stat-ontology@googlegroups.com
1.3
http://creativecommons.org/licenses/by/3.0/
Orlaith Burke
Statistical Method, Design of Experiment, Plots, Statistical Model
STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.
Camille Maumet (http://orcid.org/0000-0002-6290-553X)
Alejandra Gonzalez-Beltran (http://orcid.org/0000-0003-3499-8262)
https://github.com/ISA-tools/stato/issues
Thomas Nichols (http://orcid.org/0000-0002-4516-5103)
Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668)
Nolan Nichols (http://orcid.org/0000-0003-1099-3328)
STATO: the statistical methods ontology
This Ontology is distributed under a Creative Commons Attribution License
Chris Mungall (http://orcid.org/0000-0002-6601-2165)
http://stato-ontology.org/
0
true
true
true
true
This statement can actually be inferred from 'plan specification', because 'independent variable specification' is a subclass of 'is part of' some 'plan specification'
true
true
true
true
true
true
true
0
5
true
true
true
-1
1
2
1
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true
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0
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0
http://purl.obolibrary.org/obo/BFO_0000001
entity
http://purl.obolibrary.org/obo/BFO_0000001
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000001
entity
http://purl.obolibrary.org/obo/BFO_0000002
continuant
http://purl.obolibrary.org/obo/BFO_0000002
a heart
http://purl.obolibrary.org/obo/BFO_0000002
a person
http://purl.obolibrary.org/obo/BFO_0000002
a symphony orchestra
http://purl.obolibrary.org/obo/BFO_0000002
the color of a tomato
http://purl.obolibrary.org/obo/BFO_0000002
the disposition of blood to coagulate
http://purl.obolibrary.org/obo/BFO_0000002
the lawn and atmosphere in front of our building
http://purl.obolibrary.org/obo/BFO_0000002
the mass of a cloud
http://purl.obolibrary.org/obo/BFO_0000002
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
http://purl.obolibrary.org/obo/BFO_0000002
endurant
http://purl.obolibrary.org/obo/BFO_0000002
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000002
continuant
http://purl.obolibrary.org/obo/BFO_0000003
occurrent
http://purl.obolibrary.org/obo/BFO_0000003
a surgical operation as processual context for a nosocomical infection
http://purl.obolibrary.org/obo/BFO_0000003
the life of an organism
http://purl.obolibrary.org/obo/BFO_0000003
the most interesting part of Van Gogh's life
http://purl.obolibrary.org/obo/BFO_0000003
the spatiotemporal context occupied by a process of cellular meiosis
http://purl.obolibrary.org/obo/BFO_0000003
the spatiotemporal region occupied by the development of a cancer tumor
http://purl.obolibrary.org/obo/BFO_0000003
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
http://purl.obolibrary.org/obo/BFO_0000003
perdurant
http://purl.obolibrary.org/obo/BFO_0000003
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000003
occurrent
http://purl.obolibrary.org/obo/BFO_0000004
independent continuant
http://purl.obolibrary.org/obo/BFO_0000004
a chair
http://purl.obolibrary.org/obo/BFO_0000004
a heart
http://purl.obolibrary.org/obo/BFO_0000004
a leg
http://purl.obolibrary.org/obo/BFO_0000004
a person
http://purl.obolibrary.org/obo/BFO_0000004
a symphony orchestra
http://purl.obolibrary.org/obo/BFO_0000004
an organism
http://purl.obolibrary.org/obo/BFO_0000004
the bottom right portion of a human torso
http://purl.obolibrary.org/obo/BFO_0000004
the lawn and atmosphere in front of our building
http://purl.obolibrary.org/obo/BFO_0000004
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
http://purl.obolibrary.org/obo/BFO_0000004
substantial entity
http://purl.obolibrary.org/obo/BFO_0000004
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000004
independent continuant
http://purl.obolibrary.org/obo/BFO_0000005
dependent continuant
http://purl.obolibrary.org/obo/BFO_0000005
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
http://purl.obolibrary.org/obo/BFO_0000005
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000005
dependent continuant
http://purl.obolibrary.org/obo/BFO_0000006
spatial region
http://purl.obolibrary.org/obo/BFO_0000006
parts of the sum total of all space in the universe
http://purl.obolibrary.org/obo/BFO_0000006
the sum total of all space in the universe
http://purl.obolibrary.org/obo/BFO_0000006
A continuant that is neither bearer of quality entities nor inheres in any other entities.
http://purl.obolibrary.org/obo/BFO_0000006
All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
http://purl.obolibrary.org/obo/BFO_0000006
An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
http://purl.obolibrary.org/obo/BFO_0000006
Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
http://purl.obolibrary.org/obo/BFO_0000006
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000006
spatial region
http://purl.obolibrary.org/obo/BFO_0000007
process
http://purl.obolibrary.org/obo/BFO_0000007
the life of an organism
http://purl.obolibrary.org/obo/BFO_0000007
the process of cell-division
http://purl.obolibrary.org/obo/BFO_0000007
the process of sleeping
http://purl.obolibrary.org/obo/BFO_0000007
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
http://purl.obolibrary.org/obo/BFO_0000007
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000007
process
http://purl.obolibrary.org/obo/BFO_0000009
two dimensional region
http://purl.obolibrary.org/obo/BFO_0000009
the surface of a cube-shaped part of space
http://purl.obolibrary.org/obo/BFO_0000009
the surface of a rectilinear planar figure-shaped part of space
http://purl.obolibrary.org/obo/BFO_0000009
the surface of a sphere-shaped part of space
http://purl.obolibrary.org/obo/BFO_0000009
A spatial region with two dimensions.
http://purl.obolibrary.org/obo/BFO_0000009
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000009
two dimensional region
http://purl.obolibrary.org/obo/BFO_0000016
disposition
http://purl.obolibrary.org/obo/BFO_0000016
the disposition of a patient with a weakened immune system to contract disease
http://purl.obolibrary.org/obo/BFO_0000016
the disposition of a vase to brake if dropped
http://purl.obolibrary.org/obo/BFO_0000016
the disposition of blood to coagulate
http://purl.obolibrary.org/obo/BFO_0000016
the disposition of metal to conduct electricity
http://purl.obolibrary.org/obo/BFO_0000016
the disposition of vegetables to decay when not refrigerated
http://purl.obolibrary.org/obo/BFO_0000016
A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
http://purl.obolibrary.org/obo/BFO_0000016
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000016
disposition
http://purl.obolibrary.org/obo/BFO_0000017
realizable entity
http://purl.obolibrary.org/obo/BFO_0000017
the disposition of blood to coagulate
http://purl.obolibrary.org/obo/BFO_0000017
the disposition of metal to conduct electricity
http://purl.obolibrary.org/obo/BFO_0000017
the function of the reproductive organs
http://purl.obolibrary.org/obo/BFO_0000017
the role of being a doctor
http://purl.obolibrary.org/obo/BFO_0000017
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
http://purl.obolibrary.org/obo/BFO_0000017
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
http://purl.obolibrary.org/obo/BFO_0000017
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000017
realizable entity
http://purl.obolibrary.org/obo/BFO_0000018
zero dimensional region
http://purl.obolibrary.org/obo/BFO_0000018
a point
http://purl.obolibrary.org/obo/BFO_0000018
A spatial region with no dimensions.
http://purl.obolibrary.org/obo/BFO_0000018
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000018
zero dimensional region
http://purl.obolibrary.org/obo/BFO_0000019
quality
http://purl.obolibrary.org/obo/BFO_0000019
the ambient temperature of air
http://purl.obolibrary.org/obo/BFO_0000019
the circumference of a waist
http://purl.obolibrary.org/obo/BFO_0000019
the color of a tomato
http://purl.obolibrary.org/obo/BFO_0000019
the mass of a piece of gold
http://purl.obolibrary.org/obo/BFO_0000019
the shape of a nose
http://purl.obolibrary.org/obo/BFO_0000019
the weight of a chimpanzee
http://purl.obolibrary.org/obo/BFO_0000019
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
http://purl.obolibrary.org/obo/BFO_0000019
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000019
quality
http://purl.obolibrary.org/obo/BFO_0000020
specifically dependent continuant
http://purl.obolibrary.org/obo/BFO_0000020
the color of a tomato
http://purl.obolibrary.org/obo/BFO_0000020
the disposition of fish to decay
http://purl.obolibrary.org/obo/BFO_0000020
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
http://purl.obolibrary.org/obo/BFO_0000020
the liquidity of blood
http://purl.obolibrary.org/obo/BFO_0000020
the mass of a cloud
http://purl.obolibrary.org/obo/BFO_0000020
the role of being a doctor
http://purl.obolibrary.org/obo/BFO_0000020
the smell of mozzarella
http://purl.obolibrary.org/obo/BFO_0000020
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
http://purl.obolibrary.org/obo/BFO_0000020
mode
http://purl.obolibrary.org/obo/BFO_0000020
property
http://purl.obolibrary.org/obo/BFO_0000020
trope
http://purl.obolibrary.org/obo/BFO_0000020
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000020
specifically dependent continuant
http://purl.obolibrary.org/obo/BFO_0000023
role
http://purl.obolibrary.org/obo/BFO_0000023
the role of a biological grandfather as legal guardian in the context of a system of laws
http://purl.obolibrary.org/obo/BFO_0000023
the role of a chemical compound in an experiment
http://purl.obolibrary.org/obo/BFO_0000023
the role of a patient relative as defined by a hospital administrative form
http://purl.obolibrary.org/obo/BFO_0000023
the role of a person as a surgeon
http://purl.obolibrary.org/obo/BFO_0000023
the role of a student in a university
http://purl.obolibrary.org/obo/BFO_0000023
the role of a woman as a legal mother in the context of system of laws
http://purl.obolibrary.org/obo/BFO_0000023
the role of ingested matter in digestion
http://purl.obolibrary.org/obo/BFO_0000023
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
http://purl.obolibrary.org/obo/BFO_0000023
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000023
role
http://purl.obolibrary.org/obo/BFO_0000026
one dimensional region
http://purl.obolibrary.org/obo/BFO_0000026
an edge of a cube-shaped part of space
http://purl.obolibrary.org/obo/BFO_0000026
the part of space that is a line stretching from one end of absolute space to the other
http://purl.obolibrary.org/obo/BFO_0000026
A spatial region with one dimension.
http://purl.obolibrary.org/obo/BFO_0000026
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000026
one dimensional region
http://purl.obolibrary.org/obo/BFO_0000028
three dimensional region
http://purl.obolibrary.org/obo/BFO_0000028
a cube-shaped part of space
http://purl.obolibrary.org/obo/BFO_0000028
a sphere-shaped part of space
http://purl.obolibrary.org/obo/BFO_0000028
A spatial region with three dimensions.
http://purl.obolibrary.org/obo/BFO_0000028
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000028
three dimensional region
http://purl.obolibrary.org/obo/BFO_0000031
generically dependent continuant
http://purl.obolibrary.org/obo/BFO_0000031
a certain PDF file that exists in different and in several hard drives
http://purl.obolibrary.org/obo/BFO_0000031
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
http://purl.obolibrary.org/obo/BFO_0000031
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000031
generically dependent continuant
http://purl.obolibrary.org/obo/BFO_0000034
function
http://purl.obolibrary.org/obo/BFO_0000034
the digestive function of the stomach to nutriate the body
http://purl.obolibrary.org/obo/BFO_0000034
the function of a birth canal to enable transport
http://purl.obolibrary.org/obo/BFO_0000034
the function of a computer program to compute mathematical equations
http://purl.obolibrary.org/obo/BFO_0000034
the function of a hammer to drive in nails
http://purl.obolibrary.org/obo/BFO_0000034
the function of a judge in a court of law
http://purl.obolibrary.org/obo/BFO_0000034
the function of an automobile to provide transportation
http://purl.obolibrary.org/obo/BFO_0000034
the function of reproduction in the transmission of genetic material
http://purl.obolibrary.org/obo/BFO_0000034
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
http://purl.obolibrary.org/obo/BFO_0000034
A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
http://purl.obolibrary.org/obo/BFO_0000034
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000034
function
http://purl.obolibrary.org/obo/BFO_0000040
material entity
http://purl.obolibrary.org/obo/BFO_0000040
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
http://purl.obolibrary.org/obo/BFO_0000040
Examples: collection of random bacteria, a chair, dorsal surface of the body
http://purl.obolibrary.org/obo/BFO_0000040
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
http://purl.obolibrary.org/obo/BFO_0000040
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000040
material entity
http://purl.obolibrary.org/obo/BFO_0000050
is part of
http://purl.obolibrary.org/obo/BFO_0000050
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
http://purl.obolibrary.org/obo/BFO_0000050
part of
http://purl.obolibrary.org/obo/BFO_0000050
part_of
http://purl.obolibrary.org/obo/BFO_0000050
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000050
is part of
http://purl.obolibrary.org/obo/BFO_0000051
has part
http://purl.obolibrary.org/obo/BFO_0000051
has_part
http://purl.obolibrary.org/obo/BFO_0000051
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000051
has part
http://purl.obolibrary.org/obo/BFO_0000052
inheres in
http://purl.obolibrary.org/obo/BFO_0000052
inheres_in
http://purl.obolibrary.org/obo/BFO_0000052
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000052
inheres in
http://purl.obolibrary.org/obo/BFO_0000053
is bearer of
http://purl.obolibrary.org/obo/BFO_0000053
bearer of
http://purl.obolibrary.org/obo/BFO_0000053
bearer_of
http://purl.obolibrary.org/obo/BFO_0000053
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000053
is bearer of
http://purl.obolibrary.org/obo/BFO_0000054
is realized by
http://purl.obolibrary.org/obo/BFO_0000054
realized by
http://purl.obolibrary.org/obo/BFO_0000054
realized_by
http://purl.obolibrary.org/obo/BFO_0000054
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000054
is realized by
http://purl.obolibrary.org/obo/BFO_0000055
realizes
http://purl.obolibrary.org/obo/BFO_0000055
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000055
realizes
http://purl.obolibrary.org/obo/BFO_0000056
participates in
http://purl.obolibrary.org/obo/BFO_0000056
participates_in
http://purl.obolibrary.org/obo/BFO_0000056
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000056
participates in
http://purl.obolibrary.org/obo/BFO_0000057
has participant
http://purl.obolibrary.org/obo/BFO_0000057
has_participant
http://purl.obolibrary.org/obo/BFO_0000057
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000057
has participant
http://purl.obolibrary.org/obo/BFO_0000058
is concretized as
http://purl.obolibrary.org/obo/BFO_0000058
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000058
is concretized as
http://purl.obolibrary.org/obo/BFO_0000059
concretizes
http://purl.obolibrary.org/obo/BFO_0000059
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000059
concretizes
http://purl.obolibrary.org/obo/BFO_0000062
is preceded by
http://purl.obolibrary.org/obo/BFO_0000062
preceded by
http://purl.obolibrary.org/obo/BFO_0000062
preceded_by
http://purl.obolibrary.org/obo/BFO_0000062
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000062
is preceded by
http://purl.obolibrary.org/obo/BFO_0000063
precedes
http://purl.obolibrary.org/obo/BFO_0000063
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000063
precedes
http://purl.obolibrary.org/obo/BFO_0000070
s depends on
http://purl.obolibrary.org/obo/BFO_0000070
s_depends_on
http://purl.obolibrary.org/obo/BFO_0000070
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000070
s depends on
http://purl.obolibrary.org/obo/BFO_0000079
is function of
http://purl.obolibrary.org/obo/BFO_0000079
function of
http://purl.obolibrary.org/obo/BFO_0000079
function_of
http://purl.obolibrary.org/obo/BFO_0000079
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000079
is function of
http://purl.obolibrary.org/obo/BFO_0000081
is role of
http://purl.obolibrary.org/obo/BFO_0000081
role of
http://purl.obolibrary.org/obo/BFO_0000081
role_of
http://purl.obolibrary.org/obo/BFO_0000081
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000081
is role of
http://purl.obolibrary.org/obo/BFO_0000082
is located in
http://purl.obolibrary.org/obo/BFO_0000082
located in
http://purl.obolibrary.org/obo/BFO_0000082
located_in
http://purl.obolibrary.org/obo/BFO_0000082
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000082
is located in
http://purl.obolibrary.org/obo/BFO_0000085
has function
http://purl.obolibrary.org/obo/BFO_0000085
has_function
http://purl.obolibrary.org/obo/BFO_0000085
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000085
has function
http://purl.obolibrary.org/obo/BFO_0000086
has quality
http://purl.obolibrary.org/obo/BFO_0000086
has_quality
http://purl.obolibrary.org/obo/BFO_0000086
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000086
has quality
http://purl.obolibrary.org/obo/BFO_0000087
has role
http://purl.obolibrary.org/obo/BFO_0000087
has_role
http://purl.obolibrary.org/obo/BFO_0000087
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/BFO_0000087
has role
http://purl.obolibrary.org/obo/CARO_0001008
gross anatomical part
http://purl.obolibrary.org/obo/CARO_0001008
Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.
http://purl.obolibrary.org/obo/CARO_0001008
http://purl.obolibrary.org/obo/caro.owl
http://purl.obolibrary.org/obo/CARO_0001008
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CARO_0001008
gross anatomical part
http://purl.obolibrary.org/obo/CHEBI_16670
peptide
http://purl.obolibrary.org/obo/CHEBI_16670
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
http://purl.obolibrary.org/obo/CHEBI_16670
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_16670
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_16670
peptide
http://purl.obolibrary.org/obo/CHEBI_16991
deoxyribonucleic acid
http://purl.obolibrary.org/obo/CHEBI_16991
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
http://purl.obolibrary.org/obo/CHEBI_16991
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_16991
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_16991
deoxyribonucleic acid
http://purl.obolibrary.org/obo/CHEBI_23367
molecular entity
http://purl.obolibrary.org/obo/CHEBI_23367
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
http://purl.obolibrary.org/obo/CHEBI_23367
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
http://purl.obolibrary.org/obo/CHEBI_23367
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_23367
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_23367
molecular entity
http://purl.obolibrary.org/obo/CHEBI_33250
atom
http://purl.obolibrary.org/obo/CHEBI_33250
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
http://purl.obolibrary.org/obo/CHEBI_33250
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_33250
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_33250
atom
http://purl.obolibrary.org/obo/CHEBI_33696
nucleic acid
http://purl.obolibrary.org/obo/CHEBI_33696
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
http://purl.obolibrary.org/obo/CHEBI_33696
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_33696
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_33696
nucleic acid
http://purl.obolibrary.org/obo/CHEBI_33697
ribonucleic acid
http://purl.obolibrary.org/obo/CHEBI_33697
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
http://purl.obolibrary.org/obo/CHEBI_33697
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_33697
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_33697
ribonucleic acid
http://purl.obolibrary.org/obo/CHEBI_33839
macromolecule
http://purl.obolibrary.org/obo/CHEBI_33839
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
http://purl.obolibrary.org/obo/CHEBI_33839
polymer
http://purl.obolibrary.org/obo/CHEBI_33839
http://purl.obolibrary.org/obo/chebi.owl
http://purl.obolibrary.org/obo/CHEBI_33839
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CHEBI_33839
macromolecule
http://purl.obolibrary.org/obo/CL_0000000
cell
http://purl.obolibrary.org/obo/CL_0000000
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
http://purl.obolibrary.org/obo/CL_0000000
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
http://purl.obolibrary.org/obo/CL_0000000
http://purl.obolibrary.org/obo/cl.owl
http://purl.obolibrary.org/obo/CL_0000000
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CL_0000000
cell
http://purl.obolibrary.org/obo/CL_0000010
cultured cell
http://purl.obolibrary.org/obo/CL_0000010
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
http://purl.obolibrary.org/obo/CL_0000010
http://purl.obolibrary.org/obo/cl.owl
http://purl.obolibrary.org/obo/CL_0000010
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CL_0000010
cultured cell
http://purl.obolibrary.org/obo/CL_0000578
experimentally modified cell in vitro
http://purl.obolibrary.org/obo/CL_0000578
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
http://purl.obolibrary.org/obo/CL_0000578
http://purl.obolibrary.org/obo/cl.owl
http://purl.obolibrary.org/obo/CL_0000578
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/CL_0000578
experimentally modified cell in vitro
http://purl.obolibrary.org/obo/GO_0003674
molecular_function
http://purl.obolibrary.org/obo/GO_0003674
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
http://purl.obolibrary.org/obo/GO_0003674
http://purl.obolibrary.org/obo/go.owl
http://purl.obolibrary.org/obo/GO_0003674
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/GO_0003674
molecular_function
http://purl.obolibrary.org/obo/GO_0003824
catalytic activity
http://purl.obolibrary.org/obo/GO_0003824
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
http://purl.obolibrary.org/obo/GO_0003824
http://purl.obolibrary.org/obo/go.owl
http://purl.obolibrary.org/obo/GO_0003824
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/GO_0003824
catalytic activity
http://purl.obolibrary.org/obo/GO_0008150
biological_process
http://purl.obolibrary.org/obo/GO_0008150
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/go.owl
http://purl.obolibrary.org/obo/GO_0008150
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/GO_0008150
biological_process
http://purl.obolibrary.org/obo/GO_0010467
gene expression
http://purl.obolibrary.org/obo/GO_0010467
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
http://purl.obolibrary.org/obo/GO_0010467
http://purl.obolibrary.org/obo/go.owl
http://purl.obolibrary.org/obo/GO_0010467
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/GO_0010467
gene expression
http://purl.obolibrary.org/obo/GO_0043234
protein complex
http://purl.obolibrary.org/obo/GO_0043234
A ribosome is a protein complex
http://purl.obolibrary.org/obo/GO_0043234
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
http://purl.obolibrary.org/obo/GO_0043234
http://purl.obolibrary.org/obo/go.owl
http://purl.obolibrary.org/obo/GO_0043234
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/GO_0043234
protein complex
http://purl.obolibrary.org/obo/IAO_0000001
conditional specification
http://purl.obolibrary.org/obo/IAO_0000001
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000001
a directive information entity that specifies what should happen if the trigger condition is fulfilled
http://purl.obolibrary.org/obo/IAO_0000001
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/IAO_0000001
OBI branch derived
http://purl.obolibrary.org/obo/IAO_0000001
OBI_0000349
http://purl.obolibrary.org/obo/IAO_0000001
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000001
conditional specification
http://purl.obolibrary.org/obo/IAO_0000002
example to be eventually removed
http://purl.obolibrary.org/obo/IAO_0000002
example to be eventually removed
http://purl.obolibrary.org/obo/IAO_0000003
measurement unit label
http://purl.obolibrary.org/obo/IAO_0000003
Examples of measurement unit labels are liters, inches, weight per volume.
http://purl.obolibrary.org/obo/IAO_0000003
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000003
A data item label that denotes a unit of measure.
http://purl.obolibrary.org/obo/IAO_0000003
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
http://purl.obolibrary.org/obo/IAO_0000003
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000003
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000003
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000003
measurement unit label
http://purl.obolibrary.org/obo/IAO_0000005
objective specification
http://purl.obolibrary.org/obo/IAO_0000005
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000005
a directive information entity that describes an intended process endpoint.
http://purl.obolibrary.org/obo/IAO_0000005
Answers the question, why did you do this experiment?
http://purl.obolibrary.org/obo/IAO_0000005
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000005
PERSON: Barry Smith
http://purl.obolibrary.org/obo/IAO_0000005
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/IAO_0000005
PERSON: Jennifer Fostel
http://purl.obolibrary.org/obo/IAO_0000005
OBI Plan and Planned Process/Roles Branch
http://purl.obolibrary.org/obo/IAO_0000005
OBI_0000217
http://purl.obolibrary.org/obo/IAO_0000005
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000005
objective specification
http://purl.obolibrary.org/obo/IAO_0000007
action specification
http://purl.obolibrary.org/obo/IAO_0000007
Pour the contents of flask 1 into flask 2
http://purl.obolibrary.org/obo/IAO_0000007
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000007
a directive information entity that describes an action the bearer will take
http://purl.obolibrary.org/obo/IAO_0000007
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000007
OBI Plan and Planned Process branch
http://purl.obolibrary.org/obo/IAO_0000007
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000007
action specification
http://purl.obolibrary.org/obo/IAO_0000009
data item label
http://purl.obolibrary.org/obo/IAO_0000009
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000009
An information content entity that is part of some data item and is used to partially define the denotation of that data item.
http://purl.obolibrary.org/obo/IAO_0000009
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
http://purl.obolibrary.org/obo/IAO_0000009
GROUP: IAO
http://purl.obolibrary.org/obo/IAO_0000009
datum label
http://purl.obolibrary.org/obo/IAO_0000009
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000009
data item label
http://purl.obolibrary.org/obo/IAO_0000015
information carrier
http://purl.obolibrary.org/obo/IAO_0000015
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
http://purl.obolibrary.org/obo/IAO_0000015
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000015
A quality of an information bearer that imparts the information content
http://purl.obolibrary.org/obo/IAO_0000015
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
http://purl.obolibrary.org/obo/IAO_0000015
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000015
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
http://purl.obolibrary.org/obo/IAO_0000015
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000015
information carrier
http://purl.obolibrary.org/obo/IAO_0000027
data item
http://purl.obolibrary.org/obo/IAO_0000027
Data items include counts of things, analyte concentrations, and statistical summaries.
http://purl.obolibrary.org/obo/IAO_0000027
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000027
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method that reliably tends to produce (approximately) truthful statements.
http://purl.obolibrary.org/obo/IAO_0000027
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
http://purl.obolibrary.org/obo/IAO_0000027
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
http://purl.obolibrary.org/obo/IAO_0000027
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
http://purl.obolibrary.org/obo/IAO_0000027
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000027
PERSON: Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000027
PERSON: Jonathan Rees
http://purl.obolibrary.org/obo/IAO_0000027
data
http://purl.obolibrary.org/obo/IAO_0000027
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000027
data item
http://purl.obolibrary.org/obo/IAO_0000028
symbol
http://purl.obolibrary.org/obo/IAO_0000028
A written proper name such as “OBI”; a serial number such as “12324X”; a stop sign.
http://purl.obolibrary.org/obo/IAO_0000028
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000028
An information content entity that is a mark or character used as a conventional representation of another entity.
http://purl.obolibrary.org/obo/IAO_0000028
20091104, MC: this needs work and will most probably change
http://purl.obolibrary.org/obo/IAO_0000028
PERSON: Jonathan Rees
http://purl.obolibrary.org/obo/IAO_0000028
based on Oxford English Dictionary
http://purl.obolibrary.org/obo/IAO_0000028
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000028
symbol
http://purl.obolibrary.org/obo/IAO_0000030
information content entity
http://purl.obolibrary.org/obo/IAO_0000030
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
http://purl.obolibrary.org/obo/IAO_0000030
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000030
an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
http://purl.obolibrary.org/obo/IAO_0000030
PERSON: Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000030
OBI_0000142
http://purl.obolibrary.org/obo/IAO_0000030
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000030
information content entity
http://purl.obolibrary.org/obo/IAO_0000032
scalar measurement datum
http://purl.obolibrary.org/obo/IAO_0000032
10 feet. 3 ml.
http://purl.obolibrary.org/obo/IAO_0000032
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000032
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
http://purl.obolibrary.org/obo/IAO_0000032
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
http://purl.obolibrary.org/obo/IAO_0000032
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000032
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000032
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000032
scalar measurement datum
http://purl.obolibrary.org/obo/IAO_0000033
directive information entity
http://purl.obolibrary.org/obo/IAO_0000033
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000033
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
http://purl.obolibrary.org/obo/IAO_0000033
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
http://purl.obolibrary.org/obo/IAO_0000033
Philly2013 - AR: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
http://purl.obolibrary.org/obo/IAO_0000033
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
http://purl.obolibrary.org/obo/IAO_0000033
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000033
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/IAO_0000033
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000033
directive information entity
http://purl.obolibrary.org/obo/IAO_0000037
dot plot
http://purl.obolibrary.org/obo/IAO_0000037
Dot plot of SSC-H and FSC-H.
http://purl.obolibrary.org/obo/IAO_0000037
http://purl.obolibrary.org/obo/IAO_0000002
http://purl.obolibrary.org/obo/IAO_0000037
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
http://purl.obolibrary.org/obo/IAO_0000037
person:Allyson Lister
http://purl.obolibrary.org/obo/IAO_0000037
person:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000037
OBI_0000123
http://purl.obolibrary.org/obo/IAO_0000037
group:OBI
http://purl.obolibrary.org/obo/IAO_0000037
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000037
dot plot
http://purl.obolibrary.org/obo/IAO_0000038
graph
http://purl.obolibrary.org/obo/IAO_0000038
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/IAO_0000038
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
http://purl.obolibrary.org/obo/IAO_0000038
PERSON: Lawrence Hunter
http://purl.obolibrary.org/obo/IAO_0000038
person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000038
person:Allyson Lister
http://purl.obolibrary.org/obo/IAO_0000038
OBI_0000240
http://purl.obolibrary.org/obo/IAO_0000038
group:OBI
http://purl.obolibrary.org/obo/IAO_0000038
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000038
graph
http://purl.obolibrary.org/obo/IAO_0000039
has measurement unit label
http://purl.obolibrary.org/obo/IAO_0000039
A relation between a value specification and its unit of measurement.
http://purl.obolibrary.org/obo/IAO_0000039
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000039
has measurement unit label
http://purl.obolibrary.org/obo/IAO_0000055
rule
http://purl.obolibrary.org/obo/IAO_0000055
example to be added
http://purl.obolibrary.org/obo/IAO_0000055
http://purl.obolibrary.org/obo/IAO_0000124
http://purl.obolibrary.org/obo/IAO_0000055
a rule is an executable which guides, defines, restricts actions
http://purl.obolibrary.org/obo/IAO_0000055
MSI
http://purl.obolibrary.org/obo/IAO_0000055
PRS
http://purl.obolibrary.org/obo/IAO_0000055
OBI_0500021
http://purl.obolibrary.org/obo/IAO_0000055
PRS
http://purl.obolibrary.org/obo/IAO_0000055
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000055
rule
http://purl.obolibrary.org/obo/IAO_0000064
algorithm
http://purl.obolibrary.org/obo/IAO_0000064
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
http://purl.obolibrary.org/obo/IAO_0000064
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000064
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
http://purl.obolibrary.org/obo/IAO_0000064
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/IAO_0000064
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/IAO_0000064
OBI_0000270
http://purl.obolibrary.org/obo/IAO_0000064
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
http://purl.obolibrary.org/obo/IAO_0000064
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000064
algorithm
http://purl.obolibrary.org/obo/IAO_0000078
curation status specification
http://purl.obolibrary.org/obo/IAO_0000078
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/IAO_0000078
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
http://purl.obolibrary.org/obo/IAO_0000078
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
http://purl.obolibrary.org/obo/IAO_0000078
PERSON:Bill Bug
http://purl.obolibrary.org/obo/IAO_0000078
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000078
OBI_0000266
http://purl.obolibrary.org/obo/IAO_0000078
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000078
curation status specification
http://purl.obolibrary.org/obo/IAO_0000088
report
http://purl.obolibrary.org/obo/IAO_0000088
journal article, patent application, grant progress report, case report (not patient record)
http://purl.obolibrary.org/obo/IAO_0000088
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000088
An information content entity assembled by an author for the purpose of providing information for an audience, and that is meant to provide an accurate account of something that happened.
http://purl.obolibrary.org/obo/IAO_0000088
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
http://purl.obolibrary.org/obo/IAO_0000088
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
http://purl.obolibrary.org/obo/IAO_0000088
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
http://purl.obolibrary.org/obo/IAO_0000088
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
http://purl.obolibrary.org/obo/IAO_0000088
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000088
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000088
PERSON:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000088
GROUP: OBI
http://purl.obolibrary.org/obo/IAO_0000088
OBI_0000099
http://purl.obolibrary.org/obo/IAO_0000088
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000088
report
http://purl.obolibrary.org/obo/IAO_0000100
data set
http://purl.obolibrary.org/obo/IAO_0000100
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
http://purl.obolibrary.org/obo/IAO_0000100
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000100
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
http://purl.obolibrary.org/obo/IAO_0000100
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
http://purl.obolibrary.org/obo/IAO_0000100
person:Allyson Lister
http://purl.obolibrary.org/obo/IAO_0000100
person:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000100
OBI_0000042
http://purl.obolibrary.org/obo/IAO_0000100
group:OBI
http://purl.obolibrary.org/obo/IAO_0000100
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000100
data set
http://purl.obolibrary.org/obo/IAO_0000101
image
http://purl.obolibrary.org/obo/IAO_0000101
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000101
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
http://purl.obolibrary.org/obo/IAO_0000101
person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000101
person:Allyson
http://purl.obolibrary.org/obo/IAO_0000101
person:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000101
OBI_0000030
http://purl.obolibrary.org/obo/IAO_0000101
group:OBI
http://purl.obolibrary.org/obo/IAO_0000101
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000101
image
http://purl.obolibrary.org/obo/IAO_0000102
data about an ontology part
http://purl.obolibrary.org/obo/IAO_0000102
data about an ontology part is a data item about a part of an ontology, for example a term
http://purl.obolibrary.org/obo/IAO_0000102
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000102
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000102
data about an ontology part
http://purl.obolibrary.org/obo/IAO_0000104
plan specification
http://purl.obolibrary.org/obo/IAO_0000104
To lose weight, go running daily for at least 30 minutes. To isolate plasma from blood, centrifuge tubes at 1100-1300 rpm for 15 minutes.
http://purl.obolibrary.org/obo/IAO_0000104
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000104
a directive information entity that, when concretized, is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified.
http://purl.obolibrary.org/obo/IAO_0000104
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
http://purl.obolibrary.org/obo/IAO_0000104
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
http://purl.obolibrary.org/obo/IAO_0000104
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000104
OBI Plan and Planned Process branch
http://purl.obolibrary.org/obo/IAO_0000104
OBI_0000344
http://purl.obolibrary.org/obo/IAO_0000104
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000104
plan specification
http://purl.obolibrary.org/obo/IAO_0000109
measurement data item
http://purl.obolibrary.org/obo/IAO_0000109
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
http://purl.obolibrary.org/obo/IAO_0000109
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000109
A data item that is a recording of the output of an assay.
http://purl.obolibrary.org/obo/IAO_0000109
2/2/2009 is_specified_output of some assay?
http://purl.obolibrary.org/obo/IAO_0000109
person:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000109
measurement datum
http://purl.obolibrary.org/obo/IAO_0000109
OBI_0000305
http://purl.obolibrary.org/obo/IAO_0000109
group:OBI
http://purl.obolibrary.org/obo/IAO_0000109
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000109
measurement data item
http://purl.obolibrary.org/obo/IAO_0000111
editor preferred label
http://purl.obolibrary.org/obo/IAO_0000111
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000111
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
http://purl.obolibrary.org/obo/IAO_0000111
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000111
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000111
editor preferred label
http://purl.obolibrary.org/obo/IAO_0000111
editor preferred term
http://purl.obolibrary.org/obo/IAO_0000111
editor preferred term
http://purl.obolibrary.org/obo/IAO_0000112
example of usage
http://purl.obolibrary.org/obo/IAO_0000112
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000112
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
http://purl.obolibrary.org/obo/IAO_0000112
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000112
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000112
example of usage
http://purl.obolibrary.org/obo/IAO_0000114
has curation status
http://purl.obolibrary.org/obo/IAO_0000114
PERSON:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000114
PERSON:Bill Bug
http://purl.obolibrary.org/obo/IAO_0000114
PERSON:Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000114
OBI_0000281
http://purl.obolibrary.org/obo/IAO_0000114
has curation status
http://purl.obolibrary.org/obo/IAO_0000115
definition
http://purl.obolibrary.org/obo/IAO_0000115
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000115
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
http://purl.obolibrary.org/obo/IAO_0000115
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
http://purl.obolibrary.org/obo/IAO_0000115
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000115
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000115
definition
http://purl.obolibrary.org/obo/IAO_0000115
definition
http://purl.obolibrary.org/obo/IAO_0000115
definition
http://purl.obolibrary.org/obo/IAO_0000115
textual definition
http://purl.obolibrary.org/obo/IAO_0000116
editor note
http://purl.obolibrary.org/obo/IAO_0000116
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000116
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
http://purl.obolibrary.org/obo/IAO_0000116
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000116
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000116
editor note
http://purl.obolibrary.org/obo/IAO_0000117
term editor
http://purl.obolibrary.org/obo/IAO_0000117
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000117
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
http://purl.obolibrary.org/obo/IAO_0000117
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
http://purl.obolibrary.org/obo/IAO_0000117
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000117
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000117
term editor
http://purl.obolibrary.org/obo/IAO_0000118
alternative term
http://purl.obolibrary.org/obo/IAO_0000118
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/IAO_0000118
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
http://purl.obolibrary.org/obo/IAO_0000118
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000118
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000118
alternative term
http://purl.obolibrary.org/obo/IAO_0000119
definition source
http://purl.obolibrary.org/obo/IAO_0000119
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000119
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
http://purl.obolibrary.org/obo/IAO_0000119
PERSON:Daniel Schober
http://purl.obolibrary.org/obo/IAO_0000119
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
http://purl.obolibrary.org/obo/IAO_0000119
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000119
definition source
http://purl.obolibrary.org/obo/IAO_0000120
metadata complete
http://purl.obolibrary.org/obo/IAO_0000120
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
http://purl.obolibrary.org/obo/IAO_0000120
metadata complete
http://purl.obolibrary.org/obo/IAO_0000121
organizational term
http://purl.obolibrary.org/obo/IAO_0000121
term created to ease viewing/sort terms for development purpose, and will not be included in a release
http://purl.obolibrary.org/obo/IAO_0000121
PERSON:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000121
organizational term
http://purl.obolibrary.org/obo/IAO_0000122
ready for release
http://purl.obolibrary.org/obo/IAO_0000122
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
http://purl.obolibrary.org/obo/IAO_0000122
ready for release
http://purl.obolibrary.org/obo/IAO_0000123
metadata incomplete
http://purl.obolibrary.org/obo/IAO_0000123
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
http://purl.obolibrary.org/obo/IAO_0000123
metadata incomplete
http://purl.obolibrary.org/obo/IAO_0000124
uncurated
http://purl.obolibrary.org/obo/IAO_0000124
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
http://purl.obolibrary.org/obo/IAO_0000124
uncurated
http://purl.obolibrary.org/obo/IAO_0000125
pending final vetting
http://purl.obolibrary.org/obo/IAO_0000125
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
http://purl.obolibrary.org/obo/IAO_0000125
pending final vetting
http://purl.obolibrary.org/obo/IAO_0000129
version number
http://purl.obolibrary.org/obo/IAO_0000129
http://purl.obolibrary.org/obo/IAO_0000124
http://purl.obolibrary.org/obo/IAO_0000129
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
http://purl.obolibrary.org/obo/IAO_0000129
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
http://purl.obolibrary.org/obo/IAO_0000129
GROUP: IAO
http://purl.obolibrary.org/obo/IAO_0000129
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000129
version number
http://purl.obolibrary.org/obo/IAO_0000136
is about
http://purl.obolibrary.org/obo/IAO_0000136
This document is about information artifacts and their representations
http://purl.obolibrary.org/obo/IAO_0000136
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/IAO_0000136
is_about is a (currently) primitive relation that relates an information artifact to an entity.
http://purl.obolibrary.org/obo/IAO_0000136
person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000136
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
http://purl.obolibrary.org/obo/IAO_0000136
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000136
is about
http://purl.obolibrary.org/obo/IAO_0000144
conclusion textual entity
http://purl.obolibrary.org/obo/IAO_0000144
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
http://purl.obolibrary.org/obo/IAO_0000144
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000144
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
http://purl.obolibrary.org/obo/IAO_0000144
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
http://purl.obolibrary.org/obo/IAO_0000144
2009/10/23 Alan Ruttenberg: We need to work on the definition still
http://purl.obolibrary.org/obo/IAO_0000144
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000144
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000144
conclusion textual entity
http://purl.obolibrary.org/obo/IAO_0000178
material information bearer
http://purl.obolibrary.org/obo/IAO_0000178
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. Additional examples: a hard drive, a brain.
http://purl.obolibrary.org/obo/IAO_0000178
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000178
A material entity in which a concretization of an information content entity inheres.
http://purl.obolibrary.org/obo/IAO_0000178
GROUP: IAO
http://purl.obolibrary.org/obo/IAO_0000178
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000178
material information bearer
http://purl.obolibrary.org/obo/IAO_0000184
scatter plot
http://purl.obolibrary.org/obo/IAO_0000184
Comparison of gene expression values in two samples can be displayed in a scatter plot
http://purl.obolibrary.org/obo/IAO_0000184
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000184
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
http://purl.obolibrary.org/obo/IAO_0000184
PERSON:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000184
PERSON:James Malone
http://purl.obolibrary.org/obo/IAO_0000184
PERSON:Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000184
scattergraph
http://purl.obolibrary.org/obo/IAO_0000184
WEB: http://en.wikipedia.org/wiki/Scatterplot
http://purl.obolibrary.org/obo/IAO_0000184
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000184
scatter plot
http://purl.obolibrary.org/obo/IAO_0000219
denotes
http://purl.obolibrary.org/obo/IAO_0000219
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
http://purl.obolibrary.org/obo/IAO_0000219
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
http://purl.obolibrary.org/obo/IAO_0000219
person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000219
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
http://purl.obolibrary.org/obo/IAO_0000219
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000219
http://purl.obolibrary.org/obo/IAO_0000219
denotes
http://purl.obolibrary.org/obo/IAO_0000232
curator note
http://purl.obolibrary.org/obo/IAO_0000232
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000232
An administrative note of use for a curator but of no use for a user
http://purl.obolibrary.org/obo/IAO_0000232
PERSON:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000232
curator note
http://purl.obolibrary.org/obo/IAO_0000300
textual entity
http://purl.obolibrary.org/obo/IAO_0000300
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
http://purl.obolibrary.org/obo/IAO_0000300
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
http://purl.obolibrary.org/obo/IAO_0000300
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
http://purl.obolibrary.org/obo/IAO_0000300
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
http://purl.obolibrary.org/obo/IAO_0000300
PERSON: Lawrence Hunter
http://purl.obolibrary.org/obo/IAO_0000300
text
http://purl.obolibrary.org/obo/IAO_0000300
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000300
textual entity
http://purl.obolibrary.org/obo/IAO_0000306
table
http://purl.obolibrary.org/obo/IAO_0000306
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/IAO_0000306
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
http://purl.obolibrary.org/obo/IAO_0000306
PERSON: Lawrence Hunter
http://purl.obolibrary.org/obo/IAO_0000306
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000306
table
http://purl.obolibrary.org/obo/IAO_0000308
figure
http://purl.obolibrary.org/obo/IAO_0000308
Any picture, diagram or table
http://purl.obolibrary.org/obo/IAO_0000308
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000308
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
http://purl.obolibrary.org/obo/IAO_0000308
PERSON: Lawrence Hunter
http://purl.obolibrary.org/obo/IAO_0000308
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000308
figure
http://purl.obolibrary.org/obo/IAO_0000309
diagram
http://purl.obolibrary.org/obo/IAO_0000309
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
http://purl.obolibrary.org/obo/IAO_0000309
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000309
A figure that expresses one or more propositions
http://purl.obolibrary.org/obo/IAO_0000309
PERSON: Lawrence Hunter
http://purl.obolibrary.org/obo/IAO_0000309
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000309
diagram
http://purl.obolibrary.org/obo/IAO_0000400
cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000400
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000400
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
http://purl.obolibrary.org/obo/IAO_0000400
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
http://purl.obolibrary.org/obo/IAO_0000400
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000400
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000400
cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000400
http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
http://purl.obolibrary.org/obo/IAO_0000401
one dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000401
http://purl.obolibrary.org/obo/IAO_0000124
http://purl.obolibrary.org/obo/IAO_0000401
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000401
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000401
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
http://purl.obolibrary.org/obo/IAO_0000401
one dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000402
two dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000402
http://purl.obolibrary.org/obo/IAO_0000124
http://purl.obolibrary.org/obo/IAO_0000402
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000402
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000402
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
http://purl.obolibrary.org/obo/IAO_0000402
two dimensional cartesian spatial coordinate datum
http://purl.obolibrary.org/obo/IAO_0000404
has x coordinate value
http://purl.obolibrary.org/obo/IAO_0000404
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000404
has x coordinate value
http://purl.obolibrary.org/obo/IAO_0000406
has y coordinate value
http://purl.obolibrary.org/obo/IAO_0000406
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000406
has y coordinate value
http://purl.obolibrary.org/obo/IAO_0000407
has coordinate unit label
http://purl.obolibrary.org/obo/IAO_0000407
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000407
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
http://purl.obolibrary.org/obo/IAO_0000407
has coordinate unit label
http://purl.obolibrary.org/obo/IAO_0000412
imported from
http://purl.obolibrary.org/obo/IAO_0000412
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/IAO_0000412
For external terms/classes, the ontology from which the term was imported
http://purl.obolibrary.org/obo/IAO_0000412
PERSON:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000412
PERSON:Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000412
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
http://purl.obolibrary.org/obo/IAO_0000412
imported from
http://purl.obolibrary.org/obo/IAO_0000413
is duration of
http://purl.obolibrary.org/obo/IAO_0000413
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000413
relates a process to a time-measurement-datum that represents the duration of the process
http://purl.obolibrary.org/obo/IAO_0000413
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000413
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000413
is duration of
http://purl.obolibrary.org/obo/IAO_0000414
mass measurement datum
http://purl.obolibrary.org/obo/IAO_0000414
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/IAO_0000414
A scalar measurement datum that is the result of measurement of mass quality
http://purl.obolibrary.org/obo/IAO_0000414
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
http://purl.obolibrary.org/obo/IAO_0000414
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000414
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000414
mass measurement datum
http://purl.obolibrary.org/obo/IAO_0000416
time measurement datum
http://purl.obolibrary.org/obo/IAO_0000416
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/IAO_0000416
A scalar measurement datum that is the result of measuring a temporal interval
http://purl.obolibrary.org/obo/IAO_0000416
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
http://purl.obolibrary.org/obo/IAO_0000416
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000416
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000416
time measurement datum
http://purl.obolibrary.org/obo/IAO_0000423
to be replaced with external ontology term
http://purl.obolibrary.org/obo/IAO_0000423
Terms with this status should eventually replaced with a term from another ontology.
http://purl.obolibrary.org/obo/IAO_0000423
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000423
group:OBI
http://purl.obolibrary.org/obo/IAO_0000423
to be replaced with external ontology term
http://purl.obolibrary.org/obo/IAO_0000428
requires discussion
http://purl.obolibrary.org/obo/IAO_0000428
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
http://purl.obolibrary.org/obo/IAO_0000428
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000428
group:OBI
http://purl.obolibrary.org/obo/IAO_0000428
requires discussion
http://purl.obolibrary.org/obo/IAO_0000572
documenting
http://purl.obolibrary.org/obo/IAO_0000572
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Copying the readout from an instrument into a spreadsheet.
http://purl.obolibrary.org/obo/IAO_0000572
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000572
a planned process in which input information is used to create or add to a report
http://purl.obolibrary.org/obo/IAO_0000572
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
http://purl.obolibrary.org/obo/IAO_0000572
Bjoern Peters
http://purl.obolibrary.org/obo/IAO_0000572
wikipedia http://en.wikipedia.org/wiki/Documenting
http://purl.obolibrary.org/obo/IAO_0000572
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000572
documenting
http://purl.obolibrary.org/obo/IAO_0000573
line graph
http://purl.obolibrary.org/obo/IAO_0000573
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000573
PERSON:Chris Stoeckert
http://purl.obolibrary.org/obo/IAO_0000573
PERSON:Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000573
line chart
http://purl.obolibrary.org/obo/IAO_0000573
GROUP:OBI
http://purl.obolibrary.org/obo/IAO_0000573
WEB: http://en.wikipedia.org/wiki/Line_chart
http://purl.obolibrary.org/obo/IAO_0000573
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000573
line graph
http://purl.obolibrary.org/obo/IAO_0000577
CRID
http://purl.obolibrary.org/obo/IAO_0000577
PubMed identifier “PMID:12345”
http://purl.obolibrary.org/obo/IAO_0000577
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000577
A symbol that is sufficient to look up information about the corresponding entity from its CRID (centrally registered identifier) registry.
http://purl.obolibrary.org/obo/IAO_0000577
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
http://purl.obolibrary.org/obo/IAO_0000577
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000577
PERSON: Bill Hogan
http://purl.obolibrary.org/obo/IAO_0000577
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/IAO_0000577
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000577
centrally registered identifier
http://purl.obolibrary.org/obo/IAO_0000577
Original proposal from Bjoern, discussions at IAO calls
http://purl.obolibrary.org/obo/IAO_0000577
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000577
CRID
http://purl.obolibrary.org/obo/IAO_0000578
centrally registered identifier
http://purl.obolibrary.org/obo/IAO_0000578
Entries in a Column of which the header is "Pubmed ID"
http://purl.obolibrary.org/obo/IAO_0000578
PMID:12345
http://purl.obolibrary.org/obo/IAO_0000578
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
http://purl.obolibrary.org/obo/IAO_0000578
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
http://purl.obolibrary.org/obo/IAO_0000578
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
http://purl.obolibrary.org/obo/IAO_0000578
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
http://purl.obolibrary.org/obo/IAO_0000578
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000578
PERSON: Bill Hogan
http://purl.obolibrary.org/obo/IAO_0000578
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/IAO_0000578
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000578
Centrally Registered IDentifier (CRID)
http://purl.obolibrary.org/obo/IAO_0000578
Original proposal from Bjoern, discussions at IAO calls
http://purl.obolibrary.org/obo/IAO_0000578
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000578
centrally registered identifier
http://purl.obolibrary.org/obo/IAO_0000579
CRID registry
http://purl.obolibrary.org/obo/IAO_0000579
PubMed and GenBank both have CRID registries as parts of their database systems.
http://purl.obolibrary.org/obo/IAO_0000579
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/IAO_0000579
A data set that consists of CRIDs (centrally registered identifier) and additional information about their corresponding entities, that were recorded in the dataset through an assigning a centrally registered identifier process.
http://purl.obolibrary.org/obo/IAO_0000579
IAO call, 20101124: PubMed registry is an instance of CRID registry
http://purl.obolibrary.org/obo/IAO_0000579
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000579
PERSON: Bill Hogan
http://purl.obolibrary.org/obo/IAO_0000579
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/IAO_0000579
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/IAO_0000579
centrally registered identifier registry
http://purl.obolibrary.org/obo/IAO_0000579
Original proposal from Bjoern, discussions at IAO calls
http://purl.obolibrary.org/obo/IAO_0000579
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000579
CRID registry
http://purl.obolibrary.org/obo/IAO_0000581
has time stamp
http://purl.obolibrary.org/obo/IAO_0000581
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/IAO_0000581
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
http://purl.obolibrary.org/obo/IAO_0000581
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000581
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000581
has time stamp
http://purl.obolibrary.org/obo/IAO_0000582
time stamped measurement datum
http://purl.obolibrary.org/obo/IAO_0000582
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/IAO_0000582
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000582
time stamped measurement datum
http://purl.obolibrary.org/obo/IAO_0000583
has measurement datum
http://purl.obolibrary.org/obo/IAO_0000583
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/IAO_0000583
relates a time stamped measurement datum to the measurement datum that was measured
http://purl.obolibrary.org/obo/IAO_0000583
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000583
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000583
has measurement datum
http://purl.obolibrary.org/obo/IAO_0000584
time sampled measurement data set
http://purl.obolibrary.org/obo/IAO_0000584
pmid:20604925 - time-lapse live cell microscopy
http://purl.obolibrary.org/obo/IAO_0000584
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/IAO_0000584
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
http://purl.obolibrary.org/obo/IAO_0000584
Alan Ruttenberg
http://purl.obolibrary.org/obo/IAO_0000584
experimental time series
http://purl.obolibrary.org/obo/IAO_0000584
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/IAO_0000584
time sampled measurement data set
http://purl.obolibrary.org/obo/NCBITaxon_10239
Viruses
http://purl.obolibrary.org/obo/NCBITaxon_10239
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_10239
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_10239
Viruses
http://purl.obolibrary.org/obo/NCBITaxon_117571
Euteleostomi
http://purl.obolibrary.org/obo/NCBITaxon_117571
bony vertebrates
http://purl.obolibrary.org/obo/NCBITaxon_117571
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_117571
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_117571
Euteleostomi
http://purl.obolibrary.org/obo/NCBITaxon_2
Bacteria
http://purl.obolibrary.org/obo/NCBITaxon_2
eubacteria
http://purl.obolibrary.org/obo/NCBITaxon_2
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_2
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_2
Bacteria
http://purl.obolibrary.org/obo/NCBITaxon_2157
Archaea
http://purl.obolibrary.org/obo/NCBITaxon_2157
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_2157
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_2157
Archaea
http://purl.obolibrary.org/obo/NCBITaxon_2759
Eukaryota
http://purl.obolibrary.org/obo/NCBITaxon_2759
eucaryotes
http://purl.obolibrary.org/obo/NCBITaxon_2759
eukaryotes
http://purl.obolibrary.org/obo/NCBITaxon_2759
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_2759
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_2759
Eukaryota
http://purl.obolibrary.org/obo/NCBITaxon_314146
Euarchontoglires
http://purl.obolibrary.org/obo/NCBITaxon_314146
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_314146
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_314146
Euarchontoglires
http://purl.obolibrary.org/obo/NCBITaxon_32523
Tetrapoda
http://purl.obolibrary.org/obo/NCBITaxon_32523
tetrapods
http://purl.obolibrary.org/obo/NCBITaxon_32523
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_32523
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_32523
Tetrapoda
http://purl.obolibrary.org/obo/NCBITaxon_32524
Amniota
http://purl.obolibrary.org/obo/NCBITaxon_32524
amniotes
http://purl.obolibrary.org/obo/NCBITaxon_32524
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_32524
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_32524
Amniota
http://purl.obolibrary.org/obo/NCBITaxon_33154
Opisthokonta
http://purl.obolibrary.org/obo/NCBITaxon_33154
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_33154
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_33154
Opisthokonta
http://purl.obolibrary.org/obo/NCBITaxon_33213
Bilateria
http://purl.obolibrary.org/obo/NCBITaxon_33213
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_33213
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_33213
Bilateria
http://purl.obolibrary.org/obo/NCBITaxon_40674
Mammalia
http://purl.obolibrary.org/obo/NCBITaxon_40674
mammals
http://purl.obolibrary.org/obo/NCBITaxon_40674
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_40674
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_40674
Mammalia
http://purl.obolibrary.org/obo/NCBITaxon_7742
Vertebrata <Metazoa>
http://purl.obolibrary.org/obo/NCBITaxon_7742
Vertebrata
http://purl.obolibrary.org/obo/NCBITaxon_7742
vertebrates
http://purl.obolibrary.org/obo/NCBITaxon_7742
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_7742
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_7742
Vertebrata <Metazoa>
http://purl.obolibrary.org/obo/NCBITaxon_9606
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
human
http://purl.obolibrary.org/obo/NCBITaxon_9606
human being
http://purl.obolibrary.org/obo/NCBITaxon_9606
man
http://purl.obolibrary.org/obo/NCBITaxon_9606
http://purl.obolibrary.org/obo/ncbitaxon.owl
http://purl.obolibrary.org/obo/NCBITaxon_9606
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/NCBITaxon_9606
Homo sapiens
http://purl.obolibrary.org/obo/OBI_0000010
fluorescent reporter intensity
http://purl.obolibrary.org/obo/OBI_0000010
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000010
A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
http://purl.obolibrary.org/obo/OBI_0000010
person:Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000010
group:OBI
http://purl.obolibrary.org/obo/OBI_0000010
From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
http://purl.obolibrary.org/obo/OBI_0000010
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000010
fluorescent reporter intensity
http://purl.obolibrary.org/obo/OBI_0000011
planned process
http://purl.obolibrary.org/obo/OBI_0000011
Injecting mice with a vaccine in order to test its efficacy
http://purl.obolibrary.org/obo/OBI_0000011
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000011
A processual entity that realizes a plan which is the concretization of a plan specification.
http://purl.obolibrary.org/obo/OBI_0000011
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
http://purl.obolibrary.org/obo/OBI_0000011
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000011
branch derived
http://purl.obolibrary.org/obo/OBI_0000011
6/11/9: Edited at workshop. Used to include: is initiated by an agent
http://purl.obolibrary.org/obo/OBI_0000011
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
http://purl.obolibrary.org/obo/OBI_0000011
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000011
planned process
http://purl.obolibrary.org/obo/OBI_0000015
biological feature identification objective
http://purl.obolibrary.org/obo/OBI_0000015
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000015
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
http://purl.obolibrary.org/obo/OBI_0000015
Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000015
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000015
biological feature identification objective
http://purl.obolibrary.org/obo/OBI_0000047
processed material
http://purl.obolibrary.org/obo/OBI_0000047
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
http://purl.obolibrary.org/obo/OBI_0000047
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000047
Is a material entity that is created or changed during material processing.
http://purl.obolibrary.org/obo/OBI_0000047
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000047
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000047
processed material
http://purl.obolibrary.org/obo/OBI_0000066
investigation
http://purl.obolibrary.org/obo/OBI_0000066
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
http://purl.obolibrary.org/obo/OBI_0000066
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000066
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
http://purl.obolibrary.org/obo/OBI_0000066
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000066
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0000066
Could add specific objective specification
http://purl.obolibrary.org/obo/OBI_0000066
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000066
study
http://purl.obolibrary.org/obo/OBI_0000066
investigation
http://purl.obolibrary.org/obo/OBI_0000067
evaluant role
http://purl.obolibrary.org/obo/OBI_0000067
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
http://purl.obolibrary.org/obo/OBI_0000067
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000067
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
http://purl.obolibrary.org/obo/OBI_0000067
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
http://purl.obolibrary.org/obo/OBI_0000067
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
http://purl.obolibrary.org/obo/OBI_0000067
GROUP: Role Branch
http://purl.obolibrary.org/obo/OBI_0000067
OBI
http://purl.obolibrary.org/obo/OBI_0000067
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
http://purl.obolibrary.org/obo/OBI_0000067
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000067
evaluant role
http://purl.obolibrary.org/obo/OBI_0000070
assay
http://purl.obolibrary.org/obo/OBI_0000070
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
http://purl.obolibrary.org/obo/OBI_0000070
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000070
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
http://purl.obolibrary.org/obo/OBI_0000070
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
http://purl.obolibrary.org/obo/OBI_0000070
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0000070
measuring
http://purl.obolibrary.org/obo/OBI_0000070
scientific observation
http://purl.obolibrary.org/obo/OBI_0000070
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0000070
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000070
study assay
http://purl.obolibrary.org/obo/OBI_0000070
any method
http://purl.obolibrary.org/obo/OBI_0000070
assay
http://purl.obolibrary.org/obo/OBI_0000071
quantitative confidence value
http://purl.obolibrary.org/obo/OBI_0000071
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000071
A data item which is used to indicate the degree of uncertainty about a measurement.
http://purl.obolibrary.org/obo/OBI_0000071
person:Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000071
group:OBI
http://purl.obolibrary.org/obo/OBI_0000071
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000071
quantitative confidence value
http://purl.obolibrary.org/obo/OBI_0000079
culture medium
http://purl.obolibrary.org/obo/OBI_0000079
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
http://purl.obolibrary.org/obo/OBI_0000079
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000079
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
http://purl.obolibrary.org/obo/OBI_0000079
Person: Jennifer Fostel, Jie Zheng
http://purl.obolibrary.org/obo/OBI_0000079
OBI
http://purl.obolibrary.org/obo/OBI_0000079
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000079
culture medium
http://purl.obolibrary.org/obo/OBI_0000086
reagent role
http://purl.obolibrary.org/obo/OBI_0000086
Buffer, dye, a catalyst, a solvating agent.
http://purl.obolibrary.org/obo/OBI_0000086
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000086
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
http://purl.obolibrary.org/obo/OBI_0000086
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0000086
reagent
http://purl.obolibrary.org/obo/OBI_0000086
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0000086
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000086
reagent role
http://purl.obolibrary.org/obo/OBI_0000094
material processing
http://purl.obolibrary.org/obo/OBI_0000094
A cell lysis, production of a cloning vector, creating a buffer.
http://purl.obolibrary.org/obo/OBI_0000094
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000094
A planned process which results in physical changes in a specified input material
http://purl.obolibrary.org/obo/OBI_0000094
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000094
PERSON: Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000094
PERSON: Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000094
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000094
PERSON: Philippe Rocca Serra
http://purl.obolibrary.org/obo/OBI_0000094
material transformation
http://purl.obolibrary.org/obo/OBI_0000094
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0000094
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000094
material processing
http://purl.obolibrary.org/obo/OBI_0000097
participant under investigation role
http://purl.obolibrary.org/obo/OBI_0000097
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000097
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
http://purl.obolibrary.org/obo/OBI_0000097
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
http://purl.obolibrary.org/obo/OBI_0000097
GROUP: Role Branch
http://purl.obolibrary.org/obo/OBI_0000097
OBI
http://purl.obolibrary.org/obo/OBI_0000097
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000097
participant under investigation role
http://purl.obolibrary.org/obo/OBI_0000109
biological vector role
http://purl.obolibrary.org/obo/OBI_0000109
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
http://purl.obolibrary.org/obo/OBI_0000109
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
http://purl.obolibrary.org/obo/OBI_0000109
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000109
a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
http://purl.obolibrary.org/obo/OBI_0000109
Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
http://purl.obolibrary.org/obo/OBI_0000109
GROUP: Role Branch
http://purl.obolibrary.org/obo/OBI_0000109
OBI and Wikipedia
http://purl.obolibrary.org/obo/OBI_0000109
6/12/2009 Alan made this a material to be added role, because it was, and because this speeded up reasoning
http://purl.obolibrary.org/obo/OBI_0000109
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000109
biological vector role
http://purl.obolibrary.org/obo/OBI_0000112
specimen role
http://purl.obolibrary.org/obo/OBI_0000112
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
http://purl.obolibrary.org/obo/OBI_0000112
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000112
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
http://purl.obolibrary.org/obo/OBI_0000112
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
http://purl.obolibrary.org/obo/OBI_0000112
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
http://purl.obolibrary.org/obo/OBI_0000112
GROUP: Role Branch
http://purl.obolibrary.org/obo/OBI_0000112
OBI
http://purl.obolibrary.org/obo/OBI_0000112
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000112
specimen role
http://purl.obolibrary.org/obo/OBI_0000113
sequence feature identification objective
http://purl.obolibrary.org/obo/OBI_0000113
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000113
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
http://purl.obolibrary.org/obo/OBI_0000113
Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000113
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000113
sequence feature identification objective
http://purl.obolibrary.org/obo/OBI_0000115
intervention design
http://purl.obolibrary.org/obo/OBI_0000115
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
http://purl.obolibrary.org/obo/OBI_0000115
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000115
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
http://purl.obolibrary.org/obo/OBI_0000115
Philppe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000115
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0000115
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000115
intervention design
http://purl.obolibrary.org/obo/OBI_0000118
gene list
http://purl.obolibrary.org/obo/OBI_0000118
Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
http://purl.obolibrary.org/obo/OBI_0000118
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000118
A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
http://purl.obolibrary.org/obo/OBI_0000118
person:Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000118
group:OBI
http://purl.obolibrary.org/obo/OBI_0000118
kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.
http://purl.obolibrary.org/obo/OBI_0000118
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000118
gene list
http://purl.obolibrary.org/obo/OBI_0000124
is_supported_by_data
http://purl.obolibrary.org/obo/OBI_0000124
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
http://purl.obolibrary.org/obo/OBI_0000124
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000124
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
http://purl.obolibrary.org/obo/OBI_0000124
OBI
http://purl.obolibrary.org/obo/OBI_0000124
OBI
http://purl.obolibrary.org/obo/OBI_0000124
Philly 2011 workshop
http://purl.obolibrary.org/obo/OBI_0000124
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000124
is_supported_by_data
http://purl.obolibrary.org/obo/OBI_0000131
molecular feature identification objective
http://purl.obolibrary.org/obo/OBI_0000131
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000131
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
http://purl.obolibrary.org/obo/OBI_0000131
Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000131
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000131
molecular feature identification objective
http://purl.obolibrary.org/obo/OBI_0000164
cDNA library
http://purl.obolibrary.org/obo/OBI_0000164
PMID:6110205. collection of cDNA derived from mouse splenocytes.
http://purl.obolibrary.org/obo/OBI_0000164
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000164
PERSON: Luisa Montecchi
http://purl.obolibrary.org/obo/OBI_0000164
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000164
GROUP: PSI
http://purl.obolibrary.org/obo/OBI_0000164
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000164
cDNA library
http://purl.obolibrary.org/obo/OBI_0000175
p-value
http://purl.obolibrary.org/obo/OBI_0000175
http://purl.obolibrary.org/obo/IAO_0000121
http://purl.obolibrary.org/obo/OBI_0000175
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
http://purl.obolibrary.org/obo/OBI_0000175
Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO
http://purl.obolibrary.org/obo/OBI_0000175
May be outside the scope of OBI long term, is needed so is retained
http://purl.obolibrary.org/obo/OBI_0000175
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0000175
PERSON:Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000175
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000175
WEB: http://en.wikipedia.org/wiki/P-value
http://purl.obolibrary.org/obo/OBI_0000175
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000175
http://purl.obolibrary.org/obo/OBI_0000175
p
http://purl.obolibrary.org/obo/OBI_0000175
p-value
http://purl.obolibrary.org/obo/OBI_0000181
population
http://purl.obolibrary.org/obo/OBI_0000181
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
http://purl.obolibrary.org/obo/OBI_0000181
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000181
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
http://purl.obolibrary.org/obo/OBI_0000181
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000181
adapted from Oxford English Dictionnary
http://purl.obolibrary.org/obo/OBI_0000181
rem1: collection somehow always involve a selection process
http://purl.obolibrary.org/obo/OBI_0000181
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000181
population
http://purl.obolibrary.org/obo/OBI_0000185
imaging assay
http://purl.obolibrary.org/obo/OBI_0000185
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000185
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
http://purl.obolibrary.org/obo/OBI_0000185
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0000185
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0000185
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000185
imaging assay
http://purl.obolibrary.org/obo/OBI_0000245
organization
http://purl.obolibrary.org/obo/OBI_0000245
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
http://purl.obolibrary.org/obo/OBI_0000245
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000245
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
http://purl.obolibrary.org/obo/OBI_0000245
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000245
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000245
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000245
PERSON: Susanna Sansone
http://purl.obolibrary.org/obo/OBI_0000245
GROUP: OBI
http://purl.obolibrary.org/obo/OBI_0000245
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000245
organization
http://purl.obolibrary.org/obo/OBI_0000250
dye role
http://purl.obolibrary.org/obo/OBI_0000250
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000250
A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
http://purl.obolibrary.org/obo/OBI_0000250
Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000250
dye
http://purl.obolibrary.org/obo/OBI_0000250
A substance used to color materials www.answers.com/topic/dye 19feb09
http://purl.obolibrary.org/obo/OBI_0000250
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000250
dye role
http://purl.obolibrary.org/obo/OBI_0000272
protocol
http://purl.obolibrary.org/obo/OBI_0000272
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
http://purl.obolibrary.org/obo/OBI_0000272
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000272
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
http://purl.obolibrary.org/obo/OBI_0000272
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0000272
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
http://purl.obolibrary.org/obo/OBI_0000272
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000272
study protocol
http://purl.obolibrary.org/obo/OBI_0000272
protocol
http://purl.obolibrary.org/obo/OBI_0000274
adding a material entity into a target
http://purl.obolibrary.org/obo/OBI_0000274
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
http://purl.obolibrary.org/obo/OBI_0000274
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000274
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
http://purl.obolibrary.org/obo/OBI_0000274
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
http://purl.obolibrary.org/obo/OBI_0000274
BP
http://purl.obolibrary.org/obo/OBI_0000274
branch derived
http://purl.obolibrary.org/obo/OBI_0000274
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000274
adding a material entity into a target
http://purl.obolibrary.org/obo/OBI_0000275
analyte role
http://purl.obolibrary.org/obo/OBI_0000275
Glucose in blood (measured in an assay to determine the concentration of glucose).
http://purl.obolibrary.org/obo/OBI_0000275
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000275
A role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
http://purl.obolibrary.org/obo/OBI_0000275
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
http://purl.obolibrary.org/obo/OBI_0000275
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
http://purl.obolibrary.org/obo/OBI_0000275
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
http://purl.obolibrary.org/obo/OBI_0000275
GROUP: Role Branch
http://purl.obolibrary.org/obo/OBI_0000275
OBI
http://purl.obolibrary.org/obo/OBI_0000275
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
http://purl.obolibrary.org/obo/OBI_0000275
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000275
analyte role
http://purl.obolibrary.org/obo/OBI_0000293
has_specified_input
http://purl.obolibrary.org/obo/OBI_0000293
see is_input_of example_of_usage
http://purl.obolibrary.org/obo/OBI_0000293
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000293
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
http://purl.obolibrary.org/obo/OBI_0000293
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
http://purl.obolibrary.org/obo/OBI_0000293
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000293
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000293
PERSON: Larry Hunter
http://purl.obolibrary.org/obo/OBI_0000293
PERSON: Melanie Coutot
http://purl.obolibrary.org/obo/OBI_0000293
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000293
has_specified_input
http://purl.obolibrary.org/obo/OBI_0000295
is_specified_input_of
http://purl.obolibrary.org/obo/OBI_0000295
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
http://purl.obolibrary.org/obo/OBI_0000295
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000295
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
http://purl.obolibrary.org/obo/OBI_0000295
Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000295
PERSON:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000295
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000295
is_specified_input_of
http://purl.obolibrary.org/obo/OBI_0000299
has_specified_output
http://purl.obolibrary.org/obo/OBI_0000299
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000299
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
http://purl.obolibrary.org/obo/OBI_0000299
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000299
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000299
PERSON: Larry Hunter
http://purl.obolibrary.org/obo/OBI_0000299
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000299
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000299
has_specified_output
http://purl.obolibrary.org/obo/OBI_0000312
is_specified_output_of
http://purl.obolibrary.org/obo/OBI_0000312
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000312
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
http://purl.obolibrary.org/obo/OBI_0000312
Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000312
PERSON:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000312
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000312
is_specified_output_of
http://purl.obolibrary.org/obo/OBI_0000314
is_proxy_for
http://purl.obolibrary.org/obo/OBI_0000314
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000314
A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
http://purl.obolibrary.org/obo/OBI_0000314
Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000314
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000314
is_proxy_for
http://purl.obolibrary.org/obo/OBI_0000319
material to be added role
http://purl.obolibrary.org/obo/OBI_0000319
drug added to a buffer contained in a tube; substance injected into an animal;
http://purl.obolibrary.org/obo/OBI_0000319
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000319
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
http://purl.obolibrary.org/obo/OBI_0000319
Role Branch
http://purl.obolibrary.org/obo/OBI_0000319
OBI
http://purl.obolibrary.org/obo/OBI_0000319
9 March 09 from discussion with PA branch
http://purl.obolibrary.org/obo/OBI_0000319
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000319
material to be added role
http://purl.obolibrary.org/obo/OBI_0000338
drawing a conclusion based on data
http://purl.obolibrary.org/obo/OBI_0000338
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
http://purl.obolibrary.org/obo/OBI_0000338
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000338
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
http://purl.obolibrary.org/obo/OBI_0000338
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000338
PERSON: Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000338
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000338
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000338
drawing a conclusion based on data
http://purl.obolibrary.org/obo/OBI_0000339
planning
http://purl.obolibrary.org/obo/OBI_0000339
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
http://purl.obolibrary.org/obo/OBI_0000339
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000339
a process of creating or modifying a plan specification
http://purl.obolibrary.org/obo/OBI_0000339
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
http://purl.obolibrary.org/obo/OBI_0000339
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000339
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000339
Plans and Planned Processes Branch
http://purl.obolibrary.org/obo/OBI_0000339
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000339
planning
http://purl.obolibrary.org/obo/OBI_0000367
light emission function
http://purl.obolibrary.org/obo/OBI_0000367
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000367
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
http://purl.obolibrary.org/obo/OBI_0000367
Bill Bug
http://purl.obolibrary.org/obo/OBI_0000367
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000367
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000367
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000367
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000367
light emission function
http://purl.obolibrary.org/obo/OBI_0000370
contain function
http://purl.obolibrary.org/obo/OBI_0000370
A syringe, a beaker
http://purl.obolibrary.org/obo/OBI_0000370
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000370
A contain function is a function to constrain a material entities location in space
http://purl.obolibrary.org/obo/OBI_0000370
Bill Bug
http://purl.obolibrary.org/obo/OBI_0000370
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000370
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000370
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000370
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000370
contain function
http://purl.obolibrary.org/obo/OBI_0000371
heat function
http://purl.obolibrary.org/obo/OBI_0000371
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000371
A heat function is a function that increases the internal kinetic energy of a material
http://purl.obolibrary.org/obo/OBI_0000371
Bill Bug
http://purl.obolibrary.org/obo/OBI_0000371
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000371
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000371
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000371
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000371
heat function
http://purl.obolibrary.org/obo/OBI_0000372
material separation function
http://purl.obolibrary.org/obo/OBI_0000372
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000372
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
http://purl.obolibrary.org/obo/OBI_0000372
Bill Bug
http://purl.obolibrary.org/obo/OBI_0000372
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000372
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000372
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000372
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000372
material separation function
http://purl.obolibrary.org/obo/OBI_0000374
excitation function
http://purl.obolibrary.org/obo/OBI_0000374
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000374
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
http://purl.obolibrary.org/obo/OBI_0000374
Bill Bug
http://purl.obolibrary.org/obo/OBI_0000374
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000374
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000374
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000374
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000374
excitation function
http://purl.obolibrary.org/obo/OBI_0000378
filter function
http://purl.obolibrary.org/obo/OBI_0000378
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000378
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
http://purl.obolibrary.org/obo/OBI_0000378
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000378
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000378
filter function
http://purl.obolibrary.org/obo/OBI_0000387
cool function
http://purl.obolibrary.org/obo/OBI_0000387
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000387
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
http://purl.obolibrary.org/obo/OBI_0000387
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000387
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000387
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000387
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000387
cool function
http://purl.obolibrary.org/obo/OBI_0000399
solid support function
http://purl.obolibrary.org/obo/OBI_0000399
Taped, glued, pinned, dried or molecularly bonded to a solid support
http://purl.obolibrary.org/obo/OBI_0000399
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000399
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
http://purl.obolibrary.org/obo/OBI_0000399
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000399
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000399
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000399
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000399
solid support function
http://purl.obolibrary.org/obo/OBI_0000401
environment control function
http://purl.obolibrary.org/obo/OBI_0000401
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000401
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
http://purl.obolibrary.org/obo/OBI_0000401
Bill Bug
http://purl.obolibrary.org/obo/OBI_0000401
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000401
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000401
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000401
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000401
environment control function
http://purl.obolibrary.org/obo/OBI_0000403
sort function
http://purl.obolibrary.org/obo/OBI_0000403
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000403
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
http://purl.obolibrary.org/obo/OBI_0000403
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000403
Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000403
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000403
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000403
sort function
http://purl.obolibrary.org/obo/OBI_0000411
cloning vector role
http://purl.obolibrary.org/obo/OBI_0000411
http://purl.obolibrary.org/obo/OBI_0000411
pBluescript plays the role of a cloning vector
http://purl.obolibrary.org/obo/OBI_0000411
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000411
a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
http://purl.obolibrary.org/obo/OBI_0000411
PERSON: Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0000411
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000411
http://purl.obolibrary.org/obo/OBI_0000411
cloning vector role
http://purl.obolibrary.org/obo/OBI_0000416
cloning insert role
http://purl.obolibrary.org/obo/OBI_0000416
http://purl.obolibrary.org/obo/IAO_0000121
http://purl.obolibrary.org/obo/OBI_0000416
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
http://purl.obolibrary.org/obo/OBI_0000416
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
http://purl.obolibrary.org/obo/OBI_0000416
GROUP: Role branch
http://purl.obolibrary.org/obo/OBI_0000416
OBII and Wikipedia
http://purl.obolibrary.org/obo/OBI_0000416
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000416
cloning insert role
http://purl.obolibrary.org/obo/OBI_0000417
achieves_planned_objective
http://purl.obolibrary.org/obo/OBI_0000417
A cell sorting process achieves the objective specification 'material separation objective'
http://purl.obolibrary.org/obo/OBI_0000417
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000417
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
http://purl.obolibrary.org/obo/OBI_0000417
BP, AR, PPPB branch
http://purl.obolibrary.org/obo/OBI_0000417
PPPB branch derived
http://purl.obolibrary.org/obo/OBI_0000417
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
http://purl.obolibrary.org/obo/OBI_0000417
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000417
achieves_planned_objective
http://purl.obolibrary.org/obo/OBI_0000423
extract
http://purl.obolibrary.org/obo/OBI_0000423
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
http://purl.obolibrary.org/obo/OBI_0000423
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000423
an extract is a material entity which results from an extraction process
http://purl.obolibrary.org/obo/OBI_0000423
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000423
extracted material
http://purl.obolibrary.org/obo/OBI_0000423
GROUP: OBI Biomatrial Branch
http://purl.obolibrary.org/obo/OBI_0000423
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000423
extract
http://purl.obolibrary.org/obo/OBI_0000424
transcription profiling assay
http://purl.obolibrary.org/obo/OBI_0000424
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
http://purl.obolibrary.org/obo/OBI_0000424
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000424
An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
http://purl.obolibrary.org/obo/OBI_0000424
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000424
gene expression profiling
http://purl.obolibrary.org/obo/OBI_0000424
OBI
http://purl.obolibrary.org/obo/OBI_0000424
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000424
transcription profiling
http://purl.obolibrary.org/obo/OBI_0000424
transcription profiling assay
http://purl.obolibrary.org/obo/OBI_0000425
averaging objective
http://purl.obolibrary.org/obo/OBI_0000425
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
http://purl.obolibrary.org/obo/OBI_0000425
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000425
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
http://purl.obolibrary.org/obo/OBI_0000425
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0000425
James Malone
http://purl.obolibrary.org/obo/OBI_0000425
PERSON: Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0000425
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000425
averaging objective
http://purl.obolibrary.org/obo/OBI_0000427
enzyme
http://purl.obolibrary.org/obo/OBI_0000427
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000427
person: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000427
GROUP:OBI
http://purl.obolibrary.org/obo/OBI_0000427
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000427
enzyme
http://purl.obolibrary.org/obo/OBI_0000434
adding material objective
http://purl.obolibrary.org/obo/OBI_0000434
creating a mouse infected with LCM virus
http://purl.obolibrary.org/obo/OBI_0000434
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000434
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
http://purl.obolibrary.org/obo/OBI_0000434
BP
http://purl.obolibrary.org/obo/OBI_0000434
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000434
adding material objective
http://purl.obolibrary.org/obo/OBI_0000435
genotyping assay
http://purl.obolibrary.org/obo/OBI_0000435
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
http://purl.obolibrary.org/obo/OBI_0000435
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000435
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000435
genotype profiling, SNP genotyping
http://purl.obolibrary.org/obo/OBI_0000435
OBI Biomaterial
http://purl.obolibrary.org/obo/OBI_0000435
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000435
SNP analysis
http://purl.obolibrary.org/obo/OBI_0000435
genotyping assay
http://purl.obolibrary.org/obo/OBI_0000437
analyte measurement objective
http://purl.obolibrary.org/obo/OBI_0000437
The objective to measure the concentration of glucose in a blood sample
http://purl.obolibrary.org/obo/OBI_0000437
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000437
an assay objective to determine the presence or concentration of an analyte in the evaluant
http://purl.obolibrary.org/obo/OBI_0000437
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000437
PPPB branch
http://purl.obolibrary.org/obo/OBI_0000437
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000437
analyte measurement objective
http://purl.obolibrary.org/obo/OBI_0000441
assay objective
http://purl.obolibrary.org/obo/OBI_0000441
the objective to determine the weight of a mouse.
http://purl.obolibrary.org/obo/OBI_0000441
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000441
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
http://purl.obolibrary.org/obo/OBI_0000441
PPPB branch
http://purl.obolibrary.org/obo/OBI_0000441
PPPB branch
http://purl.obolibrary.org/obo/OBI_0000441
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000441
assay objective
http://purl.obolibrary.org/obo/OBI_0000443
analyte assay
http://purl.obolibrary.org/obo/OBI_0000443
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
http://purl.obolibrary.org/obo/OBI_0000443
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000443
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
http://purl.obolibrary.org/obo/OBI_0000443
2013-09-23: simplify equivalent axiom
http://purl.obolibrary.org/obo/OBI_0000443
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
http://purl.obolibrary.org/obo/OBI_0000443
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000443
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000443
analyte assay
http://purl.obolibrary.org/obo/OBI_0000444
target of material addition role
http://purl.obolibrary.org/obo/OBI_0000444
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
http://purl.obolibrary.org/obo/OBI_0000444
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000444
target of material addition role is a role realized by an entity into which a material is added in a material addition process
http://purl.obolibrary.org/obo/OBI_0000444
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
http://purl.obolibrary.org/obo/OBI_0000444
GROUP: Role Branch
http://purl.obolibrary.org/obo/OBI_0000444
OBI
http://purl.obolibrary.org/obo/OBI_0000444
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000444
target of material addition role
http://purl.obolibrary.org/obo/OBI_0000451
normalized data set
http://purl.obolibrary.org/obo/OBI_0000451
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000451
A data set that is produced as the output of a normalization data transformation.
http://purl.obolibrary.org/obo/OBI_0000451
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0000451
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000451
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000451
normalized data set
http://purl.obolibrary.org/obo/OBI_0000453
measure function
http://purl.obolibrary.org/obo/OBI_0000453
A glucometer measures blood glucose concentration, the glucometer has a measure function.
http://purl.obolibrary.org/obo/OBI_0000453
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000453
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
http://purl.obolibrary.org/obo/OBI_0000453
PERSON: Daniel Schober
http://purl.obolibrary.org/obo/OBI_0000453
PERSON: Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0000453
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000453
PERSON:Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000453
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000453
measure function
http://purl.obolibrary.org/obo/OBI_0000456
material transformation objective
http://purl.obolibrary.org/obo/OBI_0000456
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
http://purl.obolibrary.org/obo/OBI_0000456
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000456
an objective specifiction that creates an specific output object from input materials.
http://purl.obolibrary.org/obo/OBI_0000456
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000456
PERSON: Frank Gibson
http://purl.obolibrary.org/obo/OBI_0000456
PERSON: Jennifer Fostel
http://purl.obolibrary.org/obo/OBI_0000456
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000456
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000456
artifact creation objective
http://purl.obolibrary.org/obo/OBI_0000456
GROUP: OBI PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0000456
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000456
material transformation objective
http://purl.obolibrary.org/obo/OBI_0000471
study design execution
http://purl.obolibrary.org/obo/OBI_0000471
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
http://purl.obolibrary.org/obo/OBI_0000471
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000471
a planned process that realizes the concretization of a study design
http://purl.obolibrary.org/obo/OBI_0000471
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
http://purl.obolibrary.org/obo/OBI_0000471
branch derived
http://purl.obolibrary.org/obo/OBI_0000471
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
http://purl.obolibrary.org/obo/OBI_0000471
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000471
study design execution
http://purl.obolibrary.org/obo/OBI_0000626
DNA sequencing
http://purl.obolibrary.org/obo/OBI_0000626
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
http://purl.obolibrary.org/obo/OBI_0000626
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000626
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
http://purl.obolibrary.org/obo/OBI_0000626
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000626
OBI Branch derived
http://purl.obolibrary.org/obo/OBI_0000626
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000626
nucleotide sequencing
http://purl.obolibrary.org/obo/OBI_0000626
DNA sequencing
http://purl.obolibrary.org/obo/OBI_0000639
material separation objective
http://purl.obolibrary.org/obo/OBI_0000639
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
http://purl.obolibrary.org/obo/OBI_0000639
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000639
is an objective to transform a material entity into spatially separated components.
http://purl.obolibrary.org/obo/OBI_0000639
PPPB branch
http://purl.obolibrary.org/obo/OBI_0000639
PPPB branch
http://purl.obolibrary.org/obo/OBI_0000639
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000639
material separation objective
http://purl.obolibrary.org/obo/OBI_0000643
has grain
http://purl.obolibrary.org/obo/OBI_0000643
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000643
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
http://purl.obolibrary.org/obo/OBI_0000643
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
http://purl.obolibrary.org/obo/OBI_0000643
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000643
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
http://purl.obolibrary.org/obo/OBI_0000643
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000643
has grain
http://purl.obolibrary.org/obo/OBI_0000649
data set of features
http://purl.obolibrary.org/obo/OBI_0000649
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000649
A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
http://purl.obolibrary.org/obo/OBI_0000649
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0000649
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0000649
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000649
data set of features
http://purl.obolibrary.org/obo/OBI_0000650
differential expression analysis data transformation
http://purl.obolibrary.org/obo/OBI_0000650
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000650
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
http://purl.obolibrary.org/obo/OBI_0000650
James Malone
http://purl.obolibrary.org/obo/OBI_0000650
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000650
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0000650
WEB:
http://purl.obolibrary.org/obo/OBI_0000650
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000650
differential expression analysis data transformation
http://purl.obolibrary.org/obo/OBI_0000652
material combination
http://purl.obolibrary.org/obo/OBI_0000652
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
http://purl.obolibrary.org/obo/OBI_0000652
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000652
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
http://purl.obolibrary.org/obo/OBI_0000652
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
http://purl.obolibrary.org/obo/OBI_0000652
bp
http://purl.obolibrary.org/obo/OBI_0000652
bp
http://purl.obolibrary.org/obo/OBI_0000652
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000652
material combination
http://purl.obolibrary.org/obo/OBI_0000659
specimen collection
http://purl.obolibrary.org/obo/OBI_0000659
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
http://purl.obolibrary.org/obo/OBI_0000659
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000659
A planned process with the objective of collecting a specimen.
http://purl.obolibrary.org/obo/OBI_0000659
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
http://purl.obolibrary.org/obo/OBI_0000659
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
http://purl.obolibrary.org/obo/OBI_0000659
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
http://purl.obolibrary.org/obo/OBI_0000659
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000659
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
http://purl.obolibrary.org/obo/OBI_0000659
6/9/09: used at workshop
http://purl.obolibrary.org/obo/OBI_0000659
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000659
specimen collection
http://purl.obolibrary.org/obo/OBI_0000662
error corrected data set
http://purl.obolibrary.org/obo/OBI_0000662
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000662
A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
http://purl.obolibrary.org/obo/OBI_0000662
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0000662
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0000662
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000662
error corrected data set
http://purl.obolibrary.org/obo/OBI_0000668
error correction data transformation
http://purl.obolibrary.org/obo/OBI_0000668
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000668
An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
http://purl.obolibrary.org/obo/OBI_0000668
James Malone
http://purl.obolibrary.org/obo/OBI_0000668
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0000668
EDITORS
http://purl.obolibrary.org/obo/OBI_0000668
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000668
error correction data transformation
http://purl.obolibrary.org/obo/OBI_0000671
sample from organism
http://purl.obolibrary.org/obo/OBI_0000671
http://purl.obolibrary.org/obo/IAO_0000002
http://purl.obolibrary.org/obo/OBI_0000671
a material obtained from an organism in order to be a representative of the whole
http://purl.obolibrary.org/obo/OBI_0000671
5/29: This is a helper class for now
http://purl.obolibrary.org/obo/OBI_0000671
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
http://purl.obolibrary.org/obo/OBI_0000671
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000671
sample from organism
http://purl.obolibrary.org/obo/OBI_0000673
statistical hypothesis test
http://purl.obolibrary.org/obo/OBI_0000673
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000673
"A statistical test provides a mechanism for making quantitative decisions about a process or processes".
http://purl.obolibrary.org/obo/OBI_0000673
A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
http://purl.obolibrary.org/obo/OBI_0000673
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0000673
James Malone
http://purl.obolibrary.org/obo/OBI_0000673
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000673
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0000673
http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm
http://purl.obolibrary.org/obo/OBI_0000673
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000673
NHST
http://purl.obolibrary.org/obo/OBI_0000673
Null Hypothesis Statistical Testing
http://purl.obolibrary.org/obo/OBI_0000673
statistical hypothesis testing
http://purl.obolibrary.org/obo/OBI_0000673
statistical hypothesis test
http://purl.obolibrary.org/obo/OBI_0000674
center value
http://purl.obolibrary.org/obo/OBI_0000674
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000674
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
http://purl.obolibrary.org/obo/OBI_0000674
[STATO Definition]
The median is that value of the variate which divides the total frequency into two halves.
The median is measure of central tendency of data. It is obtained by arranging the observations in order from smallest to largest value. If there is an odd number of observations, the median is the middle value. If there is an even number of observations, the median is the average of the two middle values.
http://purl.obolibrary.org/obo/OBI_0000674
PRS and AGB added restriction about 'measure of central tendency' and quartile, june 2013
http://purl.obolibrary.org/obo/OBI_0000674
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0000674
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0000674
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0000674
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000674
median
http://purl.obolibrary.org/obo/OBI_0000674
second quartile
http://purl.obolibrary.org/obo/OBI_0000674
A Dictionary of Statistical Terms, 5th edition, prepared for the International Statistical Institute by F.H.C. Marriott. Published for the International Statistical Institute by Longman Scientific and Technical.
and
Wolfram Alpha
http://purl.obolibrary.org/obo/OBI_0000674
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000674
second quartile
http://purl.obolibrary.org/obo/OBI_0000674
center value
http://purl.obolibrary.org/obo/OBI_0000675
statistical hypothesis test objective
http://purl.obolibrary.org/obo/OBI_0000675
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000675
is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
http://purl.obolibrary.org/obo/OBI_0000675
James Malone
http://purl.obolibrary.org/obo/OBI_0000675
Person:Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0000675
hypothesis test objective
http://purl.obolibrary.org/obo/OBI_0000675
WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
http://purl.obolibrary.org/obo/OBI_0000675
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000675
statistical hypothesis test objective
http://purl.obolibrary.org/obo/OBI_0000678
portioning objective
http://purl.obolibrary.org/obo/OBI_0000678
The objective to obtain multiple aliquots of an enzyme preparation.
http://purl.obolibrary.org/obo/OBI_0000678
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000678
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
http://purl.obolibrary.org/obo/OBI_0000678
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000678
portioning objective
http://purl.obolibrary.org/obo/OBI_0000679
average value
http://purl.obolibrary.org/obo/OBI_0000679
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000679
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
http://purl.obolibrary.org/obo/OBI_0000679
[STATO definition]:
The arithmetic mean is defined as the sum of the numerical values of each and every observation divided by the total number of observations. S The arithmetic mean A is defined by the formula
A=sum[Ai] / n where i ranges from 1 to n and Ai represents the value of individual observations.
The arithmetic mean is significantly affected by extreme values and outliers. A better measure of central tendency is the median (http://purl.obolibrary.org/obo/OBI_0000674).
http://purl.obolibrary.org/obo/OBI_0000679
PRS and AGB added restriction about 'measure of central tendency', june 2013
http://purl.obolibrary.org/obo/OBI_0000679
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0000679
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0000679
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0000679
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000679
arithmetic mean
http://purl.obolibrary.org/obo/OBI_0000679
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000679
http://purl.obolibrary.org/obo/OBI_0000679
http://docs.scipy.org/doc/numpy/reference/generated/numpy.mean.html
http://purl.obolibrary.org/obo/OBI_0000679
average value
http://purl.obolibrary.org/obo/OBI_0000681
separation into different composition objective
http://purl.obolibrary.org/obo/OBI_0000681
The objective to obtain cells contained in a sample of blood.
http://purl.obolibrary.org/obo/OBI_0000681
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000681
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
http://purl.obolibrary.org/obo/OBI_0000681
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
http://purl.obolibrary.org/obo/OBI_0000681
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000681
separation into different composition objective
http://purl.obolibrary.org/obo/OBI_0000684
specimen collection objective
http://purl.obolibrary.org/obo/OBI_0000684
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
http://purl.obolibrary.org/obo/OBI_0000684
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000684
A objective specification to obtain a material entity for potential use as an input during an investigation.
http://purl.obolibrary.org/obo/OBI_0000684
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000684
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000684
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000684
specimen collection objective
http://purl.obolibrary.org/obo/OBI_0000686
material combination objective
http://purl.obolibrary.org/obo/OBI_0000686
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000686
is an objective to obtain an output material that contains several input materials.
http://purl.obolibrary.org/obo/OBI_0000686
PPPB branch
http://purl.obolibrary.org/obo/OBI_0000686
bp
http://purl.obolibrary.org/obo/OBI_0000686
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000686
material combination objective
http://purl.obolibrary.org/obo/OBI_0000722
paired-end library
http://purl.obolibrary.org/obo/OBI_0000722
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
http://purl.obolibrary.org/obo/OBI_0000722
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000722
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
http://purl.obolibrary.org/obo/OBI_0000722
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000722
mate-paired library
http://purl.obolibrary.org/obo/OBI_0000722
paired-end tag (PET) library
http://purl.obolibrary.org/obo/OBI_0000722
adapted from information provided by Solid web site
http://purl.obolibrary.org/obo/OBI_0000722
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000722
paired-end library
http://purl.obolibrary.org/obo/OBI_0000731
recombinant vector
http://purl.obolibrary.org/obo/OBI_0000731
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000731
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
http://purl.obolibrary.org/obo/OBI_0000731
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000731
recombinant vector
http://purl.obolibrary.org/obo/OBI_0000736
single fragment library
http://purl.obolibrary.org/obo/OBI_0000736
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000736
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
http://purl.obolibrary.org/obo/OBI_0000736
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000736
fragment library
http://purl.obolibrary.org/obo/OBI_0000736
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000736
single fragment library
http://purl.obolibrary.org/obo/OBI_0000737
cloning vector
http://purl.obolibrary.org/obo/OBI_0000737
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000737
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
http://purl.obolibrary.org/obo/OBI_0000737
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000737
cloning vector
http://purl.obolibrary.org/obo/OBI_0000739
Student's t-test
http://purl.obolibrary.org/obo/OBI_0000739
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000739
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000739
Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
http://purl.obolibrary.org/obo/OBI_0000739
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0000739
James Malone
http://purl.obolibrary.org/obo/OBI_0000739
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000739
t-test
http://purl.obolibrary.org/obo/OBI_0000739
WEB: http://en.wikipedia.org/wiki/T-test
http://purl.obolibrary.org/obo/OBI_0000739
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000739
http://purl.obolibrary.org/obo/OBI_0000739
t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
http://purl.obolibrary.org/obo/OBI_0000739
Student's t-test
http://purl.obolibrary.org/obo/OBI_0000740
material sample role
http://purl.obolibrary.org/obo/OBI_0000740
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
http://purl.obolibrary.org/obo/OBI_0000740
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0000740
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
http://purl.obolibrary.org/obo/OBI_0000740
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
http://purl.obolibrary.org/obo/OBI_0000740
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000740
material sample role
http://purl.obolibrary.org/obo/OBI_0000744
material sampling process
http://purl.obolibrary.org/obo/OBI_0000744
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000744
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
http://purl.obolibrary.org/obo/OBI_0000744
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000744
material sampling process
http://purl.obolibrary.org/obo/OBI_0000747
material sample
http://purl.obolibrary.org/obo/OBI_0000747
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
http://purl.obolibrary.org/obo/OBI_0000747
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000747
A material entity that has the material sample role
http://purl.obolibrary.org/obo/OBI_0000747
OBI: workshop
http://purl.obolibrary.org/obo/OBI_0000747
sample population
http://purl.obolibrary.org/obo/OBI_0000747
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000747
sample
http://purl.obolibrary.org/obo/OBI_0000747
material sample
http://purl.obolibrary.org/obo/OBI_0000750
study design independent variable
http://purl.obolibrary.org/obo/OBI_0000750
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
http://purl.obolibrary.org/obo/OBI_0000750
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000750
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
http://purl.obolibrary.org/obo/OBI_0000750
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
http://purl.obolibrary.org/obo/OBI_0000750
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
http://purl.obolibrary.org/obo/OBI_0000750
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000750
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000750
PERSON: Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000750
experimental factor
http://purl.obolibrary.org/obo/OBI_0000750
independent variable
http://purl.obolibrary.org/obo/OBI_0000750
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
http://purl.obolibrary.org/obo/OBI_0000750
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
http://purl.obolibrary.org/obo/OBI_0000750
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000750
study factor
http://purl.obolibrary.org/obo/OBI_0000750
explanatory variable
http://purl.obolibrary.org/obo/OBI_0000750
factor
http://purl.obolibrary.org/obo/OBI_0000750
study design independent variable
http://purl.obolibrary.org/obo/OBI_0000751
study design dependent variable
http://purl.obolibrary.org/obo/OBI_0000751
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
http://purl.obolibrary.org/obo/OBI_0000751
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000751
PRS-AGB: a dependent variable is a variable which assumes only values set by the operator according to a plan and are expected to influence the ranges of values assumed by a response variable aka independent variable.
http://purl.obolibrary.org/obo/OBI_0000751
dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
http://purl.obolibrary.org/obo/OBI_0000751
2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
http://purl.obolibrary.org/obo/OBI_0000751
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
http://purl.obolibrary.org/obo/OBI_0000751
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000751
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000751
PERSON: Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000751
dependent variable
http://purl.obolibrary.org/obo/OBI_0000751
WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
http://purl.obolibrary.org/obo/OBI_0000751
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
http://purl.obolibrary.org/obo/OBI_0000751
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000751
response variable
http://purl.obolibrary.org/obo/OBI_0000751
study design dependent variable
http://purl.obolibrary.org/obo/OBI_0000789
survival rate
http://purl.obolibrary.org/obo/OBI_0000789
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000789
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
http://purl.obolibrary.org/obo/OBI_0000789
Oliver He
http://purl.obolibrary.org/obo/OBI_0000789
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000789
survival rate
http://purl.obolibrary.org/obo/OBI_0000791
multiple testing correction objective
http://purl.obolibrary.org/obo/OBI_0000791
Application of the Bonferroni correction
http://purl.obolibrary.org/obo/OBI_0000791
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000791
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
http://purl.obolibrary.org/obo/OBI_0000791
multiple comparison correction objective
http://purl.obolibrary.org/obo/OBI_0000791
http://en.wikipedia.org/wiki/Multiple_Testing_Correction
http://purl.obolibrary.org/obo/OBI_0000791
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000791
multiple testing correction objective
http://purl.obolibrary.org/obo/OBI_0000806
material maintenance objective
http://purl.obolibrary.org/obo/OBI_0000806
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000806
An objective specification maintains some or all of the qualities of a material over time.
http://purl.obolibrary.org/obo/OBI_0000806
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000806
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000806
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000806
material maintenance objective
http://purl.obolibrary.org/obo/OBI_0000811
primary structure of DNA macromolecule
http://purl.obolibrary.org/obo/OBI_0000811
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000811
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
http://purl.obolibrary.org/obo/OBI_0000811
placeholder for SO
http://purl.obolibrary.org/obo/OBI_0000811
BP et al
http://purl.obolibrary.org/obo/OBI_0000811
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000811
primary structure of DNA macromolecule
http://purl.obolibrary.org/obo/OBI_0000832
measurement device
http://purl.obolibrary.org/obo/OBI_0000832
A ruler, a microarray scanner, a Geiger counter.
http://purl.obolibrary.org/obo/OBI_0000832
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000832
A device in which a measure function inheres.
http://purl.obolibrary.org/obo/OBI_0000832
GROUP:OBI Philly workshop
http://purl.obolibrary.org/obo/OBI_0000832
OBI
http://purl.obolibrary.org/obo/OBI_0000832
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000832
measurement device
http://purl.obolibrary.org/obo/OBI_0000838
material maintenance
http://purl.obolibrary.org/obo/OBI_0000838
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000838
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
http://purl.obolibrary.org/obo/OBI_0000838
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000838
material maintenance
http://purl.obolibrary.org/obo/OBI_0000846
is member of organization
http://purl.obolibrary.org/obo/OBI_0000846
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000846
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
http://purl.obolibrary.org/obo/OBI_0000846
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
http://purl.obolibrary.org/obo/OBI_0000846
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
http://purl.obolibrary.org/obo/OBI_0000846
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000846
Person:Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0000846
Person:Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0000846
Person:Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0000846
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
http://purl.obolibrary.org/obo/OBI_0000846
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000846
is member of organization
http://purl.obolibrary.org/obo/OBI_0000861
Likelihood-ratio test
http://purl.obolibrary.org/obo/OBI_0000861
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000861
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000861
Likelihood-ratio test is a statistical test which evaluates the goodness-of-fit between two models and whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one)
http://purl.obolibrary.org/obo/OBI_0000861
date: March 2013
AGB and PRS provide formal definition expressed the test in terms of output and input, specifying the nature of the variables, the purpose of the test and the distribution used.
http://purl.obolibrary.org/obo/OBI_0000861
Alejandra Gonzales-Beltran
http://purl.obolibrary.org/obo/OBI_0000861
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000861
Tina Boussard
http://purl.obolibrary.org/obo/OBI_0000861
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000861
lrtest()
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/lrtest.html
http://purl.obolibrary.org/obo/OBI_0000861
Likelihood-ratio test
http://purl.obolibrary.org/obo/OBI_0000889
survival curve
http://purl.obolibrary.org/obo/OBI_0000889
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000889
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
http://purl.obolibrary.org/obo/OBI_0000889
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0000889
PERSON:Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000889
PERSON:James Malone
http://purl.obolibrary.org/obo/OBI_0000889
PERSON:Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0000889
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0000889
WEB: http://www.graphpad.com/www/book/survive.htm
http://purl.obolibrary.org/obo/OBI_0000889
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000889
survival curve
http://purl.obolibrary.org/obo/OBI_0000916
flow cytometry assay
http://purl.obolibrary.org/obo/OBI_0000916
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
http://purl.obolibrary.org/obo/OBI_0000916
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000916
An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution.
http://purl.obolibrary.org/obo/OBI_0000916
http://purl.obolibrary.org/obo/OBI_0000916
PERSON:Randi Vita, Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000916
http://purl.obolibrary.org/obo/OBI_0000916
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000916
flow cytometry
http://purl.obolibrary.org/obo/OBI_0000916
FACS
http://purl.obolibrary.org/obo/OBI_0000916
flow cytometry assay
http://purl.obolibrary.org/obo/OBI_0000924
labeled specimen
http://purl.obolibrary.org/obo/OBI_0000924
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000924
A specimen that has been modified in order to be able to detect it in future experiments
http://purl.obolibrary.org/obo/OBI_0000924
added during call 3/1/2010
http://purl.obolibrary.org/obo/OBI_0000924
OBI group
http://purl.obolibrary.org/obo/OBI_0000924
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000924
labeled specimen
http://purl.obolibrary.org/obo/OBI_0000931
study intervention
http://purl.obolibrary.org/obo/OBI_0000931
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000931
the part of the execution of an intervention design study which is varied between two or more subjects in the study
http://purl.obolibrary.org/obo/OBI_0000931
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000931
GROUP: OBI
http://purl.obolibrary.org/obo/OBI_0000931
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000931
study intervention
http://purl.obolibrary.org/obo/OBI_0000932
material separation device
http://purl.obolibrary.org/obo/OBI_0000932
flow cytometer
http://purl.obolibrary.org/obo/OBI_0000932
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000932
A device with a separation function realized in a planed process
http://purl.obolibrary.org/obo/OBI_0000932
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000932
material separation device
http://purl.obolibrary.org/obo/OBI_0000938
categorical measurement datum
http://purl.obolibrary.org/obo/OBI_0000938
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000938
A measurement datum that is reported on a categorical scale
http://purl.obolibrary.org/obo/OBI_0000938
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000938
nominal mesurement datum
http://purl.obolibrary.org/obo/OBI_0000938
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000938
categorical measurement datum
http://purl.obolibrary.org/obo/OBI_0000953
processed specimen
http://purl.obolibrary.org/obo/OBI_0000953
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000953
A specimen that has been intentionally physically modified.
http://purl.obolibrary.org/obo/OBI_0000953
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000953
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000953
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000953
A tissue sample that has been sliced and stained for a histology study.
http://purl.obolibrary.org/obo/OBI_0000953
processed specimen
http://purl.obolibrary.org/obo/OBI_0000963
categorical label
http://purl.obolibrary.org/obo/OBI_0000963
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
http://purl.obolibrary.org/obo/OBI_0000963
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000963
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
http://purl.obolibrary.org/obo/OBI_0000963
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000963
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000963
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000963
categorical label
http://purl.obolibrary.org/obo/OBI_0000964
in live cell assay
http://purl.obolibrary.org/obo/OBI_0000964
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000964
An assay in which a measurement is made by observing entities located in a live cell.
http://purl.obolibrary.org/obo/OBI_0000964
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000964
in live cell assay
http://purl.obolibrary.org/obo/OBI_0000967
container
http://purl.obolibrary.org/obo/OBI_0000967
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000967
A device that can be used to restrict the location of material entities over time
http://purl.obolibrary.org/obo/OBI_0000967
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
http://purl.obolibrary.org/obo/OBI_0000967
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0000967
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000967
container
http://purl.obolibrary.org/obo/OBI_0000968
device
http://purl.obolibrary.org/obo/OBI_0000968
A voltmeter is a measurement device which is intended to perform some measure function.
http://purl.obolibrary.org/obo/OBI_0000968
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
http://purl.obolibrary.org/obo/OBI_0000968
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0000968
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
http://purl.obolibrary.org/obo/OBI_0000968
PERSON: Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0000968
instrument
http://purl.obolibrary.org/obo/OBI_0000968
OBI development call 2012-12-17.
http://purl.obolibrary.org/obo/OBI_0000968
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000968
device
http://purl.obolibrary.org/obo/OBI_0000973
sequence data
http://purl.obolibrary.org/obo/OBI_0000973
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
http://purl.obolibrary.org/obo/OBI_0000973
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0000973
Person:Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0000973
GROUP: OBI
http://purl.obolibrary.org/obo/OBI_0000973
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000973
sequence data
http://purl.obolibrary.org/obo/OBI_0000984
dose
http://purl.obolibrary.org/obo/OBI_0000984
An organism has been injected 1ml of vaccine
http://purl.obolibrary.org/obo/OBI_0000984
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0000984
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
http://purl.obolibrary.org/obo/OBI_0000984
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0000984
dose
http://purl.obolibrary.org/obo/OBI_0001010
nucleic acid extract
http://purl.obolibrary.org/obo/OBI_0001010
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001010
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
http://purl.obolibrary.org/obo/OBI_0001010
PERSON: Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001010
UPenn Group
http://purl.obolibrary.org/obo/OBI_0001010
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001010
nucleic acid extract
http://purl.obolibrary.org/obo/OBI_0001032
light emission device
http://purl.obolibrary.org/obo/OBI_0001032
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
http://purl.obolibrary.org/obo/OBI_0001032
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001032
a device which has a function to emit light.
http://purl.obolibrary.org/obo/OBI_0001032
Person:Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0001032
OBI
http://purl.obolibrary.org/obo/OBI_0001032
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001032
light emission device
http://purl.obolibrary.org/obo/OBI_0001034
environmental control device
http://purl.obolibrary.org/obo/OBI_0001034
A growth chamber is an environmental control device.
http://purl.obolibrary.org/obo/OBI_0001034
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001034
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
http://purl.obolibrary.org/obo/OBI_0001034
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0001034
OBI
http://purl.obolibrary.org/obo/OBI_0001034
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001034
environmental control device
http://purl.obolibrary.org/obo/OBI_0001143
labeled nucleic acid extract
http://purl.obolibrary.org/obo/OBI_0001143
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001143
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
http://purl.obolibrary.org/obo/OBI_0001143
Person: Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001143
labeled extract
http://purl.obolibrary.org/obo/OBI_0001143
MO_221 labeledExtract
http://purl.obolibrary.org/obo/OBI_0001143
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001143
labeled extract
http://purl.obolibrary.org/obo/OBI_0001143
labeled nucleic acid extract
http://purl.obolibrary.org/obo/OBI_0001172
dose response curve
http://purl.obolibrary.org/obo/OBI_0001172
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001172
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001172
A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
http://purl.obolibrary.org/obo/OBI_0001172
Bjoern Peters; Randi Vita
http://purl.obolibrary.org/obo/OBI_0001172
Philippe Rocca-Serra, Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0001172
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001172
dose response curve
http://purl.obolibrary.org/obo/OBI_0001225
genetic population background information
http://purl.obolibrary.org/obo/OBI_0001225
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
http://purl.obolibrary.org/obo/OBI_0001225
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001225
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
http://purl.obolibrary.org/obo/OBI_0001225
proposed and discussed on San Diego OBI workshop, March 2011
http://purl.obolibrary.org/obo/OBI_0001225
Group: OBI group
http://purl.obolibrary.org/obo/OBI_0001225
Group: OBI group
http://purl.obolibrary.org/obo/OBI_0001225
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001225
genetic population background information
http://purl.obolibrary.org/obo/OBI_0001265
FWER adjusted p-value
http://purl.obolibrary.org/obo/OBI_0001265
http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
http://purl.obolibrary.org/obo/OBI_0001265
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001265
A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
http://purl.obolibrary.org/obo/OBI_0001265
Addition of restriction 'output of null hypothesis testing' and specified output by AGB and PRS while working on STATO
http://purl.obolibrary.org/obo/OBI_0001265
PERS:Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0001265
adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
http://purl.obolibrary.org/obo/OBI_0001265
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001265
Family-wise type I error rate
http://purl.obolibrary.org/obo/OBI_0001265
FWER adjusted p-value
http://purl.obolibrary.org/obo/OBI_0001271
RNA-seq assay
http://purl.obolibrary.org/obo/OBI_0001271
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001271
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
http://purl.obolibrary.org/obo/OBI_0001271
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0001271
transcription profiling by high throughput sequencing
http://purl.obolibrary.org/obo/OBI_0001271
EFO_0002770 transcription profiling by high throughput sequencing
http://purl.obolibrary.org/obo/OBI_0001271
JZ: should be inferred as 'DNA sequencing'. Will check in the future.
http://purl.obolibrary.org/obo/OBI_0001271
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001271
RNA-seq assay
http://purl.obolibrary.org/obo/OBI_0001305
genotype information
http://purl.obolibrary.org/obo/OBI_0001305
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
http://purl.obolibrary.org/obo/OBI_0001305
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001305
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
http://purl.obolibrary.org/obo/OBI_0001305
discussed on San Diego OBI workshop, March 2011
http://purl.obolibrary.org/obo/OBI_0001305
Group: OBI group
http://purl.obolibrary.org/obo/OBI_0001305
Group: OBI group
http://purl.obolibrary.org/obo/OBI_0001305
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001305
genotype information
http://purl.obolibrary.org/obo/OBI_0001331
transcription profiling identification objective
http://purl.obolibrary.org/obo/OBI_0001331
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001331
A molecular feature identification objective that aims to characterize the abundance of transcripts
http://purl.obolibrary.org/obo/OBI_0001331
Person: Chris Stoeckert, Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001331
Group: Penn Group
http://purl.obolibrary.org/obo/OBI_0001331
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001331
transcription profiling identification objective
http://purl.obolibrary.org/obo/OBI_0001352
allele information
http://purl.obolibrary.org/obo/OBI_0001352
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
http://purl.obolibrary.org/obo/OBI_0001352
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001352
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
http://purl.obolibrary.org/obo/OBI_0001352
discussed on San Diego OBI workshop, March 2011
http://purl.obolibrary.org/obo/OBI_0001352
Person: Chris Stoeckert, Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001352
MO_58 Allele
http://purl.obolibrary.org/obo/OBI_0001352
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001352
allele information
http://purl.obolibrary.org/obo/OBI_0001364
genetic alteration information
http://purl.obolibrary.org/obo/OBI_0001364
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001364
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
http://purl.obolibrary.org/obo/OBI_0001364
proposed and discussed on San Diego OBI workshop, March 2011
http://purl.obolibrary.org/obo/OBI_0001364
Group: OBI group
http://purl.obolibrary.org/obo/OBI_0001364
Group: OBI group
http://purl.obolibrary.org/obo/OBI_0001364
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001364
genetic alteration information
http://purl.obolibrary.org/obo/OBI_0001404
genetic characteristics information
http://purl.obolibrary.org/obo/OBI_0001404
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001404
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
http://purl.obolibrary.org/obo/OBI_0001404
Person: Chris Stoeckert, Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001404
MO_66 IndividualGeneticCharacteristics
http://purl.obolibrary.org/obo/OBI_0001404
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001404
genetic characteristics information
http://purl.obolibrary.org/obo/OBI_0001442
q-value
http://purl.obolibrary.org/obo/OBI_0001442
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001442
Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO
http://purl.obolibrary.org/obo/OBI_0001442
PERS:Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0001442
FDR adjusted p-value
http://purl.obolibrary.org/obo/OBI_0001442
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001442
q
http://purl.obolibrary.org/obo/OBI_0001442
q-value
http://purl.obolibrary.org/obo/OBI_0001444
genotyping design
http://purl.obolibrary.org/obo/OBI_0001444
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001444
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
http://purl.obolibrary.org/obo/OBI_0001444
Person: Chris Stoeckert, Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001444
MO_560 genotyping_design
http://purl.obolibrary.org/obo/OBI_0001444
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001444
http://purl.obolibrary.org/obo/OBI_0001444
genotyping design
http://purl.obolibrary.org/obo/OBI_0001479
tissue specimen
http://purl.obolibrary.org/obo/OBI_0001479
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001479
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
http://purl.obolibrary.org/obo/OBI_0001479
PERSON: Chris Stoeckert, Jie Zheng
http://purl.obolibrary.org/obo/OBI_0001479
MO_954 organism_part
http://purl.obolibrary.org/obo/OBI_0001479
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001479
tissue specimen
http://purl.obolibrary.org/obo/OBI_0001554
rate measurement datum
http://purl.obolibrary.org/obo/OBI_0001554
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
http://purl.obolibrary.org/obo/OBI_0001554
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001554
A scalar measurement datum that represents the number of events occuring over a time interval
http://purl.obolibrary.org/obo/OBI_0001554
PERSON: Bjoern Peters, Randi Vita
http://purl.obolibrary.org/obo/OBI_0001554
IEDB
http://purl.obolibrary.org/obo/OBI_0001554
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001554
rate measurement datum
http://purl.obolibrary.org/obo/OBI_0001573
DNA sequence data
http://purl.obolibrary.org/obo/OBI_0001573
The part of a FASTA file that contains the letters ACTGGGAA
http://purl.obolibrary.org/obo/OBI_0001573
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001573
A sequence data item that is about the primary structure of DNA
http://purl.obolibrary.org/obo/OBI_0001573
OBI call; Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0001573
OBI call; Melanie Courtout
http://purl.obolibrary.org/obo/OBI_0001573
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
http://purl.obolibrary.org/obo/OBI_0001573
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001573
DNA sequence data
http://purl.obolibrary.org/obo/OBI_0001755
selection criterion
http://purl.obolibrary.org/obo/OBI_0001755
rats should be aged between 6 and 8 weeks and weight between 180-250grams
http://purl.obolibrary.org/obo/OBI_0001755
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001755
A directive information entity which defines and states a principle of standard by which selection process may take place.
http://purl.obolibrary.org/obo/OBI_0001755
Person: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0001755
selection rule
http://purl.obolibrary.org/obo/OBI_0001755
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
http://purl.obolibrary.org/obo/OBI_0001755
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001755
selection criterion
http://purl.obolibrary.org/obo/OBI_0001834
drawing a conclusion
http://purl.obolibrary.org/obo/OBI_0001834
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0001834
A planned process in which new information is inferred from existing information.
http://purl.obolibrary.org/obo/OBI_0001834
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001834
drawing a conclusion
http://purl.obolibrary.org/obo/OBI_0001847
ISA alternative term
http://purl.obolibrary.org/obo/OBI_0001847
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001847
An alternative term used by the ISA tools project (http://isa-tools.org).
http://purl.obolibrary.org/obo/OBI_0001847
Person: Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0001847
Person: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0001847
ISA tools project (http://isa-tools.org)
http://purl.obolibrary.org/obo/OBI_0001847
ISA alternative term
http://purl.obolibrary.org/obo/OBI_0001865
assay array
http://purl.obolibrary.org/obo/OBI_0001865
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001865
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
http://purl.obolibrary.org/obo/OBI_0001865
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
http://purl.obolibrary.org/obo/OBI_0001865
Penn Group
http://purl.obolibrary.org/obo/OBI_0001865
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001865
assay array
http://purl.obolibrary.org/obo/OBI_0001909
conclusion based on data
http://purl.obolibrary.org/obo/OBI_0001909
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001909
An information content entity that is inferred from data.
http://purl.obolibrary.org/obo/OBI_0001909
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
http://purl.obolibrary.org/obo/OBI_0001909
Group:2013 Philly Workshop group
http://purl.obolibrary.org/obo/OBI_0001909
Group:2013 Philly Workshop group
http://purl.obolibrary.org/obo/OBI_0001909
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001909
conclusion based on data
http://purl.obolibrary.org/obo/OBI_0001912
cell freezing medium
http://purl.obolibrary.org/obo/OBI_0001912
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001912
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
http://purl.obolibrary.org/obo/OBI_0001912
PERSON: Matthew Brush
http://purl.obolibrary.org/obo/OBI_0001912
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001912
cell freezing medium
http://purl.obolibrary.org/obo/OBI_0001927
specifies value of
http://purl.obolibrary.org/obo/OBI_0001927
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0001927
A relation between a value specification and an entity which the specification is about.
http://purl.obolibrary.org/obo/OBI_0001927
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001927
specifies value of
http://purl.obolibrary.org/obo/OBI_0001930
categorical value specification
http://purl.obolibrary.org/obo/OBI_0001930
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0001930
A value specification that is specifies one category out of a fixed number of nominal categories
http://purl.obolibrary.org/obo/OBI_0001930
PERSON:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0001930
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001930
categorical value specification
http://purl.obolibrary.org/obo/OBI_0001931
scalar value specification
http://purl.obolibrary.org/obo/OBI_0001931
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0001931
A value specification that consists of two parts: a numeral and a unit label
http://purl.obolibrary.org/obo/OBI_0001931
PERSON:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0001931
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001931
scalar value specification
http://purl.obolibrary.org/obo/OBI_0001933
value specification
http://purl.obolibrary.org/obo/OBI_0001933
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
http://purl.obolibrary.org/obo/OBI_0001933
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0001933
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
http://purl.obolibrary.org/obo/OBI_0001933
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
http://purl.obolibrary.org/obo/OBI_0001933
PERSON:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0001933
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001933
value specification
http://purl.obolibrary.org/obo/OBI_0001936
molecular-labeled material
http://purl.obolibrary.org/obo/OBI_0001936
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0001936
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
http://purl.obolibrary.org/obo/OBI_0001936
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0001936
OBI developer call, 3-12-12
http://purl.obolibrary.org/obo/OBI_0001936
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001936
molecular-labeled material
http://purl.obolibrary.org/obo/OBI_0001937
has specified value
http://purl.obolibrary.org/obo/OBI_0001937
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001937
A relation between a value specification and a number that quantifies it.
http://purl.obolibrary.org/obo/OBI_0001937
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
http://purl.obolibrary.org/obo/OBI_0001937
PERSON: James A. Overton
http://purl.obolibrary.org/obo/OBI_0001937
OBI
http://purl.obolibrary.org/obo/OBI_0001937
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001937
has specified value
http://purl.obolibrary.org/obo/OBI_0001938
has value specification
http://purl.obolibrary.org/obo/OBI_0001938
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0001938
A relation between an information content entity and a value specification that specifies its value.
http://purl.obolibrary.org/obo/OBI_0001938
PERSON: James A. Overton
http://purl.obolibrary.org/obo/OBI_0001938
OBI
http://purl.obolibrary.org/obo/OBI_0001938
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0001938
has value specification
http://purl.obolibrary.org/obo/OBI_0100026
organism
http://purl.obolibrary.org/obo/OBI_0100026
animal
http://purl.obolibrary.org/obo/OBI_0100026
fungus
http://purl.obolibrary.org/obo/OBI_0100026
plant
http://purl.obolibrary.org/obo/OBI_0100026
virus
http://purl.obolibrary.org/obo/OBI_0100026
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0100026
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
http://purl.obolibrary.org/obo/OBI_0100026
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
http://purl.obolibrary.org/obo/OBI_0100026
GROUP: OBI Biomaterial Branch
http://purl.obolibrary.org/obo/OBI_0100026
WEB: http://en.wikipedia.org/wiki/Organism
http://purl.obolibrary.org/obo/OBI_0100026
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0100026
organism
http://purl.obolibrary.org/obo/OBI_0100051
specimen
http://purl.obolibrary.org/obo/OBI_0100051
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
http://purl.obolibrary.org/obo/OBI_0100051
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0100051
A material entity that has the specimen role.
http://purl.obolibrary.org/obo/OBI_0100051
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
http://purl.obolibrary.org/obo/OBI_0100051
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0100051
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0100051
GROUP: OBI Biomaterial Branch
http://purl.obolibrary.org/obo/OBI_0100051
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0100051
specimen
http://purl.obolibrary.org/obo/OBI_0100060
cultured cell population
http://purl.obolibrary.org/obo/OBI_0100060
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0100060
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
http://purl.obolibrary.org/obo/OBI_0100060
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
http://purl.obolibrary.org/obo/OBI_0100060
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0100060
cell culture sample
http://purl.obolibrary.org/obo/OBI_0100060
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0100060
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0100060
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
http://purl.obolibrary.org/obo/OBI_0100060
cultured cell population
http://purl.obolibrary.org/obo/OBI_0100064
screening library
http://purl.obolibrary.org/obo/OBI_0100064
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
http://purl.obolibrary.org/obo/OBI_0100064
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0100064
a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
http://purl.obolibrary.org/obo/OBI_0100064
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0100064
GROUP: IEDB
http://purl.obolibrary.org/obo/OBI_0100064
7/13/09: Need to clarify if this meets reagent role definition
http://purl.obolibrary.org/obo/OBI_0100064
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0100064
screening library
http://purl.obolibrary.org/obo/OBI_0200000
data transformation
http://purl.obolibrary.org/obo/OBI_0200000
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
http://purl.obolibrary.org/obo/OBI_0200000
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200000
A planned process that produces output data from input data.
http://purl.obolibrary.org/obo/OBI_0200000
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200000
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200000
James Malone
http://purl.obolibrary.org/obo/OBI_0200000
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0200000
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200000
Richard Scheuermann
http://purl.obolibrary.org/obo/OBI_0200000
Ryan Brinkman
http://purl.obolibrary.org/obo/OBI_0200000
Tina Hernandez-Boussard
http://purl.obolibrary.org/obo/OBI_0200000
data analysis
http://purl.obolibrary.org/obo/OBI_0200000
data processing
http://purl.obolibrary.org/obo/OBI_0200000
Branch editors
http://purl.obolibrary.org/obo/OBI_0200000
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200000
data transformation
http://purl.obolibrary.org/obo/OBI_0200031
differential expression analysis objective
http://purl.obolibrary.org/obo/OBI_0200031
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
http://purl.obolibrary.org/obo/OBI_0200031
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200031
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
http://purl.obolibrary.org/obo/OBI_0200031
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200031
PERSON: Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200031
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200031
differential expression analysis objective
http://purl.obolibrary.org/obo/OBI_0200036
Benjamini and Hochberg false discovery rate correction method
http://purl.obolibrary.org/obo/OBI_0200036
Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
http://purl.obolibrary.org/obo/OBI_0200036
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200036
A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
http://purl.obolibrary.org/obo/OBI_0200036
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200036
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200036
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200036
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200036
Benjamini and Hochberg false discovery rate correction method
http://purl.obolibrary.org/obo/OBI_0200049
Benjamini and Yekutieli false discovery rate correction method
http://purl.obolibrary.org/obo/OBI_0200049
The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
http://purl.obolibrary.org/obo/OBI_0200049
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200049
A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
http://purl.obolibrary.org/obo/OBI_0200049
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200049
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200049
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200049
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200049
Benjamini and Yekutieli false discovery rate correction method
http://purl.obolibrary.org/obo/OBI_0200066
Holm-Bonferroni family-wise error rate correction method
http://purl.obolibrary.org/obo/OBI_0200066
t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
http://purl.obolibrary.org/obo/OBI_0200066
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200066
a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
http://purl.obolibrary.org/obo/OBI_0200066
Person:Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200066
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200066
WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
http://purl.obolibrary.org/obo/OBI_0200066
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200066
Bonferroni adjustment method
http://purl.obolibrary.org/obo/OBI_0200066
Holm-Bonferroni family-wise error rate correction method
http://purl.obolibrary.org/obo/OBI_0200073
family wise error rate correction method
http://purl.obolibrary.org/obo/OBI_0200073
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0200073
A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
http://purl.obolibrary.org/obo/OBI_0200073
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200073
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200073
FWER correction
http://purl.obolibrary.org/obo/OBI_0200073
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
http://purl.obolibrary.org/obo/OBI_0200073
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200073
family wise error rate correction method
http://purl.obolibrary.org/obo/OBI_0200078
descriptive statistical calculation objective
http://purl.obolibrary.org/obo/OBI_0200078
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200078
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
http://purl.obolibrary.org/obo/OBI_0200078
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200078
James Malone
http://purl.obolibrary.org/obo/OBI_0200078
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0200078
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200078
PERSON: Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200078
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200078
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0200078
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200078
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200078
descriptive statistical calculation objective
http://purl.obolibrary.org/obo/OBI_0200083
survival analysis objective
http://purl.obolibrary.org/obo/OBI_0200083
Kaplan meier data transformation
http://purl.obolibrary.org/obo/OBI_0200083
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200083
A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
http://purl.obolibrary.org/obo/OBI_0200083
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200083
PERSON: Tina Boussard
http://purl.obolibrary.org/obo/OBI_0200083
survival analysis
http://purl.obolibrary.org/obo/OBI_0200083
http://en.wikipedia.org/wiki/Survival_analysis
http://purl.obolibrary.org/obo/OBI_0200083
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200083
survival analysis objective
http://purl.obolibrary.org/obo/OBI_0200089
multiple testing correction method
http://purl.obolibrary.org/obo/OBI_0200089
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200089
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
http://purl.obolibrary.org/obo/OBI_0200089
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200089
multiple testing procedure
http://purl.obolibrary.org/obo/OBI_0200089
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
http://purl.obolibrary.org/obo/OBI_0200089
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200089
multiple testing correction method
http://purl.obolibrary.org/obo/OBI_0200094
logarithmic transformation
http://purl.obolibrary.org/obo/OBI_0200094
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200094
A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
http://purl.obolibrary.org/obo/OBI_0200094
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200094
WEB: http://en.wikipedia.org/wiki/Logarithm
http://purl.obolibrary.org/obo/OBI_0200094
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200094
logarithmic transformation
http://purl.obolibrary.org/obo/OBI_0200102
regression analysis method
http://purl.obolibrary.org/obo/OBI_0200102
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0200102
Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
http://purl.obolibrary.org/obo/OBI_0200102
Date:2013-11-15
Person: AGB,PRS
Adding restrictions, specifying model + parameter estimation process
change of label from 'regression analysis method' to 'regression analysis'
http://purl.obolibrary.org/obo/OBI_0200102
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0200102
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200102
Tina Hernandez-Boussard
http://purl.obolibrary.org/obo/OBI_0200102
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
http://purl.obolibrary.org/obo/OBI_0200102
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200102
regression analysis method
http://purl.obolibrary.org/obo/OBI_0200111
data visualization
http://purl.obolibrary.org/obo/OBI_0200111
Generation of a heatmap from a microarray dataset
http://purl.obolibrary.org/obo/OBI_0200111
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200111
An planned process that creates images, diagrams or animations from the input data.
http://purl.obolibrary.org/obo/OBI_0200111
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200111
James Malone
http://purl.obolibrary.org/obo/OBI_0200111
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0200111
Tina Boussard
http://purl.obolibrary.org/obo/OBI_0200111
data encoding as image
http://purl.obolibrary.org/obo/OBI_0200111
visualization
http://purl.obolibrary.org/obo/OBI_0200111
PERSON: Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200111
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200111
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0200111
PERSON: Tina Boussard
http://purl.obolibrary.org/obo/OBI_0200111
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200111
data visualization
http://purl.obolibrary.org/obo/OBI_0200117
mode calculation
http://purl.obolibrary.org/obo/OBI_0200117
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200117
A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
http://purl.obolibrary.org/obo/OBI_0200117
James Malone
http://purl.obolibrary.org/obo/OBI_0200117
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200117
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200117
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200117
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
http://purl.obolibrary.org/obo/OBI_0200117
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200117
mode calculation
http://purl.obolibrary.org/obo/OBI_0200119
median calculation
http://purl.obolibrary.org/obo/OBI_0200119
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200119
A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
http://purl.obolibrary.org/obo/OBI_0200119
James Malone
http://purl.obolibrary.org/obo/OBI_0200119
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200119
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200119
PERSON: Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200119
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
http://purl.obolibrary.org/obo/OBI_0200119
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200119
median calculation
http://purl.obolibrary.org/obo/OBI_0200163
false discovery rate correction method
http://purl.obolibrary.org/obo/OBI_0200163
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0200163
The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
http://purl.obolibrary.org/obo/OBI_0200163
Monnie McGee
http://purl.obolibrary.org/obo/OBI_0200163
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200163
FDR correction method
http://purl.obolibrary.org/obo/OBI_0200163
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
http://purl.obolibrary.org/obo/OBI_0200163
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200163
false discovery rate correction method
http://purl.obolibrary.org/obo/OBI_0200166
data transformation objective
http://purl.obolibrary.org/obo/OBI_0200166
normalize objective
http://purl.obolibrary.org/obo/OBI_0200166
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200166
An objective specification to transformation input data into output data
http://purl.obolibrary.org/obo/OBI_0200166
Modified definition in 2013 Philly OBI workshop
http://purl.obolibrary.org/obo/OBI_0200166
James Malone
http://purl.obolibrary.org/obo/OBI_0200166
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200166
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200166
data transformation objective
http://purl.obolibrary.org/obo/OBI_0200167
data normalization objective
http://purl.obolibrary.org/obo/OBI_0200167
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
http://purl.obolibrary.org/obo/OBI_0200167
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200167
Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200167
Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200167
James Malone
http://purl.obolibrary.org/obo/OBI_0200167
PERSON: Elisabetta Manduchi
http://purl.obolibrary.org/obo/OBI_0200167
PERSON: Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200167
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200167
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200167
data normalization objective
http://purl.obolibrary.org/obo/OBI_0200168
correction objective
http://purl.obolibrary.org/obo/OBI_0200168
Type I error correction
http://purl.obolibrary.org/obo/OBI_0200168
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200168
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
http://purl.obolibrary.org/obo/OBI_0200168
James Malone
http://purl.obolibrary.org/obo/OBI_0200168
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200168
PERSON: Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0200168
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200168
correction objective
http://purl.obolibrary.org/obo/OBI_0200169
normalization data transformation
http://purl.obolibrary.org/obo/OBI_0200169
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200169
A normalization data transformation is a data transformation that has objective normalization.
http://purl.obolibrary.org/obo/OBI_0200169
James Malone
http://purl.obolibrary.org/obo/OBI_0200169
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200169
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200169
normalization data transformation
http://purl.obolibrary.org/obo/OBI_0200170
averaging data transformation
http://purl.obolibrary.org/obo/OBI_0200170
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200170
An averaging data transformation is a data transformation that has objective averaging.
http://purl.obolibrary.org/obo/OBI_0200170
James Malone
http://purl.obolibrary.org/obo/OBI_0200170
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200170
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200170
averaging data transformation
http://purl.obolibrary.org/obo/OBI_0200176
Fisher's exact test
http://purl.obolibrary.org/obo/OBI_0200176
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200176
Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
http://purl.obolibrary.org/obo/OBI_0200176
James Malone
http://purl.obolibrary.org/obo/OBI_0200176
WEB:http://mathworld.wolfram.com/FishersExactTest.html
http://purl.obolibrary.org/obo/OBI_0200176
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200176
Fisher's exact test
http://purl.obolibrary.org/obo/OBI_0200177
center calculation objective
http://purl.obolibrary.org/obo/OBI_0200177
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
http://purl.obolibrary.org/obo/OBI_0200177
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200177
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
http://purl.obolibrary.org/obo/OBI_0200177
James Malone
http://purl.obolibrary.org/obo/OBI_0200177
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200177
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200177
center calculation objective
http://purl.obolibrary.org/obo/OBI_0200181
center calculation data transformation
http://purl.obolibrary.org/obo/OBI_0200181
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200181
A center calculation data transformation is a data transformation that has objective of center calculation.
http://purl.obolibrary.org/obo/OBI_0200181
James Malone
http://purl.obolibrary.org/obo/OBI_0200181
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200181
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200181
center calculation data transformation
http://purl.obolibrary.org/obo/OBI_0200184
descriptive statistical calculation data transformation
http://purl.obolibrary.org/obo/OBI_0200184
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0200184
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
http://purl.obolibrary.org/obo/OBI_0200184
James Malone
http://purl.obolibrary.org/obo/OBI_0200184
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200184
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200184
descriptive statistical calculation data transformation
http://purl.obolibrary.org/obo/OBI_0200186
error correction objective
http://purl.obolibrary.org/obo/OBI_0200186
Application of a multiple testing correction method
http://purl.obolibrary.org/obo/OBI_0200186
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0200186
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
http://purl.obolibrary.org/obo/OBI_0200186
James Malone, Helen Parkinson
http://purl.obolibrary.org/obo/OBI_0200186
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200186
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200186
error correction objective
http://purl.obolibrary.org/obo/OBI_0200191
gene list visualization
http://purl.obolibrary.org/obo/OBI_0200191
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200191
Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
http://purl.obolibrary.org/obo/OBI_0200191
James Malone
http://purl.obolibrary.org/obo/OBI_0200191
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200191
gene list visualization
http://purl.obolibrary.org/obo/OBI_0200194
survival analysis data transformation
http://purl.obolibrary.org/obo/OBI_0200194
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0200194
A data transformation which has the objective of performing survival analysis.
http://purl.obolibrary.org/obo/OBI_0200194
James Malone
http://purl.obolibrary.org/obo/OBI_0200194
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200194
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200194
survival analysis data transformation
http://purl.obolibrary.org/obo/OBI_0200200
chi square test
http://purl.obolibrary.org/obo/OBI_0200200
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200200
The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
http://purl.obolibrary.org/obo/OBI_0200200
negociation with OBI hence definition and definition source are missing from this class
http://purl.obolibrary.org/obo/OBI_0200200
PERSON: James Malone
http://purl.obolibrary.org/obo/OBI_0200200
PERSON: Tina Boussard
http://purl.obolibrary.org/obo/OBI_0200200
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200200
chi square test
http://purl.obolibrary.org/obo/OBI_0200201
ANOVA
http://purl.obolibrary.org/obo/OBI_0200201
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0200201
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0200201
ANalysis Of VAriance (ANOVA) is a data transformation in which a statistical test is performed to evaluate the null hypothesis that the means computed over the different groups as specified by the investigator do not differ. The test compares an F-statistics (a ratio of means) to an F-distribution and produces a p-value, used to reject or accept the null hypothesis given a false positive rate. The test assumes normality and equivariance of the data.
http://purl.obolibrary.org/obo/OBI_0200201
AGB and PRS augmented the class with formal definitions as part of STATO extension
http://purl.obolibrary.org/obo/OBI_0200201
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/OBI_0200201
James Malone
http://purl.obolibrary.org/obo/OBI_0200201
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0200201
Analysis of Variance
http://purl.obolibrary.org/obo/OBI_0200201
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0200201
http://purl.obolibrary.org/obo/OBI_0200201
stat.anova()
http://purl.obolibrary.org/obo/OBI_0200201
ANOVA
http://purl.obolibrary.org/obo/OBI_0300311
observation design
http://purl.obolibrary.org/obo/OBI_0300311
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
http://purl.obolibrary.org/obo/OBI_0300311
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0300311
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
http://purl.obolibrary.org/obo/OBI_0300311
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0300311
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0300311
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0300311
observation design
http://purl.obolibrary.org/obo/OBI_0302884
extraction
http://purl.obolibrary.org/obo/OBI_0302884
nucleic acid extraction using phenol chloroform
http://purl.obolibrary.org/obo/OBI_0302884
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0302884
A material separation in which a desired component of an input material is separated from the remainder
http://purl.obolibrary.org/obo/OBI_0302884
Person:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0302884
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0302884
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0302884
extraction
http://purl.obolibrary.org/obo/OBI_0302900
group randomization
http://purl.obolibrary.org/obo/OBI_0302900
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
http://purl.obolibrary.org/obo/OBI_0302900
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0302900
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
http://purl.obolibrary.org/obo/OBI_0302900
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0302900
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
http://purl.obolibrary.org/obo/OBI_0302900
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0302900
group randomization
http://purl.obolibrary.org/obo/OBI_0302903
nucleic acid hybridization
http://purl.obolibrary.org/obo/OBI_0302903
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
http://purl.obolibrary.org/obo/OBI_0302903
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0302903
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
http://purl.obolibrary.org/obo/OBI_0302903
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0302903
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
http://purl.obolibrary.org/obo/OBI_0302903
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0302903
hybridization assay
http://purl.obolibrary.org/obo/OBI_0302903
nucleic acid hybridization
http://purl.obolibrary.org/obo/OBI_0400043
flow cell
http://purl.obolibrary.org/obo/OBI_0400043
Biofilm Flow Cell
http://purl.obolibrary.org/obo/OBI_0400043
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400043
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
http://purl.obolibrary.org/obo/OBI_0400043
Person:John Quinn
http://purl.obolibrary.org/obo/OBI_0400043
flow_cell
http://purl.obolibrary.org/obo/OBI_0400043
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
http://purl.obolibrary.org/obo/OBI_0400043
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400043
flow cell
http://purl.obolibrary.org/obo/OBI_0400044
flow cytometer
http://purl.obolibrary.org/obo/OBI_0400044
FACS Calibur
http://purl.obolibrary.org/obo/OBI_0400044
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0400044
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
http://purl.obolibrary.org/obo/OBI_0400044
John Quinn
http://purl.obolibrary.org/obo/OBI_0400044
http://en.wikipedia.org/wiki/Flow_cytometer
http://purl.obolibrary.org/obo/OBI_0400044
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400044
flow cytometer
http://purl.obolibrary.org/obo/OBI_0400065
light source
http://purl.obolibrary.org/obo/OBI_0400065
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400065
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
http://purl.obolibrary.org/obo/OBI_0400065
Elizabeth M. Goralczyk
http://purl.obolibrary.org/obo/OBI_0400065
John Quinn
http://purl.obolibrary.org/obo/OBI_0400065
Olga Tchuvatkina
http://purl.obolibrary.org/obo/OBI_0400065
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
http://purl.obolibrary.org/obo/OBI_0400065
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400065
light source
http://purl.obolibrary.org/obo/OBI_0400078
obscuration bar
http://purl.obolibrary.org/obo/OBI_0400078
obscuration bar in a flow cytometer
http://purl.obolibrary.org/obo/OBI_0400078
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400078
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
http://purl.obolibrary.org/obo/OBI_0400078
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0400078
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
http://purl.obolibrary.org/obo/OBI_0400078
John Quinn
http://purl.obolibrary.org/obo/OBI_0400078
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400078
obscuration bar
http://purl.obolibrary.org/obo/OBI_0400079
optical filter
http://purl.obolibrary.org/obo/OBI_0400079
720 LP filter, 580/30 BP filter
http://purl.obolibrary.org/obo/OBI_0400079
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400079
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
http://purl.obolibrary.org/obo/OBI_0400079
John Quinn
http://purl.obolibrary.org/obo/OBI_0400079
http://en.wikipedia.org/wiki/Optical_filter
http://purl.obolibrary.org/obo/OBI_0400079
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400079
optical filter
http://purl.obolibrary.org/obo/OBI_0400082
photodetector
http://purl.obolibrary.org/obo/OBI_0400082
A photomultiplier tube, a photo diode
http://purl.obolibrary.org/obo/OBI_0400082
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400082
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
http://purl.obolibrary.org/obo/OBI_0400082
John Quinn
http://purl.obolibrary.org/obo/OBI_0400082
http://einstein.stanford.edu/content/glossary/glossary.html
http://purl.obolibrary.org/obo/OBI_0400082
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400082
photodetector
http://purl.obolibrary.org/obo/OBI_0400103
DNA sequencer
http://purl.obolibrary.org/obo/OBI_0400103
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
http://purl.obolibrary.org/obo/OBI_0400103
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0400103
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
http://purl.obolibrary.org/obo/OBI_0400103
Trish Whetzel
http://purl.obolibrary.org/obo/OBI_0400103
MO
http://purl.obolibrary.org/obo/OBI_0400103
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400103
DNA sequencer
http://purl.obolibrary.org/obo/OBI_0400110
hybridization chamber
http://purl.obolibrary.org/obo/OBI_0400110
Glass Array Hybridization Cassette
http://purl.obolibrary.org/obo/OBI_0400110
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0400110
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
http://purl.obolibrary.org/obo/OBI_0400110
Trish Whetzel
http://purl.obolibrary.org/obo/OBI_0400110
MO_563 hybridization_chamber
http://purl.obolibrary.org/obo/OBI_0400110
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400110
hybridization chamber
http://purl.obolibrary.org/obo/OBI_0400137
cytometer
http://purl.obolibrary.org/obo/OBI_0400137
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0400137
A cytometer is an instrument for counting and measuring cells.
http://purl.obolibrary.org/obo/OBI_0400137
Melanie Courtot
http://purl.obolibrary.org/obo/OBI_0400137
http://medical.merriam-webster.com/medical/cytometer
http://purl.obolibrary.org/obo/OBI_0400137
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400137
cytometer
http://purl.obolibrary.org/obo/OBI_0400147
microarray
http://purl.obolibrary.org/obo/OBI_0400147
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
http://purl.obolibrary.org/obo/OBI_0400147
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0400147
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
http://purl.obolibrary.org/obo/OBI_0400147
Daniel Schober
http://purl.obolibrary.org/obo/OBI_0400147
PERSON: Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0400147
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400147
microarray
http://purl.obolibrary.org/obo/OBI_0400148
DNA microarray
http://purl.obolibrary.org/obo/OBI_0400148
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
http://purl.obolibrary.org/obo/OBI_0400148
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400148
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
http://purl.obolibrary.org/obo/OBI_0400148
PERSON: Daniel Schober
http://purl.obolibrary.org/obo/OBI_0400148
PERSON: Frank Gibson
http://purl.obolibrary.org/obo/OBI_0400148
DNA Chip
http://purl.obolibrary.org/obo/OBI_0400148
DNA-array
http://purl.obolibrary.org/obo/OBI_0400148
Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
http://purl.obolibrary.org/obo/OBI_0400148
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400148
DNA microarray
http://purl.obolibrary.org/obo/OBI_0400153
droplet sorter
http://purl.obolibrary.org/obo/OBI_0400153
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/OBI_0400153
OBI Instrument branch
http://purl.obolibrary.org/obo/OBI_0400153
OBI Instrument branch
http://purl.obolibrary.org/obo/OBI_0400153
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0400153
droplet sorter
http://purl.obolibrary.org/obo/OBI_0500000
study design
http://purl.obolibrary.org/obo/OBI_0500000
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
http://purl.obolibrary.org/obo/OBI_0500000
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0500000
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
http://purl.obolibrary.org/obo/OBI_0500000
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
http://purl.obolibrary.org/obo/OBI_0500000
PERSON: Chris Stoeckert
http://purl.obolibrary.org/obo/OBI_0500000
experimental design
http://purl.obolibrary.org/obo/OBI_0500000
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
http://purl.obolibrary.org/obo/OBI_0500000
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500000
http://purl.obolibrary.org/obo/OBI_0500000
study design
http://purl.obolibrary.org/obo/OBI_0500002
repeated measure design
http://purl.obolibrary.org/obo/OBI_0500002
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
http://purl.obolibrary.org/obo/OBI_0500002
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0500002
a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
http://purl.obolibrary.org/obo/OBI_0500002
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0500002
http://www.holah.karoo.net/experimentaldesigns.htm
http://purl.obolibrary.org/obo/OBI_0500002
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500002
http://purl.obolibrary.org/obo/OBI_0500002
repeated measure design
http://purl.obolibrary.org/obo/OBI_0500003
cross over design
http://purl.obolibrary.org/obo/OBI_0500003
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
http://purl.obolibrary.org/obo/OBI_0500003
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0500003
a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
http://purl.obolibrary.org/obo/OBI_0500003
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500003
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
http://purl.obolibrary.org/obo/OBI_0500003
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500003
http://purl.obolibrary.org/obo/OBI_0500003
cross over design
http://purl.obolibrary.org/obo/OBI_0500005
matched pairs design
http://purl.obolibrary.org/obo/OBI_0500005
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
http://purl.obolibrary.org/obo/OBI_0500005
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500005
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
http://purl.obolibrary.org/obo/OBI_0500005
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500005
http://www.holah.karoo.net/experimentaldesigns.htm
http://purl.obolibrary.org/obo/OBI_0500005
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500005
http://purl.obolibrary.org/obo/OBI_0500005
matched pairs design
http://purl.obolibrary.org/obo/OBI_0500006
parallel group design
http://purl.obolibrary.org/obo/OBI_0500006
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
http://purl.obolibrary.org/obo/OBI_0500006
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500006
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
http://purl.obolibrary.org/obo/OBI_0500006
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500006
independent measure design
http://purl.obolibrary.org/obo/OBI_0500006
http://www.holah.karoo.net/experimentaldesigns.htm
http://purl.obolibrary.org/obo/OBI_0500006
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500006
parallel group design
http://purl.obolibrary.org/obo/OBI_0500007
randomized complete block design
http://purl.obolibrary.org/obo/OBI_0500007
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
http://purl.obolibrary.org/obo/OBI_0500007
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500007
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
http://purl.obolibrary.org/obo/OBI_0500007
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500007
http://www.tufts.edu/~gdallal/ranblock.htm
http://purl.obolibrary.org/obo/OBI_0500007
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500007
http://purl.obolibrary.org/obo/OBI_0500007
randomized complete block design
http://purl.obolibrary.org/obo/OBI_0500011
latin square design
http://purl.obolibrary.org/obo/OBI_0500011
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
http://purl.obolibrary.org/obo/OBI_0500011
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500011
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables). The 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
http://purl.obolibrary.org/obo/OBI_0500011
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500011
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
http://purl.obolibrary.org/obo/OBI_0500011
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500011
http://purl.obolibrary.org/obo/OBI_0500011
latin square design
http://purl.obolibrary.org/obo/OBI_0500012
graeco latin square design
http://purl.obolibrary.org/obo/OBI_0500012
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
http://purl.obolibrary.org/obo/OBI_0500012
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500012
graeco-latin square design is a block design which declares 3 blocking variables (aka nuisance variables) in addition to the treatment variable
http://purl.obolibrary.org/obo/OBI_0500012
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500012
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
http://purl.obolibrary.org/obo/OBI_0500012
only 2 articles in pubmed ->probably irrelevant
http://purl.obolibrary.org/obo/OBI_0500012
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500012
http://purl.obolibrary.org/obo/OBI_0500012
Euler square design
http://purl.obolibrary.org/obo/OBI_0500012
orthogonal latin squares design
http://purl.obolibrary.org/obo/OBI_0500012
graeco latin square design
http://purl.obolibrary.org/obo/OBI_0500013
hyper graeco latin square design
http://purl.obolibrary.org/obo/OBI_0500013
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500013
hyper graeco-latin square design is a block design which declares 4 blocking variables (aka nuisance variables) in addition to the treatment variable
http://purl.obolibrary.org/obo/OBI_0500013
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500013
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
http://purl.obolibrary.org/obo/OBI_0500013
no example found in pubmed->not in use in the community
http://purl.obolibrary.org/obo/OBI_0500013
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500013
http://purl.obolibrary.org/obo/OBI_0500013
hyper graeco latin square design
http://purl.obolibrary.org/obo/OBI_0500014
factorial design
http://purl.obolibrary.org/obo/OBI_0500014
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
http://purl.obolibrary.org/obo/OBI_0500014
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500014
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://purl.obolibrary.org/obo/OBI_0500014
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500014
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
http://purl.obolibrary.org/obo/OBI_0500014
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500014
http://purl.obolibrary.org/obo/OBI_0500014
factorial design
http://purl.obolibrary.org/obo/OBI_0500015
2x2 factorial design
http://purl.obolibrary.org/obo/OBI_0500015
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
http://purl.obolibrary.org/obo/OBI_0500015
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0500015
a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
http://purl.obolibrary.org/obo/OBI_0500015
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500015
PMID: 17561240
http://purl.obolibrary.org/obo/OBI_0500015
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500015
http://purl.obolibrary.org/obo/OBI_0500015
2x2 factorial design
http://purl.obolibrary.org/obo/OBI_0500016
fractional factorial design
http://purl.obolibrary.org/obo/OBI_0500016
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500016
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
http://purl.obolibrary.org/obo/OBI_0500016
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0500016
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
http://purl.obolibrary.org/obo/OBI_0500016
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500016
fractional factorial design
http://purl.obolibrary.org/obo/OBI_0500017
dye swap design
http://purl.obolibrary.org/obo/OBI_0500017
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
http://purl.obolibrary.org/obo/OBI_0500017
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500017
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
http://purl.obolibrary.org/obo/OBI_0500017
Philippe Rocca-Serra on behalf of MO
http://purl.obolibrary.org/obo/OBI_0500017
MO_858
http://purl.obolibrary.org/obo/OBI_0500017
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500017
http://purl.obolibrary.org/obo/OBI_0500017
dye swap design
http://purl.obolibrary.org/obo/OBI_0500020
time series design
http://purl.obolibrary.org/obo/OBI_0500020
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
http://purl.obolibrary.org/obo/OBI_0500020
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0500020
Groups of assays that are related as part of a time series.
http://purl.obolibrary.org/obo/OBI_0500020
PRS-AGB adding formal restriction on independent variable specification about time (march 2013) and making time series design class a defined class.
http://purl.obolibrary.org/obo/OBI_0500020
Philippe Rocca-Serra on behalf of MO
http://purl.obolibrary.org/obo/OBI_0500020
MO_887
http://purl.obolibrary.org/obo/OBI_0500020
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0500020
http://purl.obolibrary.org/obo/OBI_0500020
time series design
http://purl.obolibrary.org/obo/OBI_0600005
collecting specimen from organism
http://purl.obolibrary.org/obo/OBI_0600005
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
http://purl.obolibrary.org/obo/OBI_0600005
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0600005
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
http://purl.obolibrary.org/obo/OBI_0600005
PERSON:Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0600005
IEDB
http://purl.obolibrary.org/obo/OBI_0600005
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600005
collecting specimen from organism
http://purl.obolibrary.org/obo/OBI_0600014
material component separation
http://purl.obolibrary.org/obo/OBI_0600014
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
http://purl.obolibrary.org/obo/OBI_0600014
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0600014
a material processing in which components of an input material become segregated in space
http://purl.obolibrary.org/obo/OBI_0600014
Bjoern Peters
http://purl.obolibrary.org/obo/OBI_0600014
IEDB
http://purl.obolibrary.org/obo/OBI_0600014
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600014
material component separation
http://purl.obolibrary.org/obo/OBI_0600015
group assignment
http://purl.obolibrary.org/obo/OBI_0600015
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
http://purl.obolibrary.org/obo/OBI_0600015
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_0600015
group assignment is a process which has an organism as specified input and during which a role is assigned
http://purl.obolibrary.org/obo/OBI_0600015
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_0600015
cohort assignment
http://purl.obolibrary.org/obo/OBI_0600015
study assignment
http://purl.obolibrary.org/obo/OBI_0600015
OBI Plan
http://purl.obolibrary.org/obo/OBI_0600015
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600015
group assignment
http://purl.obolibrary.org/obo/OBI_0600024
maintaining cell culture
http://purl.obolibrary.org/obo/OBI_0600024
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
http://purl.obolibrary.org/obo/OBI_0600024
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0600024
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
http://purl.obolibrary.org/obo/OBI_0600024
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0600024
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0600024
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600024
maintaining cell culture
http://purl.obolibrary.org/obo/OBI_0600036
establishing cell culture
http://purl.obolibrary.org/obo/OBI_0600036
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0600036
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
http://purl.obolibrary.org/obo/OBI_0600036
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0600036
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0600036
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600036
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
http://purl.obolibrary.org/obo/OBI_0600036
establishing cell culture
http://purl.obolibrary.org/obo/OBI_0600038
addition of molecular label
http://purl.obolibrary.org/obo/OBI_0600038
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
http://purl.obolibrary.org/obo/OBI_0600038
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0600038
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
http://purl.obolibrary.org/obo/OBI_0600038
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/OBI_0600038
labeling
http://purl.obolibrary.org/obo/OBI_0600038
OBI developer call, 3-12-12
http://purl.obolibrary.org/obo/OBI_0600038
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600038
addition of molecular label
http://purl.obolibrary.org/obo/OBI_0600047
sequencing assay
http://purl.obolibrary.org/obo/OBI_0600047
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
http://purl.obolibrary.org/obo/OBI_0600047
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0600047
the use of a chemical or biochemical means to infer the sequence of a biomaterial
http://purl.obolibrary.org/obo/OBI_0600047
has_output should be sequence of input; we don't have sequence well defined yet
http://purl.obolibrary.org/obo/OBI_0600047
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0600047
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0600047
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600047
sequencing assay
http://purl.obolibrary.org/obo/OBI_0600064
recombinant vector cloning
http://purl.obolibrary.org/obo/OBI_0600064
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_0600064
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
http://purl.obolibrary.org/obo/OBI_0600064
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
http://purl.obolibrary.org/obo/OBI_0600064
molecular cloning
http://purl.obolibrary.org/obo/OBI_0600064
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0600064
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0600064
recombinant vector cloning
http://purl.obolibrary.org/obo/OBI_0666667
nucleic acid extraction
http://purl.obolibrary.org/obo/OBI_0666667
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
http://purl.obolibrary.org/obo/OBI_0666667
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/OBI_0666667
a material separation to recover the nucleic acid fraction of an input material
http://purl.obolibrary.org/obo/OBI_0666667
PlanAndPlannedProcess Branch
http://purl.obolibrary.org/obo/OBI_0666667
OBI branch derived
http://purl.obolibrary.org/obo/OBI_0666667
requested by Helen Parkinson for MO. Could be defined class
http://purl.obolibrary.org/obo/OBI_0666667
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_0666667
nucleic acid extraction
http://purl.obolibrary.org/obo/OBI_1000029
phage display library
http://purl.obolibrary.org/obo/OBI_1000029
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
http://purl.obolibrary.org/obo/OBI_1000029
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/OBI_1000029
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
http://purl.obolibrary.org/obo/OBI_1000029
PERSON: Bjoern Peters
http://purl.obolibrary.org/obo/OBI_1000029
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/OBI_1000029
display library
http://purl.obolibrary.org/obo/OBI_1000029
WEB: http://www.immuneepitope.org/home.do
http://purl.obolibrary.org/obo/OBI_1000029
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_1000029
phage display library
http://purl.obolibrary.org/obo/OBI_1110108
material to be added
http://purl.obolibrary.org/obo/OBI_1110108
A mixture of peptides that is being added into a cell culture.
http://purl.obolibrary.org/obo/OBI_1110108
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_1110108
a material that is added to another one in a material combination process
http://purl.obolibrary.org/obo/OBI_1110108
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
http://purl.obolibrary.org/obo/OBI_1110108
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
http://purl.obolibrary.org/obo/OBI_1110108
IEDB
http://purl.obolibrary.org/obo/OBI_1110108
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_1110108
material to be added
http://purl.obolibrary.org/obo/OBI_1110109
target of material addition
http://purl.obolibrary.org/obo/OBI_1110109
A cell culture into which a mixture of peptides is being added.
http://purl.obolibrary.org/obo/OBI_1110109
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_1110109
A material entity into which another is being added in a material combinatino process
http://purl.obolibrary.org/obo/OBI_1110109
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
http://purl.obolibrary.org/obo/OBI_1110109
IEDB
http://purl.obolibrary.org/obo/OBI_1110109
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OBI_1110109
target of material addition
http://purl.obolibrary.org/obo/OBI_9991118
IEDB alternative term
http://purl.obolibrary.org/obo/OBI_9991118
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/OBI_9991118
An alternative term used by the IEDB.
http://purl.obolibrary.org/obo/OBI_9991118
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
http://purl.obolibrary.org/obo/OBI_9991118
IEDB
http://purl.obolibrary.org/obo/OBI_9991118
IEDB alternative term
http://purl.obolibrary.org/obo/OGMS_0000023
phenotype
http://purl.obolibrary.org/obo/OGMS_0000023
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
http://purl.obolibrary.org/obo/OGMS_0000023
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/OGMS_0000023
http://purl.obolibrary.org/obo/ogms.owl
http://purl.obolibrary.org/obo/OGMS_0000023
phenotype
http://purl.obolibrary.org/obo/PR_000000001
protein
http://purl.obolibrary.org/obo/PR_000000001
antithrombin III is a protein
http://purl.obolibrary.org/obo/PR_000000001
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
http://purl.obolibrary.org/obo/PR_000000001
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/PR_000000001
http://purl.obolibrary.org/obo/pr.owl
http://purl.obolibrary.org/obo/PR_000000001
protein
http://purl.obolibrary.org/obo/REO_0000171
molecular label role
http://purl.obolibrary.org/obo/REO_0000171
a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
http://purl.obolibrary.org/obo/REO_0000171
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
http://purl.obolibrary.org/obo/REO_0000171
molecular tracer role
http://purl.obolibrary.org/obo/REO_0000171
OBI developer call, 3-12-12
http://purl.obolibrary.org/obo/REO_0000171
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/REO_0000171
http://purl.obolibrary.org/obo/reo.owl
http://purl.obolibrary.org/obo/REO_0000171
molecular label role
http://purl.obolibrary.org/obo/REO_0000280
molecular label
http://purl.obolibrary.org/obo/REO_0000280
a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
http://purl.obolibrary.org/obo/REO_0000280
molecular tracer
http://purl.obolibrary.org/obo/REO_0000280
OBI developer call, 3-12-12
http://purl.obolibrary.org/obo/REO_0000280
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/REO_0000280
http://purl.obolibrary.org/obo/reo.owl
http://purl.obolibrary.org/obo/REO_0000280
molecular label
http://purl.obolibrary.org/obo/RO_0001000
derives from
http://purl.obolibrary.org/obo/RO_0001000
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/RO_0001000
http://purl.obolibrary.org/obo/ro.owl
http://purl.obolibrary.org/obo/RO_0001000
derives from
http://purl.obolibrary.org/obo/SO_0000001
region
http://purl.obolibrary.org/obo/SO_0000001
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
http://purl.obolibrary.org/obo/SO_0000001
primary structure of sequence macromolecule
http://purl.obolibrary.org/obo/SO_0000001
sequence
http://purl.obolibrary.org/obo/SO_0000001
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/SO_0000001
http://purl.obolibrary.org/obo/so.owl
http://purl.obolibrary.org/obo/SO_0000001
region
http://purl.obolibrary.org/obo/STATO_0000001
property to indicate that a design declares a variable; the inverse property is 'is declared by'
http://purl.obolibrary.org/obo/STATO_0000001
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000001
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000001
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000001
declares
http://purl.obolibrary.org/obo/STATO_0000002
digital images may be stored as electronic file in TIFF format on mass memory storage devices
http://purl.obolibrary.org/obo/STATO_0000002
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000002
an electronic file is an information content entity which conforms to a specification or format and which is meant to hold data and information in digital form, accessible to software agents
http://purl.obolibrary.org/obo/STATO_0000002
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000002
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000002
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000002
STATO
http://purl.obolibrary.org/obo/STATO_0000002
digital file
http://purl.obolibrary.org/obo/STATO_0000003
a balanced design is a an experimental design where all experimental group have the an equal number of subject observations
http://purl.obolibrary.org/obo/STATO_0000003
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000003
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000003
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000003
STATO
http://purl.obolibrary.org/obo/STATO_0000003
http://purl.obolibrary.org/obo/STATO_0000003
balanced design
http://purl.obolibrary.org/obo/STATO_0000004
property to indicate the variables declared by a design; the inverse property is 'declares'
http://purl.obolibrary.org/obo/STATO_0000004
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000004
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000004
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000004
is declared by
http://purl.obolibrary.org/obo/STATO_0000005
a single factor design is a study design which declares exactly 1 independent variable
http://purl.obolibrary.org/obo/STATO_0000005
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000005
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000005
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000005
STATO
http://purl.obolibrary.org/obo/STATO_0000005
http://purl.obolibrary.org/obo/STATO_0000005
single factor design
http://purl.obolibrary.org/obo/STATO_0000006
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000006
x-axis is a cartesian coordinate axis which is orthogonal to the y-axis and the z-axis
http://purl.obolibrary.org/obo/STATO_0000006
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000006
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000006
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000006
STATO
http://purl.obolibrary.org/obo/STATO_0000006
x-axis
http://purl.obolibrary.org/obo/STATO_0000007
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000007
an axis is a line graph used as reference line for the measurement of coordinates.
http://purl.obolibrary.org/obo/STATO_0000007
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000007
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000007
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000007
http://www.oxforddictionaries.com/definition/english/axis
http://purl.obolibrary.org/obo/STATO_0000007
axis
http://purl.obolibrary.org/obo/STATO_0000008
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000008
y-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the z-axis
http://purl.obolibrary.org/obo/STATO_0000008
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000008
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000008
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000008
STATO
http://purl.obolibrary.org/obo/STATO_0000008
y-axis
http://purl.obolibrary.org/obo/STATO_0000009
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000009
A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.
http://purl.obolibrary.org/obo/STATO_0000009
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000009
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000009
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000009
http://en.wikipedia.org/wiki/Cartesian_coordinate_system
http://purl.obolibrary.org/obo/STATO_0000009
http://purl.obolibrary.org/obo/STATO_0000009
cartesian coordinate system
http://purl.obolibrary.org/obo/STATO_0000010
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000010
In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space.
http://purl.obolibrary.org/obo/STATO_0000010
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000010
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000010
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000010
http://en.wikipedia.org/wiki/Coordinate_system
http://purl.obolibrary.org/obo/STATO_0000010
http://purl.obolibrary.org/obo/STATO_0000010
coordinate system
http://purl.obolibrary.org/obo/STATO_0000011
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000011
a cartesian axis is one of 3 the axis in a cartesian coordinate system defining a referential in 3 dimensions. each of the axis is orthogonal to the other 2
http://purl.obolibrary.org/obo/STATO_0000011
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000011
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000011
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000011
rectangular coordinate axis
http://purl.obolibrary.org/obo/STATO_0000011
adapted from Wolfram Alpha:
https://www.wolframalpha.com/input/?i=cartesian+coordinates&lk=4&num=6&lk=4&num=6
http://purl.obolibrary.org/obo/STATO_0000011
cartesian coordinate axis
http://purl.obolibrary.org/obo/STATO_0000012
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000012
z-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the y-axis
http://purl.obolibrary.org/obo/STATO_0000012
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000012
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000012
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000012
STATO
http://purl.obolibrary.org/obo/STATO_0000012
z-axis
http://purl.obolibrary.org/obo/STATO_0000013
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000013
a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region
http://purl.obolibrary.org/obo/STATO_0000013
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000013
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000013
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000013
http://purl.obolibrary.org/obo/STATO_0000013
two dimensional cartesian coordinate system
http://purl.obolibrary.org/obo/STATO_0000014
http://purl.obolibrary.org/obo/IAO_0000226
http://purl.obolibrary.org/obo/STATO_0000014
In mathematics, a spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.
http://purl.obolibrary.org/obo/STATO_0000014
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000014
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000014
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000014
https://en.wikipedia.org/wiki/Spherical_coordinate_system
http://purl.obolibrary.org/obo/STATO_0000014
http://purl.obolibrary.org/obo/STATO_0000014
spherical coordinate system
http://purl.obolibrary.org/obo/STATO_0000015
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000015
A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. The latter distance is given as a positive or negative number depending on which side of the reference plane faces the point.
http://purl.obolibrary.org/obo/STATO_0000015
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000015
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000015
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000015
https://en.wikipedia.org/wiki/Cylindrical_coordinate_system
http://purl.obolibrary.org/obo/STATO_0000015
http://purl.obolibrary.org/obo/STATO_0000015
cylindrical coordinate system
http://purl.obolibrary.org/obo/STATO_0000016
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000016
In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.
http://purl.obolibrary.org/obo/STATO_0000016
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000016
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000016
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000016
http://en.wikipedia.org/wiki/Polar_coordinate_system
http://purl.obolibrary.org/obo/STATO_0000016
http://purl.obolibrary.org/obo/STATO_0000016
polar coordinate system
http://purl.obolibrary.org/obo/STATO_0000017
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000017
Wilks' lambda distribution (named for Samuel S. Wilks), is a probability distribution used in multivariate hypothesis testing, especially with regard to the likelihood-ratio test and Multivariate analysis of variance. It is a multivariate generalization of the univariate F-distribution, and generalizes the F-distribution in the same way that the Hotelling's T-squared distribution generalizes Student's t-distribution.
http://purl.obolibrary.org/obo/STATO_0000017
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000017
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000017
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000017
wikipedia:
last accessed: 2013-09-11
http://en.wikipedia.org/wiki/Wilks%27_lambda_distribution
http://purl.obolibrary.org/obo/STATO_0000017
Wilk's lambda distribution
http://purl.obolibrary.org/obo/STATO_0000018
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000018
A cartesian spatial coordinate datum chosen as a fixed point of reference in a three dimensional spatial region.
http://purl.obolibrary.org/obo/STATO_0000018
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000018
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000018
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000018
three dimensional cartesian spatial coordinate origin
http://purl.obolibrary.org/obo/STATO_0000019
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000019
normal distribution hypothesis is a goodness of fit hypothesis stating that the distribution computed from the sample population fits a normal distribution
http://purl.obolibrary.org/obo/STATO_0000019
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000019
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000019
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000019
STATO
http://purl.obolibrary.org/obo/STATO_0000019
normal distribution hypothesis
http://purl.obolibrary.org/obo/STATO_0000020
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000020
A cartesian spatial coordinate datum chosen as a fixed point of reference in a two dimensional spatial region.
http://purl.obolibrary.org/obo/STATO_0000020
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000020
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000020
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000020
two dimensional cartesian spatial coordinate origin
http://purl.obolibrary.org/obo/STATO_0000021
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000021
a confidence interval which covers 90% of the sampling distribution, meaning that there is a 90% risk of false positive (type I error)
http://purl.obolibrary.org/obo/STATO_0000021
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000021
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000021
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000021
STATO
http://purl.obolibrary.org/obo/STATO_0000021
http://purl.obolibrary.org/obo/STATO_0000021
90% confidence interval
http://purl.obolibrary.org/obo/STATO_0000022
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000022
a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axis and which may be used to describe a 3 dimensional spatial region
http://purl.obolibrary.org/obo/STATO_0000022
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000022
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000022
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000022
http://purl.obolibrary.org/obo/STATO_0000022
one dimensional cartesian coordinate system
http://purl.obolibrary.org/obo/STATO_0000023
http://www.stat.duke.edu/courses/Spring98/sta110c/qtable.html
http://purl.obolibrary.org/obo/STATO_0000023
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000023
The studentized range (q) distribution is a probability distribution used by the Tukey Honestly Significant Difference test.
The distribution of the statistic
[x̄(k)- x̄(1)]/(s/√n)
where random samples of size n have been taken from k independent and identically distributed normal populations, with x̄(1) and x̄(k) being, respectively, the smallest and largest of the k sample means, and s2 being the pooled estimate of the common variance. This statistic is particularly used in multiple comparison tests.
http://purl.obolibrary.org/obo/STATO_0000023
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000023
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000023
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000023
q distribution
http://purl.obolibrary.org/obo/STATO_0000023
A Dictionary of Statistics (2 rev ed.), OUP. ISBN-13: 9780199541454
http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1588
http://purl.obolibrary.org/obo/STATO_0000023
http://purl.obolibrary.org/obo/STATO_0000023
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Tukey.html
http://purl.obolibrary.org/obo/STATO_0000023
studentized range distribution
http://purl.obolibrary.org/obo/STATO_0000024
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000024
a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region
http://purl.obolibrary.org/obo/STATO_0000024
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000024
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000024
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000024
http://purl.obolibrary.org/obo/STATO_0000024
three dimensional cartesian coordinate system
http://purl.obolibrary.org/obo/STATO_0000025
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000025
A cartesian spatial coordinate datum chosen as a fixed point of reference in a one dimensional spatial region.
http://purl.obolibrary.org/obo/STATO_0000025
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000025
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000025
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000025
one dimensional cartesian spatial coordinate origin
http://purl.obolibrary.org/obo/STATO_0000026
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000026
A cartesian spatial coordinate datum chosen as a fixed point of reference in a spatial region.
http://purl.obolibrary.org/obo/STATO_0000026
placeholder, more work needed
http://purl.obolibrary.org/obo/STATO_0000026
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000026
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000026
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000026
cartesian spatial coordinate origin
http://purl.obolibrary.org/obo/STATO_0000027
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000027
linkage between 2 categorical variable test is a statistical test which evaluates if there is an association between a predictor variable assuming discrete values and a response variable also assuming discrete values
http://purl.obolibrary.org/obo/STATO_0000027
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000027
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000027
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000027
test of association
http://purl.obolibrary.org/obo/STATO_0000027
STATO
http://purl.obolibrary.org/obo/STATO_0000027
test of independence
http://purl.obolibrary.org/obo/STATO_0000027
test of independence between variables
http://purl.obolibrary.org/obo/STATO_0000027
test of association between categorical variables
http://purl.obolibrary.org/obo/STATO_0000028
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000028
measure of variation or statistical dispersion is a data item which describes how much a theoritical distribution or dataset is spread.
http://purl.obolibrary.org/obo/STATO_0000028
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000028
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000028
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000028
STATO
http://purl.obolibrary.org/obo/STATO_0000028
measure of dispersion
http://purl.obolibrary.org/obo/STATO_0000028
measure of variation
http://purl.obolibrary.org/obo/STATO_0000028
measure of variation
http://purl.obolibrary.org/obo/STATO_0000029
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000029
a measure of central tendency is a data item which attempts to describe a set of data by identifying the value of its centre.
http://purl.obolibrary.org/obo/STATO_0000029
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000029
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000029
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000029
measure of central tendency
http://purl.obolibrary.org/obo/STATO_0000029
measure of central tendency
http://purl.obolibrary.org/obo/STATO_0000030
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000030
Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution.
http://purl.obolibrary.org/obo/STATO_0000030
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000030
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000030
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000030
STATO
http://purl.obolibrary.org/obo/STATO_0000030
Chi-Squared statistic
http://purl.obolibrary.org/obo/STATO_0000031
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000031
binary classification (or binomial classification) is a data transformation which aims to cast members of a set into 2 disjoint groups depending on whether the element have a given property/feature or not.
http://purl.obolibrary.org/obo/STATO_0000031
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000031
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000031
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000031
adapted from wikipedia:
http://en.wikipedia.org/wiki/Binary_classifier
last accessed: 2013-11-21
http://purl.obolibrary.org/obo/STATO_0000031
binomial classification
http://purl.obolibrary.org/obo/STATO_0000031
binary classification
http://purl.obolibrary.org/obo/STATO_0000032
an alternative term used for STATO statistical ontology and ISA team
http://purl.obolibrary.org/obo/STATO_0000032
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000032
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000032
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000032
STATO alternative term
http://purl.obolibrary.org/obo/STATO_0000033
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000033
The mode is a data item which corresponds to the most frequently occurring number in a set of numbers.
http://purl.obolibrary.org/obo/STATO_0000033
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000033
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000033
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000033
http://www.sagepub.com/upm-data/47775_ch_3.pdf
http://purl.obolibrary.org/obo/STATO_0000033
mode
http://purl.obolibrary.org/obo/STATO_0000033
scipy.stats.mode(a, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mode.html#scipy.stats.mode
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L586
http://purl.obolibrary.org/obo/STATO_0000033
mode
http://purl.obolibrary.org/obo/STATO_0000034
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000034
a model parameter is a data item which is part of a model and which is meant to characterize an theoritecal or unknown population. a model parameter may be estimated by considering the properties of samples presumably taken from the theoritecal population
http://purl.obolibrary.org/obo/STATO_0000034
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000034
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000034
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000034
STATO
http://purl.obolibrary.org/obo/STATO_0000034
model parameter
http://purl.obolibrary.org/obo/STATO_0000035
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000035
the range is a measure of variation which describes the difference between the lowest score and the highest score in a set of numbers (a data set)
http://purl.obolibrary.org/obo/STATO_0000035
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000035
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000035
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000035
http://www.sagepub.com/upm-data/47775_ch_3.pdf
http://purl.obolibrary.org/obo/STATO_0000035
http://purl.obolibrary.org/obo/STATO_0000035
range(..., na.rm = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/base/html/range.html
http://purl.obolibrary.org/obo/STATO_0000035
range
http://purl.obolibrary.org/obo/STATO_0000036
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000036
Outliers are deviant scores that have been legitimately gathered and are not due to equipment failures.
http://purl.obolibrary.org/obo/STATO_0000036
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000036
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000036
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000036
http://www.sagepub.com/upm-data/47775_ch_3.pdf
http://purl.obolibrary.org/obo/STATO_0000036
outlier
http://purl.obolibrary.org/obo/STATO_0000037
http://stats.stackexchange.com/questions/50623/r-calculating-mean-and-standard-error-of-mean-for-factors-with-lm-vs-direct
http://purl.obolibrary.org/obo/STATO_0000037
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000037
The standard error of the mean (SEM) is data item denoting the standard deviation of the sample-mean's estimate of a population mean.
It is calculated by dividing the sample standard deviation (i.e., the sample-based estimate of the standard deviation of the population) by the square root of n , the size (number of observations) of the sample.
http://purl.obolibrary.org/obo/STATO_0000037
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000037
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000037
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000037
SEM
http://purl.obolibrary.org/obo/STATO_0000037
adapted from wikipedia (https://en.wikipedia.org/wiki/Standard_error)
http://purl.obolibrary.org/obo/STATO_0000037
http://purl.obolibrary.org/obo/STATO_0000037
scipy.stats.sem(a, axis=0, ddof=1)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.sem.html#scipy.stats.sem
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L1928
http://purl.obolibrary.org/obo/STATO_0000037
standard error of the mean
http://purl.obolibrary.org/obo/STATO_0000038
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000038
a set of 2 subjects which result from a pairing process which assigns subject to a set based on a pairing rule/criteria
http://purl.obolibrary.org/obo/STATO_0000038
possibly submit to 'Population and Community Ontology'
http://purl.obolibrary.org/obo/STATO_0000038
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000038
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000038
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000038
STATO
http://purl.obolibrary.org/obo/STATO_0000038
http://purl.obolibrary.org/obo/STATO_0000038
matched pair of subjects
http://purl.obolibrary.org/obo/STATO_0000039
http://purl.obolibrary.org/obo/STATO_0000039
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000039
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
http://purl.obolibrary.org/obo/STATO_0000039
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000039
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000039
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000039
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
http://purl.obolibrary.org/obo/STATO_0000039
statistic
http://purl.obolibrary.org/obo/STATO_0000039
statistic
http://purl.obolibrary.org/obo/STATO_0000040
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000040
an MA plot is a scatter plot of the log intensity ratios M = log_2(T/R) versus the average log intensities A = log_2(T*T)/2, where T and R represent the signal intensities in the test and reference channels respectively.
http://purl.obolibrary.org/obo/STATO_0000040
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000040
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000040
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000040
M vs A plot
http://purl.obolibrary.org/obo/STATO_0000040
http://www.stat.berkeley.edu/users/terry/zarray/Software/SMAcode/html/plot.mva.html
http://purl.obolibrary.org/obo/STATO_0000040
MA plot
http://purl.obolibrary.org/obo/STATO_0000040
plot.mva()
http://purl.obolibrary.org/obo/STATO_0000040
MA plot
http://purl.obolibrary.org/obo/STATO_0000041
a R command syntax or link to a R documentation in support of Statistical Ontology Classes or Data Transformations
http://purl.obolibrary.org/obo/STATO_0000041
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000041
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000041
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000041
R command
http://purl.obolibrary.org/obo/STATO_0000042
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000042
The Anderson–Darling test is a statistical test of whether a given sample of data is drawn from a given probability distribution.
http://purl.obolibrary.org/obo/STATO_0000042
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000042
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000042
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000042
http://en.wikipedia.org/wiki/Anderson_Darling_test
http://purl.obolibrary.org/obo/STATO_0000042
http://purl.obolibrary.org/obo/STATO_0000042
ad.test(x) function, where x is a numeric vector
http://purl.obolibrary.org/obo/STATO_0000042
scipy.stats.anderson(x, dist='norm')
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.anderson.html#scipy.stats.anderson
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1017
http://purl.obolibrary.org/obo/STATO_0000042
Anderson-Darling test
http://purl.obolibrary.org/obo/STATO_0000043
a false positive rate whose value is 5 per cent
http://purl.obolibrary.org/obo/STATO_0000043
Following discussion with OBCS, deprecated of class STATO_0000043 and creation of instance
http://purl.obolibrary.org/obo/STATO_0000043
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000043
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000043
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000043
STATO
http://purl.obolibrary.org/obo/STATO_0000043
5 % false positive rate
http://purl.obolibrary.org/obo/STATO_0000044
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000044
one-way anova is an analysis of variance where the different groups being compared are associated with the factor levels of only one independent variable. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
http://purl.obolibrary.org/obo/STATO_0000044
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000044
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000044
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000044
one factor ANOVA
http://purl.obolibrary.org/obo/STATO_0000044
STATO
http://purl.obolibrary.org/obo/STATO_0000044
http://purl.obolibrary.org/obo/STATO_0000044
http://statland.org/R/R/R1way.htm
http://purl.obolibrary.org/obo/STATO_0000044
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f_oneway.html#scipy.stats.f_oneway
http://purl.obolibrary.org/obo/STATO_0000044
one-way ANOVA
http://purl.obolibrary.org/obo/STATO_0000045
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000045
two-way anova is an analysis of variance where the different groups being compared are associated the factor levels of exatly 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
http://purl.obolibrary.org/obo/STATO_0000045
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000045
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000045
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000045
two factor ANOVA
http://purl.obolibrary.org/obo/STATO_0000045
STATO
http://purl.obolibrary.org/obo/STATO_0000045
http://purl.obolibrary.org/obo/STATO_0000045
http://courses.statistics.com/software/R/Rtwoway.htm
http://purl.obolibrary.org/obo/STATO_0000045
two-way ANOVA
http://purl.obolibrary.org/obo/STATO_0000046
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000046
a block design is a kind of study design which declares a blocking variable (also known as nuisance variable) in order to account for a known source of variation and reduce its impact on the acquisition of the signal
http://purl.obolibrary.org/obo/STATO_0000046
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000046
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000046
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000046
adapted from several sources including Wikipedia
http://purl.obolibrary.org/obo/STATO_0000046
http://purl.obolibrary.org/obo/STATO_0000046
block design
http://purl.obolibrary.org/obo/STATO_0000047
a count of 4 resulting from counting limbs in humans
http://purl.obolibrary.org/obo/STATO_0000047
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000047
a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
http://purl.obolibrary.org/obo/STATO_0000047
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000047
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000047
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000047
STATO
http://purl.obolibrary.org/obo/STATO_0000047
http://purl.obolibrary.org/obo/STATO_0000047
count
http://purl.obolibrary.org/obo/STATO_0000048
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000048
Multi-way anova is an analysis of variance where the difference groups being compared are associated to the factor levels of more than 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
http://purl.obolibrary.org/obo/STATO_0000048
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000048
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000048
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000048
STATO
http://purl.obolibrary.org/obo/STATO_0000048
http://purl.obolibrary.org/obo/STATO_0000048
multiway ANOVA
http://purl.obolibrary.org/obo/STATO_0000049
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581961/
http://purl.obolibrary.org/obo/STATO_0000049
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000049
Hardy-Weinberg equilibrium hypothesis is a good of fit hypothesis which states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences (non-random mating, mutation, selection, genetic drift, gene flow and meiotic drive).
http://purl.obolibrary.org/obo/STATO_0000049
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000049
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000049
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000049
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)
http://purl.obolibrary.org/obo/STATO_0000049
http://purl.obolibrary.org/obo/STATO_0000049
Hardy-Weinberg equilibrium hypothesis
http://purl.obolibrary.org/obo/STATO_0000050
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000050
signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation
http://purl.obolibrary.org/obo/STATO_0000050
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000050
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000050
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000050
adapted from Wikipedia:
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
last accessed: 2013-10-18
http://purl.obolibrary.org/obo/STATO_0000050
S/N
http://purl.obolibrary.org/obo/STATO_0000050
SNR
http://purl.obolibrary.org/obo/STATO_0000050
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.signaltonoise.html#scipy.stats.signaltonoise
http://purl.obolibrary.org/obo/STATO_0000050
signal to noise ratio
http://purl.obolibrary.org/obo/STATO_0000051
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000051
Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function.
The expected value of a Poisson-distributed random variable is equal to λ and so is its variance.
http://purl.obolibrary.org/obo/STATO_0000051
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000051
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000051
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000051
http://purl.obolibrary.org/obo/STATO_0000051
dpois(x, lambda, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html
http://purl.obolibrary.org/obo/STATO_0000051
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.poisson.html#scipy.stats.poisson
http://purl.obolibrary.org/obo/STATO_0000051
NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm
http://purl.obolibrary.org/obo/STATO_0000051
Poisson distribution
http://purl.obolibrary.org/obo/STATO_0000052
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000052
Z-test is a statistical test which evaluate the null hypothesis that the means of 2 populations are equal and returns a p-value.
http://purl.obolibrary.org/obo/STATO_0000052
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000052
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000052
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000052
http://reference.wolfram.com/mathematica/ref/ZTest.html
http://purl.obolibrary.org/obo/STATO_0000052
http://purl.obolibrary.org/obo/STATO_0000052
simple.z.test(x, sigma, conf.level=0.95)
http://www.inside-r.org/packages/cran/UsingR/docs/simple.z.test
http://purl.obolibrary.org/obo/STATO_0000052
Z-test
http://purl.obolibrary.org/obo/STATO_0000053
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000053
a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis.
http://purl.obolibrary.org/obo/STATO_0000053
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000053
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000053
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000053
PRS,AGB adapted from wikipedia and wolfram alpha
http://purl.obolibrary.org/obo/STATO_0000053
significance level
http://purl.obolibrary.org/obo/STATO_0000053
type I error rate
http://purl.obolibrary.org/obo/STATO_0000053
α
http://purl.obolibrary.org/obo/STATO_0000053
false positive rate
http://purl.obolibrary.org/obo/STATO_0000054
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000054
homoskedasticity is a null hypothesis stating that all variances under consideration are homogenous
http://purl.obolibrary.org/obo/STATO_0000054
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000054
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000054
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000054
equality of variance
http://purl.obolibrary.org/obo/STATO_0000054
STATO
http://purl.obolibrary.org/obo/STATO_0000054
http://purl.obolibrary.org/obo/STATO_0000054
homoskedasticity hypothesis
http://purl.obolibrary.org/obo/STATO_0000055
http://www.ncbi.nlm.nih.gov/assembly/model/
chrX:35,000,000-36,000,000.
http://purl.obolibrary.org/obo/STATO_0000055
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000055
chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build.
http://purl.obolibrary.org/obo/STATO_0000055
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000055
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000055
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000055
http://purl.obolibrary.org/obo/STATO_0000055
chromosome coordinate system
http://purl.obolibrary.org/obo/STATO_0000056
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000056
a null hypothesis which states that no linkage exists between 2 categorical variables
http://purl.obolibrary.org/obo/STATO_0000056
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000056
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000056
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000056
STATO
http://purl.obolibrary.org/obo/STATO_0000056
no relationship between the variables
http://purl.obolibrary.org/obo/STATO_0000056
variables are independent
http://purl.obolibrary.org/obo/STATO_0000056
absence of association hypothesis
http://purl.obolibrary.org/obo/STATO_0000057
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000057
A null hypothesis is a statistical hypothesis that is tested for possible rejection under the assumption that it is true (usually that observations are the result of chance). The concept was introduced by R. A. Fisher.
The hypothesis contrary to the null hypothesis, usually that the observations are the result of a real effect, is known as the alternative hypothesis.[wolfram alpha]
http://purl.obolibrary.org/obo/STATO_0000057
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000057
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000057
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000057
http://mathworld.wolfram.com/NullHypothesis.html
http://purl.obolibrary.org/obo/STATO_0000057
http://purl.obolibrary.org/obo/STATO_0000057
null hypothesis
http://purl.obolibrary.org/obo/STATO_0000058
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000058
goodness of fit hypothesis is a null hypothesis stating that the distribution computed from the sample population fits a theoretical distribution or that a dataset can be correctly explained by a model
http://purl.obolibrary.org/obo/STATO_0000058
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000058
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000058
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000058
STATO
http://purl.obolibrary.org/obo/STATO_0000058
http://purl.obolibrary.org/obo/STATO_0000058
goodness of fit hypothesis
http://purl.obolibrary.org/obo/STATO_0000059
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000059
the Student's t distribution is a continuous probability distribution which arises when estimating the mean of a normally distributed population in situations where the sample size is small and population standard deviation is unknown.
http://purl.obolibrary.org/obo/STATO_0000059
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000059
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000059
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000059
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Student's_t-distribution)
http://purl.obolibrary.org/obo/STATO_0000059
t distribution
http://purl.obolibrary.org/obo/STATO_0000059
dt(x, df, ncp, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TDist.html
http://purl.obolibrary.org/obo/STATO_0000059
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.t.html#scipy.stats.t
http://purl.obolibrary.org/obo/STATO_0000059
Student's t distribution
http://purl.obolibrary.org/obo/STATO_0000060
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000060
hypergeometric distribution is a probability distribution that describes the probability of k successes in n draws from a finite population of size N containing K successes without replacement
http://purl.obolibrary.org/obo/STATO_0000060
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000060
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000060
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000060
http://en.wikipedia.org/wiki/Hypergeometric_distribution
http://purl.obolibrary.org/obo/STATO_0000060
http://purl.obolibrary.org/obo/STATO_0000060
dhyper(x, m, n, k, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html
http://purl.obolibrary.org/obo/STATO_0000060
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.hypergeom.html#scipy.stats.hypergeom
http://purl.obolibrary.org/obo/STATO_0000060
hypergeometric distribution
http://purl.obolibrary.org/obo/STATO_0000061
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000061
It is a null hypothesis stating that there are no differences observed between group of subjects.
http://purl.obolibrary.org/obo/STATO_0000061
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000061
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000061
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000061
STATO
http://purl.obolibrary.org/obo/STATO_0000061
http://purl.obolibrary.org/obo/STATO_0000061
absence of between group difference hypothesis
http://purl.obolibrary.org/obo/STATO_0000062
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000062
is a null hypothesis stating that there are no difference observed across a series of measurements made one same subject.
http://purl.obolibrary.org/obo/STATO_0000062
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000062
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000062
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000062
STATO
http://purl.obolibrary.org/obo/STATO_0000062
http://purl.obolibrary.org/obo/STATO_0000062
absence of within subject difference hypothesis
http://purl.obolibrary.org/obo/STATO_0000063
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000063
genomic coordinate datum is a data item which denotes a genomic position expressed using a genomic coordinate system
http://purl.obolibrary.org/obo/STATO_0000063
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000063
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000063
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000063
STATO
http://purl.obolibrary.org/obo/STATO_0000063
http://purl.obolibrary.org/obo/STATO_0000063
genomic coordinate datum
http://purl.obolibrary.org/obo/STATO_0000064
http://left.subtree.org/2012/04/13/counting-the-number-of-reads-in-a-bam-file/
http://purl.obolibrary.org/obo/STATO_0000064
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000064
sequence read count is a data item determining how many sequence reads generated by a DNA sequencing assay for a given stretch of DNA can counted
http://purl.obolibrary.org/obo/STATO_0000064
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000064
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000064
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000064
AGB-PRS, STATO
http://purl.obolibrary.org/obo/STATO_0000064
http://purl.obolibrary.org/obo/STATO_0000064
sequence read count
http://purl.obolibrary.org/obo/STATO_0000065
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000065
In statistics, a statement that can be tested.[wolfram alpha]
http://purl.obolibrary.org/obo/STATO_0000065
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000065
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000065
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000065
STATO
http://purl.obolibrary.org/obo/STATO_0000065
http://mathworld.wolfram.com/Hypothesis.html
http://purl.obolibrary.org/obo/STATO_0000065
http://purl.obolibrary.org/obo/STATO_0000065
hypothesis
http://purl.obolibrary.org/obo/STATO_0000066
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000066
Cleveland dot plot is a dot plot which plots points that each belong to one of several categories. They are an alternative to bar charts or pie charts, and look somewhat like a horizontal bar chart where the bars are replaced by a dots at the values associated with each category. Compared to (vertical) bar charts and pie charts, Cleveland argues that dot plots allow more accurate interpretation of the graph by readers by making the labels easier to read, reducing non-data ink (or graph clutter) and supporting table look-up.which
http://purl.obolibrary.org/obo/STATO_0000066
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000066
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000066
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000066
adapted from Wikipedia:
http://en.wikipedia.org/wiki/Dot_plot_(statistics)
and
Cleveland, William S. (1993). Visualizing Data. Hobart Press. ISBN 0-9634884-0-6. hdl:2027/mdp.39015026891187.
http://purl.obolibrary.org/obo/STATO_0000066
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/dotchart.html
dotchart(x, labels = NULL, groups = NULL, gdata = NULL,
cex = par("cex"), pch = 21, gpch = 21, bg = par("bg"),
color = par("fg"), gcolor = par("fg"), lcolor = "gray",
xlim = range(x[is.finite(x)]),
main = NULL, xlab = NULL, ylab = NULL, ...)
http://purl.obolibrary.org/obo/STATO_0000066
Cleveland dot plot
http://purl.obolibrary.org/obo/STATO_0000067
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000067
a continuousprobability distribution is a probability distribution which is defined by a probability density function
http://purl.obolibrary.org/obo/STATO_0000067
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000067
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000067
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000067
adapted from Wikipedia
http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution
last accessed:
14/01/2014
http://purl.obolibrary.org/obo/STATO_0000067
http://purl.obolibrary.org/obo/STATO_0000067
continuous probability distribution
http://purl.obolibrary.org/obo/STATO_0000068
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000068
Skewness is a data item indicating of the degree of asymmetry of a distribution.
http://purl.obolibrary.org/obo/STATO_0000068
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000068
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000068
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000068
http://mathworld.wolfram.com/Skewness.html
http://purl.obolibrary.org/obo/STATO_0000068
http://purl.obolibrary.org/obo/STATO_0000068
skewness(x, na.rm = FALSE, type = 3)
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/e1071/html/skewness.html
http://purl.obolibrary.org/obo/STATO_0000068
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.skew.html#scipy.stats.skew
http://purl.obolibrary.org/obo/STATO_0000068
skewness
http://purl.obolibrary.org/obo/STATO_0000069
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000069
The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations.
http://purl.obolibrary.org/obo/STATO_0000069
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000069
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000069
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000069
http://stats.stackexchange.com/questions/16921/how-to-understand-degrees-of-freedom
http://purl.obolibrary.org/obo/STATO_0000069
http://www.optique-ingenieur.org/en/courses/OPI_ang_M07_C01/co/Contenu_07.html
http://purl.obolibrary.org/obo/STATO_0000069
the rank of the quadratic form (mathematical definition)
http://purl.obolibrary.org/obo/STATO_0000069
http://purl.obolibrary.org/obo/STATO_0000069
number of degrees of freedom
http://purl.obolibrary.org/obo/STATO_0000070
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000070
Yate's corrected Chi-Squared test is a statistical test which is used to test the association/linkage/independence of 2 dichotomous variables while introducing a correction for using the continous Chi-squared distribution for the test.
To reduce the error in approximation, Frank Yates, an English statistician, suggested a correction for continuity that adjusts the formula for Pearson's chi-squared test by subtracting 0.5 from the difference between each observed value and its expected value in a 2 × 2 contingency table. This reduces the chi-squared value obtained and thus increases its p-value.
http://purl.obolibrary.org/obo/STATO_0000070
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000070
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000070
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000070
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Yates's_correction_for_continuity) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000070
Yate's correction for continuity
http://purl.obolibrary.org/obo/STATO_0000070
chisq.test(x, y = NULL, correct = TRUE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
http://purl.obolibrary.org/obo/STATO_0000070
Yate's corrected Chi-Squared test
http://purl.obolibrary.org/obo/STATO_0000071
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000071
reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval
http://purl.obolibrary.org/obo/STATO_0000071
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000071
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000071
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000071
STATO
http://purl.obolibrary.org/obo/STATO_0000071
reaction rate
http://purl.obolibrary.org/obo/STATO_0000072
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000072
substrate concentration is a scalar measurement datum which denotes the amount of molecular entity involved in an enzymatic reaction (or catalytic chemical reaction) and whose role in that reaction is as substrate.
http://purl.obolibrary.org/obo/STATO_0000072
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000072
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000072
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000072
STATO
http://purl.obolibrary.org/obo/STATO_0000072
substrate concentration
http://purl.obolibrary.org/obo/STATO_0000073
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000073
Fisher's exact test is a statistical test used to determine if there are nonrandom associations between two categorical variables.
http://purl.obolibrary.org/obo/STATO_0000073
duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI
http://purl.obolibrary.org/obo/STATO_0000073
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000073
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000073
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000073
http://mathworld.wolfram.com/FishersExactTest.html
http://purl.obolibrary.org/obo/STATO_0000073
http://purl.obolibrary.org/obo/STATO_0000073
fisher.test(x) function, where x is a matrix
http://purl.obolibrary.org/obo/STATO_0000073
scipy.stats.fisher_exact(table, alternative='two-sided')
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html#scipy.stats.fisher_exact
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2485
http://purl.obolibrary.org/obo/STATO_0000073
Fisher's exact test
http://purl.obolibrary.org/obo/STATO_0000074
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000074
Cochran-Mantel-Haenzel test for repeated tests of independence is a statitiscal test which allows the comparison of two groups on a dichotomous/categorical response. It is used when the effect of the explanatory variable on the response variable is influenced by covariates that can be controlled. It is often used in observational studies where random assignment of subjects to different treatments cannot be controlled, but influencing covariates can.
The null hypothesis is that the two nominal variables that are tested within each repetition are independent of each other. So there are 3 variables to consider: two categorical variables to be tested for independence of each other, and the third variable identifies the repeats.
http://purl.obolibrary.org/obo/STATO_0000074
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000074
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000074
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000074
STATO adapted from wikipedia (http://en.wikipedia.org/wiki/Cochran–Mantel–Haenszel_statistics) and from the Handbook of Biological Statistics (http://udel.edu/~mcdonald/statcmh.html)
http://purl.obolibrary.org/obo/STATO_0000074
CHM test
http://purl.obolibrary.org/obo/STATO_0000074
Mantel–Haenszel test
http://purl.obolibrary.org/obo/STATO_0000074
cmh.test(x,y,z)
http://purl.obolibrary.org/obo/STATO_0000074
Cochran-Mantel-Haenzel test for repeated tests of independence
http://purl.obolibrary.org/obo/STATO_0000075
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000075
a rarefaction curve is a graph used for estimating species richness in ecology studies
http://purl.obolibrary.org/obo/STATO_0000075
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000075
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000075
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000075
STATO
http://purl.obolibrary.org/obo/STATO_0000075
http://purl.obolibrary.org/obo/STATO_0000075
>library(vegan)
>rarefaction(x, subsample=5, plot=TRUE, color=TRUE, error=FALSE, legend=TRUE, symbol)
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vegan/html/vegan-package.html
http://purl.obolibrary.org/obo/STATO_0000075
rarefaction curve
http://purl.obolibrary.org/obo/STATO_0000076
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000076
The Mann-Whitney U-test is a null hypothesis statistical testing procedure which allows two groups (or conditions or treatments) to be compared without making the assumption that values are normally distributed.
The Mann-Whitney test is the non-parametric equivalent of the t-test for independent samples
http://purl.obolibrary.org/obo/STATO_0000076
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000076
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000076
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000076
U test
http://purl.obolibrary.org/obo/STATO_0000076
Wilcoxon rank-sum test
http://purl.obolibrary.org/obo/STATO_0000076
rank-sum test for the comparison of two samples
http://purl.obolibrary.org/obo/STATO_0000076
adapted from http://udel.edu/~mcdonald/statkruskalwallis.html
and from http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U
last accessed [2014-03-04]
http://purl.obolibrary.org/obo/STATO_0000076
Wilcoxon Rank-Sum test
http://purl.obolibrary.org/obo/STATO_0000076
wilcox.test(dependent variable ~ independant variable, data = dataset)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/wilcox.test.html
http://purl.obolibrary.org/obo/STATO_0000076
scipy.stats.mannwhitneyu(x, y, use_continuity=True)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mannwhitneyu.html#scipy.stats.mannwhitneyu
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4049
http://purl.obolibrary.org/obo/STATO_0000076
scipy.stats.ranksums(x, y)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ranksums.html#scipy.stats.ranksums
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4103
http://purl.obolibrary.org/obo/STATO_0000076
Mann-Whitney U-test
http://purl.obolibrary.org/obo/STATO_0000077
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000077
Shapiro-Wilk test is a goodness of fit test which evaluates the null hypothesis that the sample is drawn from a population following a normal distribution
http://purl.obolibrary.org/obo/STATO_0000077
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000077
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000077
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000077
S-W test
http://purl.obolibrary.org/obo/STATO_0000077
STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Shapiro–Wilk_test)
http://purl.obolibrary.org/obo/STATO_0000077
http://purl.obolibrary.org/obo/STATO_0000077
shapiro.test(x) function, where x is a numeric vector
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/shapiro.test.html
http://purl.obolibrary.org/obo/STATO_0000077
scipy.stats.shapiro(x, a=None, reta=False)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.shapiro.html#scipy.stats.shapiro
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L944
http://purl.obolibrary.org/obo/STATO_0000077
Shapiro-Wilk test
http://purl.obolibrary.org/obo/STATO_0000078
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000078
Levene's test is a null hypothesis statistical test which evaluates the null hypothesis of equality of variance in several populations.
http://purl.obolibrary.org/obo/STATO_0000078
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000078
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000078
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000078
http://en.wikipedia.org/wiki/Levene_test
http://purl.obolibrary.org/obo/STATO_0000078
http://purl.obolibrary.org/obo/STATO_0000078
levene.test(x) function, where x is a numeric vector
http://purl.obolibrary.org/obo/STATO_0000078
scipy.stats.levene(*args, **kwds)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.levene.html#scipy.stats.levene
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1496
http://purl.obolibrary.org/obo/STATO_0000078
Levene's test
http://purl.obolibrary.org/obo/STATO_0000079
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000079
Bartlett's test (see Snedecor and Cochran, 1989) is used to test if k samples are from populations with equal variances. Equal variances across samples is called homoscedasticity or homogeneity of variances. Some statistical tests, for example the analysis of variance, assume that variances are equal across groups or samples. The Bartlett test can be used to verify that assumption.
Bartlett's test is sensitive to departures from normality. That is, if the samples come from non-normal distributions, then Bartlett's test may simply be testing for non-normality. Levene's test and the Brown–Forsythe test are alternatives to the Bartlett test that are less sensitive to departures from normality.
http://purl.obolibrary.org/obo/STATO_0000079
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000079
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000079
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000079
http://en.wikipedia.org/wiki/Bartlett_test
http://purl.obolibrary.org/obo/STATO_0000079
http://purl.obolibrary.org/obo/STATO_0000079
bartlett.test(x) function, where x is a numeric vector
http://purl.obolibrary.org/obo/STATO_0000079
scipy.stats.bartlett(*args)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.bartlett.html#scipy.stats.bartlett
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1450
http://purl.obolibrary.org/obo/STATO_0000079
Barlett's test
http://purl.obolibrary.org/obo/STATO_0000080
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000080
the Brown Forsythe test is a statistical test which evaluates if the variance of different groups are equal. It relies on computing the median rather than the mean, as used in the Levene's test for homoschedacity.
This test maybe used to, for instance, ensure that the conditions of applications of ANOVA are met.
http://purl.obolibrary.org/obo/STATO_0000080
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000080
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000080
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000080
adapted from Wikipedia and Brown, M. B., and A. B. Forsythe. 1974a. The small sample behavior of some statistics which test the equality of several means. Technometrics, 16, 129-132.
http://purl.obolibrary.org/obo/STATO_0000080
http://purl.obolibrary.org/obo/STATO_0000080
http://www.statmethods.net/stats/anovaAssumptions.html
The hovPlot( ) function in the HH package provides a graphic test of homogeneity of variances based on Brown-Forsyth. In the following example, y is numeric and G is a grouping factor. Note that G must be of type factor.
# Homogeneity of Variance Plot
library(HH)
hov(y~G, data=mydata)
hovPlot(y~G,data=mydata)
http://purl.obolibrary.org/obo/STATO_0000080
Brown Forsythe test
http://purl.obolibrary.org/obo/STATO_0000081
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000081
Pearson's Chi-Squared test is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution or used to test independence of 2 categorical variables (ie absence of association between those variables).
http://purl.obolibrary.org/obo/STATO_0000081
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000081
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000081
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000081
Chi2 test for independence
http://purl.obolibrary.org/obo/STATO_0000081
adapted from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
and
http://en.wikipedia.org/wiki/Pearson's_chi-squared_test
http://purl.obolibrary.org/obo/STATO_0000081
http://purl.obolibrary.org/obo/STATO_0000081
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
chisq.test(x, y = NULL, correct = TRUE,
p = rep(1/length(x), length(x)), rescale.p = FALSE,
simulate.p.value = FALSE, B = 2000)
http://purl.obolibrary.org/obo/STATO_0000081
http://www.inside-r.org/packages/cran/nortest/docs/pearson.test
pearson.test(x) function, where x is a numeric vector
http://purl.obolibrary.org/obo/STATO_0000081
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chi2_contingency.html#scipy.stats.chi2_contingency
http://purl.obolibrary.org/obo/STATO_0000081
Pearson's Chi square test of independence between categorical variables
http://purl.obolibrary.org/obo/STATO_0000082
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000082
a fixed effect model is a statistical model which represents the observed quantities in terms of explanatory variables that are treated as if the quantities were non-random.
http://purl.obolibrary.org/obo/STATO_0000082
PRS: this is a stub and more work is needed to reconcile conflicting definitions
http://purl.obolibrary.org/obo/STATO_0000082
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000082
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000082
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000082
adapted from wikipedia:
http://en.wikipedia.org/wiki/Fixed_effects_model
http://purl.obolibrary.org/obo/STATO_0000082
http://purl.obolibrary.org/obo/STATO_0000082
fixed effects model
http://purl.obolibrary.org/obo/STATO_0000083
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000083
Kolmogorov-Smirnov test is a goodness of fit test which evaluates the null hypothesis that a sample is drawn from a population that follows a specific continuous probability distribution.
http://purl.obolibrary.org/obo/STATO_0000083
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000083
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000083
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000083
K-S test
http://purl.obolibrary.org/obo/STATO_0000083
STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Kolmogorov–Smirnov_test)
http://purl.obolibrary.org/obo/STATO_0000083
http://www.itl.nist.gov/div898/handbook/eda/section3/eda35g.htm
http://purl.obolibrary.org/obo/STATO_0000083
http://purl.obolibrary.org/obo/STATO_0000083
ks.test(dataset, distribution)
http://purl.obolibrary.org/obo/STATO_0000083
scipy.stats.kstwobign = <scipy.stats._continuous_distns.kstwobign_gen object at 0x7f6169f842d0>
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kstwobign.html#scipy.stats.kstwobign
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/_continuous_distns.py
http://purl.obolibrary.org/obo/STATO_0000083
scipy.stats.mstats.ks_twosamp(data1, data2,alternative='two-sided')
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mstats.ks_twosamp.html
source code:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/mstats_basic.py#L821
http://purl.obolibrary.org/obo/STATO_0000083
Kolmogorov-Smirnov test
http://purl.obolibrary.org/obo/STATO_0000084
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000084
multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is probit function.
http://purl.obolibrary.org/obo/STATO_0000084
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000084
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000084
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000084
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_probit) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000084
http://purl.obolibrary.org/obo/STATO_0000084
http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf
http://purl.obolibrary.org/obo/STATO_0000084
multinomial probit regression for analysis of polychotomous dependent variable
http://purl.obolibrary.org/obo/STATO_0000085
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
http://purl.obolibrary.org/obo/STATO_0000085
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000085
effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval
http://purl.obolibrary.org/obo/STATO_0000085
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000085
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000085
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000085
AGB,PRS
http://purl.obolibrary.org/obo/STATO_0000085
effect size
http://purl.obolibrary.org/obo/STATO_0000085
effect size estimate
http://purl.obolibrary.org/obo/STATO_0000086
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000086
an F-test is a statistical test which evaluates that the computed test statistics follows an F-distribution under the null hypothesis. The F-test is sensitive to departure from normality. F-test arise when decomposing the variability in a data set in terms of sum of squares.
http://purl.obolibrary.org/obo/STATO_0000086
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000086
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000086
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000086
STATO
http://purl.obolibrary.org/obo/STATO_0000086
http://purl.obolibrary.org/obo/STATO_0000086
F-test
http://purl.obolibrary.org/obo/STATO_0000087
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000087
a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values
http://purl.obolibrary.org/obo/STATO_0000087
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000087
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000087
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000087
STATO
http://purl.obolibrary.org/obo/STATO_0000087
http://udel.edu/~mcdonald/statvartypes.html
http://purl.obolibrary.org/obo/STATO_0000087
http://purl.obolibrary.org/obo/STATO_0000087
polychotomous variable
http://purl.obolibrary.org/obo/STATO_0000088
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000088
statistical sample size is a count evaluating the number of individual experimental units
http://purl.obolibrary.org/obo/STATO_0000088
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000088
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000088
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000088
AGB-PRS
http://purl.obolibrary.org/obo/STATO_0000088
http://purl.obolibrary.org/obo/STATO_0000088
statistical sample size
http://purl.obolibrary.org/obo/STATO_0000088
study group population size
http://purl.obolibrary.org/obo/STATO_0000089
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000089
a case-control study design is a observation study design which assess the risk of particular outcome (a trait or a disease) associated with an event (either an exposure or endogenous factor). A case-control study design therefore declares an exposure variable which is dichotomous in nature (exposed/non-exposed) and an outcome variable, which is also dichotomous (case or control), thus giving the name to the design. During the execution of the design, a case control study defines a population and counts the events to determine their frequency.
http://purl.obolibrary.org/obo/STATO_0000089
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000089
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000089
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000089
STATO, adapted from:
http://www.drcath.net/toolkit/casecontrol.html
http://purl.obolibrary.org/obo/STATO_0000089
http://purl.obolibrary.org/obo/STATO_0000089
case-control study design
http://purl.obolibrary.org/obo/STATO_0000090
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000090
a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values
http://purl.obolibrary.org/obo/STATO_0000090
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000090
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000090
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000090
AGB-PRS
http://purl.obolibrary.org/obo/STATO_0000090
http://udel.edu/~mcdonald/statvartypes.html
http://purl.obolibrary.org/obo/STATO_0000090
http://purl.obolibrary.org/obo/STATO_0000090
'has part' exactly 1 ('categorical measurement datum'
and ('has category label' exactly 2 'categorical label'))
http://purl.obolibrary.org/obo/STATO_0000090
dichotomous variable
http://purl.obolibrary.org/obo/STATO_0000091
Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design
http://purl.obolibrary.org/obo/STATO_0000091
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000091
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000091
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000091
AGB, PRS
http://purl.obolibrary.org/obo/STATO_0000091
http://purl.obolibrary.org/obo/STATO_0000091
GWAS study
http://purl.obolibrary.org/obo/STATO_0000091
whole genome association study
http://purl.obolibrary.org/obo/STATO_0000091
genome-wide association study
http://purl.obolibrary.org/obo/STATO_0000092
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000092
The Wilcoxon signed rank test is a statistical test which tests the null hypothesis that the median difference between pairs of observations is zero. This is the non-parametric analogue to the paired t-test, and should be used if the distribution of differences between pairs may be non-normally distributed.
The procedure involves a ranking, hence the name. The absolute value of the differences between observations are ranked from smallest to largest, with the smallest difference getting a rank of 1, then next larger difference getting a rank of 2, etc. Ties are given average ranks. The ranks of all differences in one direction are summed, and the ranks of all differences in the other direction are summed. The smaller of these two sums is the test statistic, W (sometimes symbolized Ts). Unlike most test statistics, smaller values of W are less likely under the null hypothesis.
http://purl.obolibrary.org/obo/STATO_0000092
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000092
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000092
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000092
http://udel.edu/~mcdonald/statsignedrank.html
http://purl.obolibrary.org/obo/STATO_0000092
http://purl.obolibrary.org/obo/STATO_0000092
signrank()
http://purl.obolibrary.org/obo/STATO_0000092
scipy.stats.wilcoxon(x, y=None, zero_method='wilcox', correction=False)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.wilcoxon.html#scipy.stats.wilcoxon
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4103
http://purl.obolibrary.org/obo/STATO_0000092
Wilcoxon signed rank test
http://purl.obolibrary.org/obo/STATO_0000093
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000093
http://purl.obolibrary.org/obo/STATO_0000093
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000093
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000093
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000093
http://purl.obolibrary.org/obo/STATO_0000093
date
http://purl.obolibrary.org/obo/STATO_0000094
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000094
The Kruskal–Wallis test is a null hypothesis statistical testing objective which allows multiple (n>=2) groups (or conditions or treatments) to be compared, without making the assumption that values are normally distributed. The Kruskal–Wallis test is the non-parametric equivalent of the independent samples ANOVA
The Kruskal–Wallis test is most commonly used when there is one nominal variable and one measurement variable, and the measurement variable does not meet the normality assumption of an anova.
http://purl.obolibrary.org/obo/STATO_0000094
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000094
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000094
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000094
H test
http://purl.obolibrary.org/obo/STATO_0000094
rank-sum test for the comparison of multiple (more than 2) samples
http://purl.obolibrary.org/obo/STATO_0000094
http://udel.edu/~mcdonald/statkruskalwallis.html
http://purl.obolibrary.org/obo/STATO_0000094
http://purl.obolibrary.org/obo/STATO_0000094
kruskal.test()
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/kruskal.test.html
http://purl.obolibrary.org/obo/STATO_0000094
scipy.stats.mstats.kruskalwallis(*args)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mstats.kruskalwallis.html
source code:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/mstats_basic.py#L800
http://purl.obolibrary.org/obo/STATO_0000094
Kruskal Wallis test
http://purl.obolibrary.org/obo/STATO_0000095
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000095
paired t-test is a statistical test which is specifically designed to analysis differences between paired observations in the case of studies realizing repeated measures design with only 2 repeated measurements per subject (before and after treatment for example)
http://purl.obolibrary.org/obo/STATO_0000095
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000095
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000095
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000095
http://udel.edu/~mcdonald/statpaired.html
http://purl.obolibrary.org/obo/STATO_0000095
http://udel.edu/~mcdonald/statsignedrank.html
http://purl.obolibrary.org/obo/STATO_0000095
t-test for dependent means
http://purl.obolibrary.org/obo/STATO_0000095
t-test for repeated measures
http://purl.obolibrary.org/obo/STATO_0000095
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE, paired= TRUE)
http://purl.obolibrary.org/obo/STATO_0000095
scipy.stats.ttest_rel(a, b, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_rel.html#scipy.stats.ttest_rel
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3389
http://purl.obolibrary.org/obo/STATO_0000095
paired t-test
http://purl.obolibrary.org/obo/STATO_0000096
stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule
http://purl.obolibrary.org/obo/STATO_0000096
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000096
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000096
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000096
PRS+AGB adapted from wikipedia:
http://en.wikipedia.org/wiki/Stratified_sampling
polled on June 7th,2013
http://purl.obolibrary.org/obo/STATO_0000096
stratifying population
http://purl.obolibrary.org/obo/STATO_0000096
population stratification prior to sampling
http://purl.obolibrary.org/obo/STATO_0000097
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000097
stastical test power analysis is a data transformation which aims to determine the size of a statistical sample required to reach a desired significance level given a particular statistical test
http://purl.obolibrary.org/obo/STATO_0000097
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000097
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000097
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000097
http://www.statmethods.net/stats/power.html
http://purl.obolibrary.org/obo/STATO_0000097
http://purl.obolibrary.org/obo/STATO_0000097
http://www.statmethods.net/stats/power.html
http://purl.obolibrary.org/obo/STATO_0000097
statistical test power analysis
http://purl.obolibrary.org/obo/STATO_0000098
http://arxiv.org/pdf/1007.1094.pdf
http://purl.obolibrary.org/obo/STATO_0000098
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000098
Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis
http://purl.obolibrary.org/obo/STATO_0000098
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000098
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000098
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000098
STATO
http://purl.obolibrary.org/obo/STATO_0000098
http://purl.obolibrary.org/obo/STATO_0000098
http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html
http://purl.obolibrary.org/obo/STATO_0000098
two sample Hotelling T2 test
http://purl.obolibrary.org/obo/STATO_0000099
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000099
a random effect(s) model, also called a variance components model, is a kind of hierarchical linear model. It assumes that the dataset being analysed consists of a hierarchy of different populations whose differences relate to that hierarchy.
http://purl.obolibrary.org/obo/STATO_0000099
PRS: this is a stub and more work is needed to reconcile conflicting definitions
http://purl.obolibrary.org/obo/STATO_0000099
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000099
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000099
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000099
variance components model
http://purl.obolibrary.org/obo/STATO_0000099
adapted from wikipedia:
http://en.wikipedia.org/wiki/Random_effects_model#Qualitative_description
http://purl.obolibrary.org/obo/STATO_0000099
http://purl.obolibrary.org/obo/STATO_0000099
random effects model
http://purl.obolibrary.org/obo/STATO_0000100
standardized mean difference is data item computed by forming the difference between two means, divided by an estimate of the within-group standard deviation.
It is used to provide an estimatation of the effect size between two treatments when the predictor (independent variable) is categorical and the response(dependent) variable is continuous
http://purl.obolibrary.org/obo/STATO_0000100
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000100
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000100
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000100
SMD
http://purl.obolibrary.org/obo/STATO_0000100
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000100
adapted from "Effect size, confidence interval and statistical significance: a practical guide for biologists" Nakagawa and Cuthill
DOI: 10.1111/j.1469-185X.2007.00027.x
http://purl.obolibrary.org/obo/STATO_0000100
adapted from http://htaglossary.net/standardised+mean+difference+(SMD)
http://purl.obolibrary.org/obo/STATO_0000100
Cohen's d statistic
http://purl.obolibrary.org/obo/STATO_0000100
standardized mean difference
http://purl.obolibrary.org/obo/STATO_0000101
the relationship between a fraction and the number above the line
http://purl.obolibrary.org/obo/STATO_0000101
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000101
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000101
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000101
AGB
http://purl.obolibrary.org/obo/STATO_0000101
has numerator
http://purl.obolibrary.org/obo/STATO_0000102
relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes)
http://purl.obolibrary.org/obo/STATO_0000102
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000102
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000102
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000102
AGB
http://purl.obolibrary.org/obo/STATO_0000102
executes
http://purl.obolibrary.org/obo/STATO_0000103
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000103
the multinomial distribution is a probability distribution which gives the probability of any particular combination of numbers of successes for various categories defined in the context of n independent trials each of which leads to a success for exactly one of k categories, with each category having a given fixed success probability.
http://purl.obolibrary.org/obo/STATO_0000103
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000103
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000103
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000103
adapted from
http://mathworld.wolfram.com/MultinomialDistribution.html
and
http://en.wikipedia.org/wiki/Multinomial_distribution
http://purl.obolibrary.org/obo/STATO_0000103
dmultinom(x, size = NULL, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Multinom.html
http://purl.obolibrary.org/obo/STATO_0000103
multinomial distribution
http://purl.obolibrary.org/obo/STATO_0000104
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000104
A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
http://purl.obolibrary.org/obo/STATO_0000104
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000104
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000104
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000104
https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores
http://purl.obolibrary.org/obo/STATO_0000104
normal score
http://purl.obolibrary.org/obo/STATO_0000104
standard score
http://purl.obolibrary.org/obo/STATO_0000104
scipy.stats.zscore(a, axis=0, ddof=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.zscore.html#scipy.stats.zscore
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L1977
http://purl.obolibrary.org/obo/STATO_0000104
z-score
http://purl.obolibrary.org/obo/STATO_0000105
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000105
log signal intensity ratio is a data item which corresponding the logarithmitic base 2 of the ratio between 2 signal intensity, each corresponding to a condition.
http://purl.obolibrary.org/obo/STATO_0000105
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000105
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000105
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000105
adapted from wikipedia:
http://en.wikipedia.org/wiki/MA_plot
last accessed: 2014-03-13
http://purl.obolibrary.org/obo/STATO_0000105
M-value
http://purl.obolibrary.org/obo/STATO_0000105
http://purl.obolibrary.org/obo/STATO_0000105
log signal intensity ratio
http://purl.obolibrary.org/obo/STATO_0000106
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000106
probit regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the probit function aka the quantile function, i.e., the inverse cumulative distribution function (CDF), associated with the standard normal distribution.
http://purl.obolibrary.org/obo/STATO_0000106
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000106
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000106
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000106
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000106
http://purl.obolibrary.org/obo/STATO_0000106
probit regression for analysis of polychotomous dependent variable
http://purl.obolibrary.org/obo/STATO_0000107
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000107
a statistical model is an information content entity which is a formalization of relationships between variables in the form of mathematical equations. A statistical model describes how one or more random variables are related to one or more other variables. The model is statistical as the variables are not deterministically but stochastically related.
http://purl.obolibrary.org/obo/STATO_0000107
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000107
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000107
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000107
adapted from Wikipedia:
http://en.wikipedia.org/wiki/Statistical_model
last accessed: 14/01/2014
http://purl.obolibrary.org/obo/STATO_0000107
statistical model
http://purl.obolibrary.org/obo/STATO_0000107
statistical model
http://purl.obolibrary.org/obo/STATO_0000108
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000108
linear regression model is a model which attempts to explain data distribution associated with response/dependent variable in terms of values assumed by the independent variable uses a linear function or linear combination of the regression parameters and the predictor/independent variable(s).
linear regression modeling makes a number of assumptions, which includes homoskedasticity (constance of variance)
http://purl.obolibrary.org/obo/STATO_0000108
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000108
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000108
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000108
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Linear_regression) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000108
http://purl.obolibrary.org/obo/STATO_0000108
linear regression for analysis of continuous dependent variable
http://purl.obolibrary.org/obo/STATO_0000109
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000109
multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.
http://purl.obolibrary.org/obo/STATO_0000109
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000109
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000109
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000109
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_logistic_regression) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000109
http://purl.obolibrary.org/obo/STATO_0000109
http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf
http://purl.obolibrary.org/obo/STATO_0000109
multinomial logistic regression for analysis of dichotomous dependent variable
http://purl.obolibrary.org/obo/STATO_0000110
This is the inverse of 'specifies value of' and it is intended to say things such as 'compound' 'assumes values specified by' 'independent variable specification'
http://purl.obolibrary.org/obo/STATO_0000110
A relation between an entity and a value specification, where the value specification is about the entity.
http://purl.obolibrary.org/obo/STATO_0000110
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000110
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000110
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000110
AGB
http://purl.obolibrary.org/obo/STATO_0000110
assumes values specified by
http://purl.obolibrary.org/obo/STATO_0000111
a sequence read is a DNA sequence data which is generated by a DNA sequencer
http://purl.obolibrary.org/obo/STATO_0000111
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000111
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000111
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000111
sequence read
http://purl.obolibrary.org/obo/STATO_0000112
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000112
a Funnel plot is a scatter plot of treatment effect versus a measure of study size and aims to provide a visual aid to detecting bias or systematic heterogeneity. A symmetric inverted funnel shape arises from a ‘well-behaved’ data set, in which publication bias is unlikely. An asymmetric funnel indicates a relationship between treatment effect and study size.
Known caveats: If high precision studies really are different from low precision studies with respect to effect size (e.g., due to different populations examined) a funnel plot may give a wrong impression of publication bias. The appearance of the funnel plot can change quite dramatically depending on the scale on the y-axis — whether it is the inverse square error or the trial size.
Funnel plot was introduced by Light and Palmer in 1984.
http://purl.obolibrary.org/obo/STATO_0000112
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000112
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000112
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000112
adapted from Wikipedia:
http://en.wikipedia.org/wiki/Funnel_plot
http://purl.obolibrary.org/obo/STATO_0000112
Funnel plot
http://purl.obolibrary.org/obo/STATO_0000113
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000113
variance is a data item about a random variable or probability distribution. it is equivalent to the square of the standard deviation. It is one of several descriptors of a probability distribution, describing how far the numbers lie from the mean (expected value).The variance is the second moment of a distribution.
http://purl.obolibrary.org/obo/STATO_0000113
Alejandra Gonzalez-Belran
http://purl.obolibrary.org/obo/STATO_0000113
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000113
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000113
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000113
σ2
http://purl.obolibrary.org/obo/STATO_0000113
http://purl.obolibrary.org/obo/STATO_0000113
var(x, y = NULL, na.rm = FALSE, use)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html
http://purl.obolibrary.org/obo/STATO_0000113
variance
http://purl.obolibrary.org/obo/STATO_0000114
relationship between an element and a set it belongs to
http://purl.obolibrary.org/obo/STATO_0000114
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000114
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000114
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000114
AGB
http://purl.obolibrary.org/obo/STATO_0000114
is member of
http://purl.obolibrary.org/obo/STATO_0000115
relationship between a set and one of its elements
http://purl.obolibrary.org/obo/STATO_0000115
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000115
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000115
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000115
AGB
http://purl.obolibrary.org/obo/STATO_0000115
has member
http://purl.obolibrary.org/obo/STATO_0000116
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000116
the process of using statistical analysis for interpreting and communicating "what the data say".
http://purl.obolibrary.org/obo/STATO_0000116
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000116
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000116
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000116
From "The strenght of statistical evidence" by Richard Royall.
https://www.stat.fi/isi99/proceedings/arkisto/varasto/roya0578.pdf
http://purl.obolibrary.org/obo/STATO_0000116
assess stastistical evidence
http://purl.obolibrary.org/obo/STATO_0000116
assess statistical evidence
http://purl.obolibrary.org/obo/STATO_0000117
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000117
a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values
http://purl.obolibrary.org/obo/STATO_0000117
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000117
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000117
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000117
adapted from Wikipedia
http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution
last accessed:
14/01/2014
http://purl.obolibrary.org/obo/STATO_0000117
discrete probability distribution
http://purl.obolibrary.org/obo/STATO_0000118
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000118
ranking is a data transformation which turns a non-ordinal variable into a Ordinal variable by sorting the values of the input variable and replacing their value by their position in the sorting result
http://purl.obolibrary.org/obo/STATO_0000118
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000118
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000118
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000118
STATO
http://purl.obolibrary.org/obo/STATO_0000118
http://purl.obolibrary.org/obo/STATO_0000118
ranking
http://purl.obolibrary.org/obo/STATO_0000119
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000119
model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model.
http://purl.obolibrary.org/obo/STATO_0000119
textual definition modified following contributiong by Thomas Nichols:
https://github.com/ISA-tools/stato/issues/18
http://purl.obolibrary.org/obo/STATO_0000119
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000119
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000119
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000119
http://purl.obolibrary.org/obo/STATO_0000119
model parameter estimation
http://purl.obolibrary.org/obo/STATO_0000120
http://www.r-bloggers.com/boxplots-beyond-iv-beanplots/
http://purl.obolibrary.org/obo/STATO_0000120
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000120
beanplot is a plot in which (one or) multiple batches ("beans") are shown. Each bean consists of a density trace, which is mirrored to
form a polygon shape. Next to that, a one-dimensional scatter plot shows all the individual measurements, like in a stripchart.
The name beanplot stems from green beans. The density shape can be seen as the pod of a green bean, while the scatter plot shows the seeds inside the pod.
http://purl.obolibrary.org/obo/STATO_0000120
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000120
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000120
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000120
http://www.jstatsoft.org/v28/c01/paper
http://purl.obolibrary.org/obo/STATO_0000120
http://cran.r-project.org/web/packages/beanplot/index.html
http://purl.obolibrary.org/obo/STATO_0000120
bean plot
http://purl.obolibrary.org/obo/STATO_0000121
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000121
the objective of a data transformation to evaluate a null hypothesis of absence of linkage between variables.
http://purl.obolibrary.org/obo/STATO_0000121
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000121
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000121
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000121
STATO
http://purl.obolibrary.org/obo/STATO_0000121
http://purl.obolibrary.org/obo/STATO_0000121
association between categorical variables testing objective
http://purl.obolibrary.org/obo/STATO_0000122
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000122
a pedigree chart is a graph which plots parent child relations
http://purl.obolibrary.org/obo/STATO_0000122
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000122
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000122
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000122
STATO adapted from wikipedia (https://en.wikipedia.org/wiki/Pedigree_chart)
http://purl.obolibrary.org/obo/STATO_0000122
family tree
http://purl.obolibrary.org/obo/STATO_0000122
plot.pedigree {kinship}
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/kinship/html/plot.pedigree.html
http://purl.obolibrary.org/obo/STATO_0000122
pedigree chart
http://purl.obolibrary.org/obo/STATO_0000123
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000123
r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot
http://purl.obolibrary.org/obo/STATO_0000123
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000123
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000123
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000123
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580747/
http://purl.obolibrary.org/obo/STATO_0000123
r2
http://purl.obolibrary.org/obo/STATO_0000123
r2
http://purl.obolibrary.org/obo/STATO_0000124
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000124
a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum
http://purl.obolibrary.org/obo/STATO_0000124
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000124
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000124
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000124
STATO
http://purl.obolibrary.org/obo/STATO_0000124
adapted from wikipedia:
http://en.wikipedia.org/wiki/Stratified_sampling
polled on June 7th,2013
http://purl.obolibrary.org/obo/STATO_0000124
http://purl.obolibrary.org/obo/STATO_0000124
stratification rule
http://purl.obolibrary.org/obo/STATO_0000125
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000125
The dot plot as a representation of a distribution consists of group of data points plotted on a simple scale. Dot plots are used for continuous, quantitative, univariate data. Data points may be labelled if there are few of them.
http://purl.obolibrary.org/obo/STATO_0000125
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000125
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000125
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000125
adapted from Wikipedia:
Wilkinson, Leland (1999). "Dot plots". The American Statistician (American Statistical Association) 53 (3): 276–281. doi:10.2307/2686111
http://purl.obolibrary.org/obo/STATO_0000125
http://purl.obolibrary.org/obo/STATO_0000125
Wilkinson dot plot
http://purl.obolibrary.org/obo/STATO_0000126
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000126
volcano plot is a kind of scatter plot which graphs the negative log of the p-value (significance) on the y-axis versus log2 of fold-change between 2 conditions on the x-axis.
It is a popular method for visualizing differential occurence of variables between 2 conditions.
http://purl.obolibrary.org/obo/STATO_0000126
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000126
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000126
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000126
http://en.wikipedia.org/wiki/Volcano_plot_(statistics)
http://purl.obolibrary.org/obo/STATO_0000126
volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, ...)
http://rss.acs.unt.edu/Rdoc/library/limma/html/volcanoplot.html
http://purl.obolibrary.org/obo/STATO_0000126
volcano plot
http://purl.obolibrary.org/obo/STATO_0000127
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
http://purl.obolibrary.org/obo/STATO_0000127
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000127
a confidence interval which covers 99% of the sampling distribution, meaning that there is a 1% risk of false positive (type I error)
http://purl.obolibrary.org/obo/STATO_0000127
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000127
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000127
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000127
confidence interval at 1% of type I error rate
http://purl.obolibrary.org/obo/STATO_0000127
STATO
http://purl.obolibrary.org/obo/STATO_0000127
http://purl.obolibrary.org/obo/STATO_0000127
99% confidence interval
http://purl.obolibrary.org/obo/STATO_0000128
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000128
Altman Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Altman to create the 'whisker' of the plot.
http://purl.obolibrary.org/obo/STATO_0000128
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000128
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000128
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000128
Altman, D.G. Practical Statistics for Medical Research (Chapman and Hall, 1991).
http://purl.obolibrary.org/obo/STATO_0000128
Altman box and whisker plot
http://purl.obolibrary.org/obo/STATO_0000129
A relationship (data property) between an entity and its value.
http://purl.obolibrary.org/obo/STATO_0000129
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000129
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000129
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000129
has value
http://purl.obolibrary.org/obo/STATO_0000130
http://www.biomedcentral.com/1471-2288/11/58#B9
http://purl.obolibrary.org/obo/STATO_0000130
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000130
the Breslow-Day test is a statistical test which evaluates if the odds ratios are homogenous across N 2x2 contingency tables, for instance several 2x2 contingency tables associated with different strata of a stratified population when evaluating the relationship between exposure and outcome or associated with the different samples coming from several centres in a multicentric study in clinical trial context.
http://purl.obolibrary.org/obo/STATO_0000130
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000130
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000130
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000130
adapted from wikipedia:
http://en.wikipedia.org/wiki/Odds_ratio#Statistical_inference
polled on June 8th,2013
http://purl.obolibrary.org/obo/STATO_0000130
Breslow-Day test
http://purl.obolibrary.org/obo/STATO_0000130
http://www.math.montana.edu/~jimrc/classes/stat524/Rcode/breslowday.test.r
http://purl.obolibrary.org/obo/STATO_0000130
Breslow-Day test for homogeneity of odds ratio
http://purl.obolibrary.org/obo/STATO_0000131
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000131
a sphericity test is a null hypothesis statistical testing procedure which posits a null hypothesis of equality of the variances of the differences between levels of the repeated measures factor
http://purl.obolibrary.org/obo/STATO_0000131
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000131
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000131
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000131
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Sphericity#Sphericity_in_statistics)
http://purl.obolibrary.org/obo/STATO_0000131
test of data sphericity
http://purl.obolibrary.org/obo/STATO_0000131
sphericity test
http://purl.obolibrary.org/obo/STATO_0000132
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000132
Hotelling T squared distribution is a probability distribution used in multivariate hypothesis testing, which is a univariate distribution proportional to the F-distribution and arises importantly as the distribution of a set of statistics which are natural generalizations of the statistics underlying Student's t-distribution.
In particular, the distribution arises in multivariate statistics in undertaking tests of the differences between the (multivariate) means of different populations, where tests for univariate problems would make use of a t-test.
The distribution is named for Harold Hotelling, who developed it[1] as a generalization of Student's t-distribution.
This distribution is commonly used to describe the sample Mahalanobis distance between two populations.
http://purl.obolibrary.org/obo/STATO_0000132
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000132
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000132
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000132
adapted from Wikipedia
"http://en.wikipedia.org/wiki/Hotelling's_T-squared_distribution"
last polled: 2013-11-09
http://purl.obolibrary.org/obo/STATO_0000132
Hotelling T2 distribution
http://purl.obolibrary.org/obo/STATO_0000133
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000133
A post-hoc analysis is a statistical test carried out following an analysis of variance which ruled out the null hypothesis of absence of difference between group which allows identifying which groups differ.
http://purl.obolibrary.org/obo/STATO_0000133
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000133
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000133
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000133
a posteriori test
http://purl.obolibrary.org/obo/STATO_0000133
adapted from wikipedia: http://en.wikipedia.org/wiki/Post-hoc_analysis
last accessed: 2013-11-15
http://purl.obolibrary.org/obo/STATO_0000133
post-hoc analysis
http://purl.obolibrary.org/obo/STATO_0000134
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000134
specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1
http://purl.obolibrary.org/obo/STATO_0000134
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000134
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000134
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000134
specificity
http://purl.obolibrary.org/obo/STATO_0000134
http://purl.obolibrary.org/obo/STATO_0000134
true negative rate
http://purl.obolibrary.org/obo/STATO_0000135
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/
http://purl.obolibrary.org/obo/STATO_0000135
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000135
strictly standardized mean difference (SSMS) is a standardized mean difference which corresponds to the ratio of mean to the standard deviation of the difference between two groups.
SSMD directly measures the magnitude of difference between two groups.
SSMD is widely used in High Content Screen for hit selection and quality control.
When the data is preprocessed using log-transformation as normally done in HTS experiments, SSMD is the mean of log fold change divided by the standard deviation of log fold change with respect to a negative reference.
In other words, SSMD is the average fold change (on the log scale) penalized by the variability of fold change (on the log scale).
For quality control, one index for the quality of an HTS assay is the magnitude of difference between a positive control and a negative reference in an assay plate. For hit selection, the size of effects of a compound (i.e., a small molecule or an siRNA) is represented by the magnitude of difference between the compound and a negative reference. SSMD directly measures the magnitude of difference between two groups. Therefore, SSMD can be used for both quality control and hit selection in HTS experiments.
http://purl.obolibrary.org/obo/STATO_0000135
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000135
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000135
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000135
http://en.wikipedia.org/wiki/SSMD
http://purl.obolibrary.org/obo/STATO_0000135
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/
http://purl.obolibrary.org/obo/STATO_0000135
http://purl.obolibrary.org/obo/STATO_0000135
strictly standardized mean difference
http://purl.obolibrary.org/obo/STATO_0000136
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000136
Tarone's test for homogeneity of odds ratio is a statistical test which evaluates the null hypothesis that odds ratio are homogeneous
http://purl.obolibrary.org/obo/STATO_0000136
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000136
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000136
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000136
> library("metafor")
> calcTaronesTest <- function(mylist,referencerow=2)
http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/en/latest/src/biomedicalstats.html#calculating-the-mantel-haenszel-odds-ratio-when-there-is-a-stratifying-variable
http://purl.obolibrary.org/obo/STATO_0000136
Tarone's test for homogeneity of odds ratio
http://purl.obolibrary.org/obo/STATO_0000137
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000137
an homoskedasticity test is a statistical test aiming at evaluate if the variances from several random samples are similar
http://purl.obolibrary.org/obo/STATO_0000137
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000137
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000137
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000137
STATO
http://purl.obolibrary.org/obo/STATO_0000137
equivariance test
http://purl.obolibrary.org/obo/STATO_0000137
homoskedasticity test
http://purl.obolibrary.org/obo/STATO_0000138
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000138
a 2x2 contingency table is a contingency table build for 2 dichotomous variables (i.e. 2 categorical variables, each with only 2 possible outcomes). It is the simplest of contingency tables
http://purl.obolibrary.org/obo/STATO_0000138
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000138
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000138
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000138
STATO
http://purl.obolibrary.org/obo/STATO_0000138
2x2 contingency table
http://purl.obolibrary.org/obo/STATO_0000138
xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE,
na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html
flat contingency tables:
ftable(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html
http://purl.obolibrary.org/obo/STATO_0000138
2 by 2 contingency table
http://purl.obolibrary.org/obo/STATO_0000139
pairing patients by age, pairing animals by body weight range
http://purl.obolibrary.org/obo/STATO_0000139
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000139
a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria
http://purl.obolibrary.org/obo/STATO_0000139
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000139
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000139
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000139
STATO
http://purl.obolibrary.org/obo/STATO_0000139
http://purl.obolibrary.org/obo/STATO_0000139
subject pairing
http://purl.obolibrary.org/obo/STATO_0000140
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000140
a contigency table is a data item which displays the (multivariate) frequency distribution of the possible values of categorical variables.
The first row of the table corresponds to categories of one categorical variable, the first column of the table corresponds to categories of the other categorical variable, the cells corresponding to each combination of categories is filled with the observed occurences in the sample being considered.
The table also contains marginal total (marginal sums) and grand total of the occurences
The term contingency table was first used by Karl Pearson in "On the Theory of Contingency and Its Relation to Association and Normal Correlation", part of the Drapers' Company Research Memoirs Biometric Series I published in 1904.
http://purl.obolibrary.org/obo/STATO_0000140
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000140
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000140
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000140
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Contingency_table)
http://purl.obolibrary.org/obo/STATO_0000140
http://purl.obolibrary.org/obo/STATO_0000140
xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE,
na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html
flat contingency tables:
ftable(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html
http://purl.obolibrary.org/obo/STATO_0000140
contingency table
http://purl.obolibrary.org/obo/STATO_0000141
acute toxicity study is an investigation which use interventions organized according to a factorial design and a parallel group design to observe the effect of use of high dose xenobiotics in animal models or cellular models
http://purl.obolibrary.org/obo/STATO_0000141
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000141
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000141
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000141
acute toxicity study
http://purl.obolibrary.org/obo/STATO_0000141
acute toxicity study
http://purl.obolibrary.org/obo/STATO_0000142
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000142
The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
http://purl.obolibrary.org/obo/STATO_0000142
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000142
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000142
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000142
STATO
http://purl.obolibrary.org/obo/STATO_0000142
r
http://purl.obolibrary.org/obo/STATO_0000142
r statistics
http://purl.obolibrary.org/obo/STATO_0000142
correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000143
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000143
a Bayesian model selection is a data transformation which is based on Bayesian statistics to compute Bayes factor in order to evaluate which model best explains data.
http://purl.obolibrary.org/obo/STATO_0000143
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000143
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000143
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000143
adapted from wikipedia
http://purl.obolibrary.org/obo/STATO_0000143
Bayesian model selection
http://purl.obolibrary.org/obo/STATO_0000144
for example , model parameter estimates could be produced using regression analysis (used in a model estimation process) , which attempts to express the response variable in terms of function of predictor variable and model parameters.
http://purl.obolibrary.org/obo/STATO_0000144
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000144
a model parameter estimate is a data item which results from a model parameter estimation process and which provides a numerical value about a model parameter.
http://purl.obolibrary.org/obo/STATO_0000144
textual definition modified following contributiong by Thomas Nichols:
https://github.com/ISA-tools/stato/issues/18
http://purl.obolibrary.org/obo/STATO_0000144
Alejandra Gonzalez Beltran
http://purl.obolibrary.org/obo/STATO_0000144
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000144
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000144
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000144
STATO
http://purl.obolibrary.org/obo/STATO_0000144
model parameter estimate
http://purl.obolibrary.org/obo/STATO_0000145
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000145
the geometric distribution is a negative binomial distribution where r is 1.
It is useful for modeling the runs of consecutive successes (or failures) in repeated independent trials of a system.
The geometric distribution models the number of successes before one failure in an independent succession of tests where each test results in success or failure.
The geometric distribution with prob = p has density
p(x) = p (1-p)^x
for x = 0, 1, 2, …, 0 < p ≤ 1.
If an element of x is not integer, the result of dgeom is zero, with a warning.
The quantile is defined as the smallest value x such that F(x) ≥ p, where F is the distribution function.
http://purl.obolibrary.org/obo/STATO_0000145
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000145
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000145
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000145
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html
http://purl.obolibrary.org/obo/STATO_0000145
http://www.mathworks.co.uk/help/stats/geometric-distribution.html
http://purl.obolibrary.org/obo/STATO_0000145
http://purl.obolibrary.org/obo/STATO_0000145
dgeom(x, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html
http://purl.obolibrary.org/obo/STATO_0000145
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.geom.html#scipy.stats.geom
http://purl.obolibrary.org/obo/STATO_0000145
geometric distribution
http://purl.obolibrary.org/obo/STATO_0000146
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000146
a null hypothesis stating that there are differences observed between group of subjects
http://purl.obolibrary.org/obo/STATO_0000146
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000146
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000146
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000146
STATO
http://purl.obolibrary.org/obo/STATO_0000146
presence of between group difference hypothesis
http://purl.obolibrary.org/obo/STATO_0000147
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000147
Linkage Disequilibrium plot is a graph which represents pairwise linkage disequilibrium measures between SNP as a heatmap
http://purl.obolibrary.org/obo/STATO_0000147
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000147
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000147
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000147
STATO, adapted from R documentation (http://cran.r-project.org/web/packages/LDheatmap/index.html)
http://purl.obolibrary.org/obo/STATO_0000147
LD plot
http://purl.obolibrary.org/obo/STATO_0000147
Linkage Disequilibrium plot
http://purl.obolibrary.org/obo/STATO_0000147
http://purl.obolibrary.org/obo/STATO_0000147
LD plot
http://purl.obolibrary.org/obo/STATO_0000148
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000148
The Cochran-Armitage test is a statistical test used in categorical data analysis when the aim is to assess for the presence of an association between a dichotomous variable (variable with two categories) and a polychotomous variable (a variable with k categories).
The two-level variable represents the response, and the other represents an explanatory variable with ordered levels. The null hypothesis is the hypothesis of no trend, which means that the binomial proportion is the same for all levels of the explanatory variable
For example, doses of a treatment can be ordered as 'low', 'medium', and 'high', and we may suspect that the treatment benefit cannot become smaller as the dose increases. The trend test is often used as a genotype-based test for case-control genetic association studies.
http://purl.obolibrary.org/obo/STATO_0000148
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000148
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000148
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000148
CATT
http://purl.obolibrary.org/obo/STATO_0000148
http://en.wikipedia.org/wiki/Cochran%E2%80%93Armitage_test_for_trend
http://purl.obolibrary.org/obo/STATO_0000148
http://purl.obolibrary.org/obo/STATO_0000148
http://purl.obolibrary.org/obo/STATO_0000148
Cochran-Armitage test for trend
http://purl.obolibrary.org/obo/STATO_0000149
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000149
binomial logistic regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.
http://purl.obolibrary.org/obo/STATO_0000149
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000149
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000149
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000149
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Logistic_regression) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000149
http://purl.obolibrary.org/obo/STATO_0000149
binomial logistic regression for analysis of dichotomous dependent variable
http://purl.obolibrary.org/obo/STATO_0000150
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000150
a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation.
http://purl.obolibrary.org/obo/STATO_0000150
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000150
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000150
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000150
STATO
http://purl.obolibrary.org/obo/STATO_0000150
minimum value
http://purl.obolibrary.org/obo/STATO_0000151
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000151
maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation.
http://purl.obolibrary.org/obo/STATO_0000151
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000151
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000151
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000151
STATO
http://purl.obolibrary.org/obo/STATO_0000151
maximum value
http://purl.obolibrary.org/obo/STATO_0000152
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000152
a quartile is a quantile which splits data into sections accrued of 25% of data, so the first quartile delineates 25% of the data, the second quartile delineates 50% of the data and the third quartile, 75 % of the data
http://purl.obolibrary.org/obo/STATO_0000152
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000152
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000152
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000152
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Quartile)
http://purl.obolibrary.org/obo/STATO_0000152
http://purl.obolibrary.org/obo/STATO_0000152
quartile
http://purl.obolibrary.org/obo/STATO_0000153
http://arxiv.org/pdf/1007.1094.pdf
http://purl.obolibrary.org/obo/STATO_0000153
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000153
Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis
http://purl.obolibrary.org/obo/STATO_0000153
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000153
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000153
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000153
STATO
http://purl.obolibrary.org/obo/STATO_0000153
http://purl.obolibrary.org/obo/STATO_0000153
http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html
http://purl.obolibrary.org/obo/STATO_0000153
one sample Hotelling T2 test
http://purl.obolibrary.org/obo/STATO_0000154
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000154
a violin plot is a plot combining the features of box plot and kernel density plot. The violin plot is therefore similar to box plot but it incorporated in the display the probability density of the data at different values.
Typically violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard box plots.
http://purl.obolibrary.org/obo/STATO_0000154
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000154
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000154
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000154
http://en.wikipedia.org/wiki/Violin_plot
and
Hintze, J. L. and R. D. Nelson (1998). Violin plots: a box plot-density trace synergism. The American Statistician, 52(2):181-4.
http://purl.obolibrary.org/obo/STATO_0000154
http://www.inside-r.org/packages/cran/vioplot/docs/vioplot
vioplot( x, ..., range=1.5, h, ylim, names, horizontal=FALSE,
col="magenta", border="black", lty=1, lwd=1, rectCol="black",
colMed="white", pchMed=19, at, add=FALSE, wex=1,
drawRect=TRUE)
http://purl.obolibrary.org/obo/STATO_0000154
violin plot
http://purl.obolibrary.org/obo/STATO_0000155
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000155
meta-analysis is a data transformation which uses the effect size estimates from several independent quantitative scientific studies addressing the same question in order to assess finding consistency.
http://purl.obolibrary.org/obo/STATO_0000155
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000155
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000155
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000155
adapted from wikipedia:
http://en.wikipedia.org/wiki/Metaanalysis
last accessed: 2013-11-15
http://purl.obolibrary.org/obo/STATO_0000155
meta analysis
http://purl.obolibrary.org/obo/STATO_0000156
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000156
the Scheffe test is a data transformation which evaluates all possible contrasts and adjusting the levels significance by accounting for multiple comparison. The test is therefore conservative. Confidence intervals can be constructed for the corresponding linear regression. It was developped by American statistician Henry Scheffe in 1959.
http://purl.obolibrary.org/obo/STATO_0000156
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000156
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000156
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000156
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Scheffé's_method)
http://purl.obolibrary.org/obo/STATO_0000156
http://purl.obolibrary.org/obo/STATO_0000156
http://www.inside-r.org/packages/cran/agricolae/docs/scheffe.test
http://purl.obolibrary.org/obo/STATO_0000156
Scheffe test
http://purl.obolibrary.org/obo/STATO_0000157
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000157
the LSD test is a statistical test for multiple comparisons of treatments by means of least significant difference following an ANOVA analysis
http://purl.obolibrary.org/obo/STATO_0000157
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000157
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000157
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000157
R
http://purl.obolibrary.org/obo/STATO_0000157
LSD test
http://purl.obolibrary.org/obo/STATO_0000157
http://rss.acs.unt.edu/Rdoc/library/agricolae/html/LSD.test.html
http://purl.obolibrary.org/obo/STATO_0000157
Least significance different test
http://purl.obolibrary.org/obo/STATO_0000158
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000158
a null hypothesis which states that a linkage exists between 2 categorical variables
http://purl.obolibrary.org/obo/STATO_0000158
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000158
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000158
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000158
STATO
http://purl.obolibrary.org/obo/STATO_0000158
presence of association hypothesis
http://purl.obolibrary.org/obo/STATO_0000159
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000159
Stacked bar chart is a bar which is used to compare overall quantities across items while showing the contribution of category to the total amount. Stacked bar chart can be used for highlighting the total as they visually aggregate all of the categories in a group while indicating a part to whole relationship. The downside is that it becomes harder to compare the sizes of the individual categories.
http://purl.obolibrary.org/obo/STATO_0000159
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000159
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000159
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000159
adapter from
http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts
and
http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/
[last accessed: 2014-03-04]
http://purl.obolibrary.org/obo/STATO_0000159
barplot(height....)
set argument " beside = FALSE "
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html
http://purl.obolibrary.org/obo/STATO_0000159
stacked bar chart
http://purl.obolibrary.org/obo/STATO_0000160
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000160
The exponential distribution (a.k.a. negative exponential distribution) is the probability distribution that describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate. It is the continuous analogue of the geometric distribution, and it has the key property of being memoryless.
http://purl.obolibrary.org/obo/STATO_0000160
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000160
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000160
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000160
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Exponential.html
dexp(x, rate = 1, log = FALSE)
pexp(q, rate = 1, lower.tail = TRUE, log.p = FALSE)
qexp(p, rate = 1, lower.tail = TRUE, log.p = FALSE)
rexp(n, rate = 1)
http://purl.obolibrary.org/obo/STATO_0000160
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.expon.html#scipy.stats.expon
http://purl.obolibrary.org/obo/STATO_0000160
exponential distribution
http://purl.obolibrary.org/obo/STATO_0000161
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000161
variable distribution is data item which denotes the spatial resolution of data point making up a variable. variable distribution may be compared to a known probability distribution using goodness of fit test or plotting a quantile-quantile plot for visual assessment of the fit.
http://purl.obolibrary.org/obo/STATO_0000161
TODO: Probably need to drop it
http://purl.obolibrary.org/obo/STATO_0000161
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000161
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000161
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000161
STATO
http://purl.obolibrary.org/obo/STATO_0000161
data distribution
http://purl.obolibrary.org/obo/STATO_0000161
data distribution
http://purl.obolibrary.org/obo/STATO_0000162
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000162
the role played by an entity part of study group as defined by an experimental design and realized in a data analysis and data interpretation
http://purl.obolibrary.org/obo/STATO_0000162
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000162
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000162
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000162
experimental unit role
http://purl.obolibrary.org/obo/STATO_0000163
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000163
trimmed mean or truncated mean is a measure of central tendency which involves the calculation of the mean after discarding given parts of a probability distribution or sample at the high and low end, and typically discarding an equal amount of both
http://purl.obolibrary.org/obo/STATO_0000163
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000163
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000163
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000163
adapted from wikipedia [last accessed 2014-03-04]
http://en.wikipedia.org/wiki/Truncated_mean
http://purl.obolibrary.org/obo/STATO_0000163
truncated mean
http://purl.obolibrary.org/obo/STATO_0000163
scipy.stats.tmean(a, limits=None, inclusive=(True, True))
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.tmean.html#scipy.stats.tmean
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L684
http://purl.obolibrary.org/obo/STATO_0000163
trimmed mean
http://purl.obolibrary.org/obo/STATO_0000164
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000164
The interquartile range is a data item which corresponds to the difference between the upper quartile (3rd quartile) and lower quartile (1st quartile).
The interquartile range contains the second quartile or median.
The interquartile range is a data item providing a measure of data dispersion
http://purl.obolibrary.org/obo/STATO_0000164
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000164
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000164
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000164
STATO adapted from wikipedia, wolfram alpha and oxford dictionary of statistics
http://purl.obolibrary.org/obo/STATO_0000164
IQR(x, na.rm = FALSE, type = 7)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/IQR.html
http://purl.obolibrary.org/obo/STATO_0000164
inter quartile range
http://purl.obolibrary.org/obo/STATO_0000165
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000165
a pie chart is a graph in which a circular graph is divided into sector illustrating numerical proportion, meaning that the arc length of each sector (and consequently its central angle and area), is proportional to the quantity it represents.
http://purl.obolibrary.org/obo/STATO_0000165
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000165
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000165
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000165
adapted from Wikipedia, last accessed [2014-03-05]
http://en.wikipedia.org/wiki/Pie_chart
http://purl.obolibrary.org/obo/STATO_0000165
pie(x, labels = names(x), edges = 200, radius = 0.8,
clockwise = FALSE, init.angle = if(clockwise) 90 else 0,
density = NULL, angle = 45, col = NULL, border = NULL,
lty = NULL, main = NULL, ...)
https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/pie.html
http://purl.obolibrary.org/obo/STATO_0000165
pie chart
http://purl.obolibrary.org/obo/STATO_0000166
A bar chart is appropriate to represent counts of data.
http://purl.obolibrary.org/obo/STATO_0000166
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000166
the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent.
http://purl.obolibrary.org/obo/STATO_0000166
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000166
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000166
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000166
adapted from wikipedia (http://en.wikipedia.org/wiki/Bar_chart) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000166
bar plot
http://purl.obolibrary.org/obo/STATO_0000166
barplot(height, ...)
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html
http://purl.obolibrary.org/obo/STATO_0000166
bar chart
http://purl.obolibrary.org/obo/STATO_0000167
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000167
the first quartile is a quartile which splits the lower 25 % of the data
http://purl.obolibrary.org/obo/STATO_0000167
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000167
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000167
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000167
STATO
http://purl.obolibrary.org/obo/STATO_0000167
first quartile
http://purl.obolibrary.org/obo/STATO_0000168
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000168
a real time quantitative pcr plot is a line graph which plots the signal fluorescence intensity as a function of the number of PCR cycle
http://purl.obolibrary.org/obo/STATO_0000168
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000168
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000168
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000168
real time quantitative pcr plot
http://purl.obolibrary.org/obo/STATO_0000169
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000169
Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition
http://purl.obolibrary.org/obo/STATO_0000169
30/04/2014
- removed restriction:
'is about' exactly 2 'study group population'
- need more discussion for the relationship of fold change to study group populations for particular examples.
http://purl.obolibrary.org/obo/STATO_0000169
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000169
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000169
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000169
http://en.wikipedia.org/wiki/Fold_change
http://purl.obolibrary.org/obo/STATO_0000169
http://purl.obolibrary.org/obo/STATO_0000169
fold change
http://purl.obolibrary.org/obo/STATO_0000170
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000170
the first quartile is a quartile which splits the 75 % of the data
http://purl.obolibrary.org/obo/STATO_0000170
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000170
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000170
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000170
STATO
http://purl.obolibrary.org/obo/STATO_0000170
http://purl.obolibrary.org/obo/STATO_0000170
third quartile
http://purl.obolibrary.org/obo/STATO_0000171
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000171
Spear Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Spear to create the 'whisker' of the plot.
http://purl.obolibrary.org/obo/STATO_0000171
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000171
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000171
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000171
Spear, M.E. Charting Statistics (McGraw-Hill, 1952)
http://purl.obolibrary.org/obo/STATO_0000171
Spear box and whisker plot
http://purl.obolibrary.org/obo/STATO_0000172
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000172
expected fragments per kilobase of transcript per million fragments mapped is a metric used to report transcript expression event as generated by RNA-Seq using paired-end library. The calculated value results from 2 types of normalization, one to take into account the difference in reads counts associated with transcript length (at equal abundance, longer transcripts will have more reads than shorter transcripts) , (hence the 'per kilobase of transcript') and the other one to take into account different sequencing depth during distinct sequencing runs (hence the 'per millions mapped fragment'. The metric is specifically produced by cufflink software.
http://purl.obolibrary.org/obo/STATO_0000172
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000172
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000172
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000172
FPKM
http://purl.obolibrary.org/obo/STATO_0000172
adapted from:
http://seqanswers.com/forums/showthread.php?t=3254
and from
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
http://purl.obolibrary.org/obo/STATO_0000172
fragments per kilobase of transcript per million fragments mapped
http://purl.obolibrary.org/obo/STATO_0000173
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000173
homogeneity testing objective is the objective of a data transformation to test a null hypothesis that two or more sub-groups of a population share the same distribution of a single categorical variable.
For example, do people of different countries have the same proportion of smokers to non-smokers
http://purl.obolibrary.org/obo/STATO_0000173
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000173
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000173
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000173
STATO
http://purl.obolibrary.org/obo/STATO_0000173
http://purl.obolibrary.org/obo/STATO_0000173
homogeneity test objective
http://purl.obolibrary.org/obo/STATO_0000174
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000174
A forest plot is a graph designed to illustrate the relative strength of treatment effects in multiple quantitative scientific studies addressing the same question.
http://purl.obolibrary.org/obo/STATO_0000174
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000174
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000174
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000174
http://en.wikipedia.org/wiki/Forest_plot
http://purl.obolibrary.org/obo/STATO_0000174
http://purl.obolibrary.org/obo/STATO_0000174
metaplot(mn, se, nn=NULL, labels=NULL, conf.level=0.95,
xlab="Odds ratio", ylab="Study Reference",xlim=NULL,
summn=NULL, sumse=NULL, sumnn=NULL, summlabel="Summary",
logeffect=FALSE, lwd=2, boxsize=1,
zero=as.numeric(logeffect), colors=meta.colors(),
xaxt="s", logticks=TRUE, ...)
http://rss.acs.unt.edu/Rdoc/library/rmeta/html/metaplot.html
http://purl.obolibrary.org/obo/STATO_0000174
Forest plot
http://purl.obolibrary.org/obo/STATO_0000175
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/confint.html
http://purl.obolibrary.org/obo/STATO_0000175
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000175
confidence interval calculation is a data transformation which determines a confidence interval for a given statistical parameter
http://purl.obolibrary.org/obo/STATO_0000175
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000175
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000175
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000175
STATO
http://purl.obolibrary.org/obo/STATO_0000175
http://purl.obolibrary.org/obo/STATO_0000175
confidence interval calculation
http://purl.obolibrary.org/obo/STATO_0000176
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000176
t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution.
http://purl.obolibrary.org/obo/STATO_0000176
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000176
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000176
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000176
STATO
http://purl.obolibrary.org/obo/STATO_0000176
http://purl.obolibrary.org/obo/STATO_0000176
T
http://purl.obolibrary.org/obo/STATO_0000176
t-statistic
http://purl.obolibrary.org/obo/STATO_0000177
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000177
the beta distribution is a continuous probability distributions defined on the interval [0, 1] parametrized by two positive shape parameters, denoted by α and β, that appear as exponents of the random variable and control the shape of the distribution
http://purl.obolibrary.org/obo/STATO_0000177
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000177
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000177
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000177
adapted from Wikipedia:
http://en.wikipedia.org/wiki/Beta_distribution
http://purl.obolibrary.org/obo/STATO_0000177
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Beta.html
dbeta(x, shape1, shape2, ncp = 0, log = FALSE)
pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)
qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)
rbeta(n, shape1, shape2, ncp = 0)
http://purl.obolibrary.org/obo/STATO_0000177
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.beta.html#scipy.stats.beta
http://purl.obolibrary.org/obo/STATO_0000177
beta distribution
http://purl.obolibrary.org/obo/STATO_0000178
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000178
Kurtosis is a data item which denotes the degree of peakedness of a distribution. It is defined as a normalized form of the fourth central moment of a distribution.
http://purl.obolibrary.org/obo/STATO_0000178
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000178
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000178
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000178
http://mathworld.wolfram.com/Kurtosis.html
http://purl.obolibrary.org/obo/STATO_0000178
http://purl.obolibrary.org/obo/STATO_0000178
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kurtosis.html#scipy.stats.kurtosis
http://purl.obolibrary.org/obo/STATO_0000178
kurtosis
http://purl.obolibrary.org/obo/STATO_0000179
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000179
ANCOVA or analysis of covariance is a data transformation which evaluates if population means of a dependent variable are equal across levels of a categorical independent variables while controlling for the effects of other continuous variable s, known as covariates. Therefore, when performing ANCOVA, we are adjusting the dependent variable means to what they would be if all groups were equal on the covariates.
It augments the ANOVA model with one or more additional quantitative variables, called covariates, which are related to the response variable. The covariates are included to reduce the variance in the error terms and provide more precise measurement of the treatment effects. ANCOVA is used to test the main and interaction effects of the factors, while controlling for the effects of the covariate
http://purl.obolibrary.org/obo/STATO_0000179
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000179
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000179
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000179
adapted from wikipedia
http://purl.obolibrary.org/obo/STATO_0000179
http://purl.obolibrary.org/obo/STATO_0000179
ANCOVA
http://purl.obolibrary.org/obo/STATO_0000180
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000180
standard normal distribution is a normal distribution with variance = 1 and mean=0
http://purl.obolibrary.org/obo/STATO_0000180
we need to formally set value for mean and variance
http://purl.obolibrary.org/obo/STATO_0000180
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000180
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000180
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000180
http://purl.obolibrary.org/obo/STATO_0000180
dnorm(x, mean = 0, sd = 1, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Normal.html
http://purl.obolibrary.org/obo/STATO_0000180
standard normal distribution
http://purl.obolibrary.org/obo/STATO_0000181
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000181
Hardy-Weinberg equilibrium test is a statistical test which aims to evaluate if a population's proportion of allele is stable or not. It is used as means of quality control to evaluate possibility of genotyping error or population structure.
http://purl.obolibrary.org/obo/STATO_0000181
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000181
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000181
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000181
STATO: adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)
http://purl.obolibrary.org/obo/STATO_0000181
http://purl.obolibrary.org/obo/STATO_0000181
> library(HardyWeinberg)
> x <- c(298,489,213)
> HW.test <- HWChisq(x,verbose=TRUE)
http://cran.r-project.org/web/packages/HardyWeinberg/index.html
http://purl.obolibrary.org/obo/STATO_0000181
Hardy-Weinberg equilibrium testing
http://purl.obolibrary.org/obo/STATO_0000182
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000182
Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome.
It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups.
http://purl.obolibrary.org/obo/STATO_0000182
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000182
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000182
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000182
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/
http://www.stats.org/stories/2008/odds_ratios_april4_2008.html
http://purl.obolibrary.org/obo/STATO_0000182
OR
http://purl.obolibrary.org/obo/STATO_0000182
odds ratio
http://purl.obolibrary.org/obo/STATO_0000183
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000183
sphericity testing objective is a statistical objective of a data transformation which aims to test a null hypothesis of sphericity holds.
http://purl.obolibrary.org/obo/STATO_0000183
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000183
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000183
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000183
STATO
http://purl.obolibrary.org/obo/STATO_0000183
sphericity testing objective
http://purl.obolibrary.org/obo/STATO_0000183
sphericity testing objective
http://purl.obolibrary.org/obo/STATO_0000184
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000184
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
http://purl.obolibrary.org/obo/STATO_0000184
review formal definition as both numerator and denominator should be of the same type, not just some data item
http://purl.obolibrary.org/obo/STATO_0000184
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000184
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000184
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000184
adapted from Wolfram Alpha:
https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7
http://purl.obolibrary.org/obo/STATO_0000184
ratio
http://purl.obolibrary.org/obo/STATO_0000185
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000185
a 2 by n contingency table is a contingency table built for one dichotomous variable (a categorical variable with only 2 outcomes) and one polychotomous variable (a polychomotomous variable with at least 2 outcomes)
http://purl.obolibrary.org/obo/STATO_0000185
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000185
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000185
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000185
STATO
http://purl.obolibrary.org/obo/STATO_0000185
http://purl.obolibrary.org/obo/STATO_0000185
xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE,
na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html
flat contingency tables:
ftable(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html
http://purl.obolibrary.org/obo/STATO_0000185
2 by n contingency table
http://purl.obolibrary.org/obo/STATO_0000186
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000186
Lineweaver-Burk plot is a graph which is the graphical representation of the Lineweaver–Burk equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934. The plot provides a useful graphical method for analysis of the Michaelis–Menten equation.
It was widely used to determine important terms in enzymology and enzyme kinetics as the x-intercept of the graph represents −1/Km and the y-intercept of such a graph is equivalent to the inverse of Vmax
http://purl.obolibrary.org/obo/STATO_0000186
TODO: create 'inverse function' and replace 'data transformation' in the assertions
http://purl.obolibrary.org/obo/STATO_0000186
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000186
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000186
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000186
double reciprocal plot
http://purl.obolibrary.org/obo/STATO_0000186
Lineweaver-Burk plot
http://purl.obolibrary.org/obo/STATO_0000187
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000187
Tukey Honestly Significant Difference (HSD) test is a statistical test used following an ANOVA test yielding a statistically significant p-value in order to determine which means are different, to a given level of significance. The Tukey HSD test relies on the q-distribution.
The procedure is conservative, meaning that if sample sizes (the sizes of different study groups) are equal, the risk of a Type I error is exactly α, and if sample sizes are unequal it’s less than α.
http://purl.obolibrary.org/obo/STATO_0000187
IMPORTANT: Do Not to confuse the Tukey HSD test with Tukey Mean Difference Test (Bland-Altman test)
http://purl.obolibrary.org/obo/STATO_0000187
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000187
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000187
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000187
http://www.tc3.edu/instruct/sbrown/stat/anova1.htm#ANOVAprereq
http://purl.obolibrary.org/obo/STATO_0000187
Tukey's honestly significant difference
http://purl.obolibrary.org/obo/STATO_0000187
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TukeyHSD.html
http://purl.obolibrary.org/obo/STATO_0000187
Tukey HSD for Post-Hoc Analysis
http://purl.obolibrary.org/obo/STATO_0000188
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000188
average log signal intensity is a data time which corresponds to the sum of 2 distinct logarithm base 2 transformed signal intensity, each corresponding to a distinct condition of signal acquisition, divided by 2.
http://purl.obolibrary.org/obo/STATO_0000188
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000188
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000188
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000188
adapted from wikipedia:
http://en.wikipedia.org/wiki/MA_plot
last accessed: 2014-03-13
http://purl.obolibrary.org/obo/STATO_0000188
A-value
http://purl.obolibrary.org/obo/STATO_0000188
average log signal intensity
http://purl.obolibrary.org/obo/STATO_0000189
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000189
A mixed model is a statistical model containing both fixed effects and random effects
http://purl.obolibrary.org/obo/STATO_0000189
PRS: this is a stub and more work is needed to reconcile conflicting definitions
http://purl.obolibrary.org/obo/STATO_0000189
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000189
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000189
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000189
adapted from wikipedia
http://purl.obolibrary.org/obo/STATO_0000189
http://purl.obolibrary.org/obo/STATO_0000189
mixed model
http://purl.obolibrary.org/obo/STATO_0000190
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000190
Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.
http://purl.obolibrary.org/obo/STATO_0000190
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000190
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000190
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000190
Cq
http://purl.obolibrary.org/obo/STATO_0000190
Ct
http://purl.obolibrary.org/obo/STATO_0000190
http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml
http://purl.obolibrary.org/obo/STATO_0000190
threshold cycle
http://purl.obolibrary.org/obo/STATO_0000191
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000191
a goodness of fit statistical test is a statistical test which aim to evaluate if a sample distribution can be considered equivalent to a theoretical distribution used as input
http://purl.obolibrary.org/obo/STATO_0000191
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000191
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000191
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000191
http://purl.obolibrary.org/obo/STATO_0000191
goodness of fit statistical test
http://purl.obolibrary.org/obo/STATO_0000192
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000192
a cartesian product is a data transformation which operates on a n Sets to produce a set of all possible ordered n-tuples where each element of the tuple comes from a Set
http://purl.obolibrary.org/obo/STATO_0000192
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000192
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000192
PERSON: Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000192
adapted from math wolfram (http://mathworld.wolfram.com/CartesianProduct.html)
http://purl.obolibrary.org/obo/STATO_0000192
http://purl.obolibrary.org/obo/STATO_0000192
cartesian product
http://purl.obolibrary.org/obo/STATO_0000193
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000193
is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.
http://purl.obolibrary.org/obo/STATO_0000193
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000193
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000193
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000193
STATO
http://purl.obolibrary.org/obo/STATO_0000193
statistical sample
http://purl.obolibrary.org/obo/STATO_0000193
study group population
http://purl.obolibrary.org/obo/STATO_0000194
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000194
self explanatory
http://purl.obolibrary.org/obo/STATO_0000194
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000194
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000194
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000194
http://purl.obolibrary.org/obo/STATO_0000194
cartesian product 2 sets
http://purl.obolibrary.org/obo/STATO_0000195
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000195
A non-negative integer defining how many combination of factor levels (or treatments in the statistical sense) are to be used in a study.
http://purl.obolibrary.org/obo/STATO_0000195
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000195
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000195
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000195
STATO
http://purl.obolibrary.org/obo/STATO_0000195
http://purl.obolibrary.org/obo/STATO_0000195
number of factor level combinations
http://purl.obolibrary.org/obo/STATO_0000196
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
http://purl.obolibrary.org/obo/STATO_0000196
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000196
A confidence interval is a data item which defines an range of values in which a measurement or trial falls corresponding to a given probability.
http://purl.obolibrary.org/obo/STATO_0000196
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000196
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000196
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000196
http://mathworld.wolfram.com/ConfidenceInterval.html
http://purl.obolibrary.org/obo/STATO_0000196
http://purl.obolibrary.org/obo/STATO_0000196
confidence interval
http://purl.obolibrary.org/obo/STATO_0000197
http://purl.obolibrary.org/obo/STATO_0000197
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000197
a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....)
http://purl.obolibrary.org/obo/STATO_0000197
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000197
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000197
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000197
ensembl, ucsc
http://purl.obolibrary.org/obo/STATO_0000197
http://purl.obolibrary.org/obo/STATO_0000197
genomic coordinate system
http://purl.obolibrary.org/obo/STATO_0000198
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000198
a statistical test which makes no assumption about the underlying data distribution
http://purl.obolibrary.org/obo/STATO_0000198
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000198
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000198
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000198
STATO
http://purl.obolibrary.org/obo/STATO_0000198
non-parametric test
http://purl.obolibrary.org/obo/STATO_0000199
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000199
the Mauchly's test for sphericity is a statistical test which evaluates if the variance of the differences between all combinations of the groups are equal, a property known as 'sphericity' in the context of repeated measures. It is used for instance prior to repeated measure ANOVA.
The test works by assessing if a Wishart-distributed covariance matrix (or transformation thereof) is proportional to a given matrix.
http://purl.obolibrary.org/obo/STATO_0000199
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000199
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000199
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000199
AGB-PRS, adapted from wikipedia (http://en.wikipedia.org/wiki/Mauchly's_sphericity_test)
polled on june,10th, 2013
and from R manual:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html
http://purl.obolibrary.org/obo/STATO_0000199
Mauchly's test for sphericity
http://purl.obolibrary.org/obo/STATO_0000199
mauchly.test(object, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html
http://purl.obolibrary.org/obo/STATO_0000199
Mauchly's test for sphericity
http://purl.obolibrary.org/obo/STATO_0000200
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000200
the statistical test power is data item which is about a statistical test and is obtained by subtracting the false negative rate (type II error rate) to 1.
The power of a statistical test is the probability that it will correctly lead to the rejection of a false null hypothesis (Greene 2000). The statistical power is the ability of a test to detect an effect, if the effect actually exists (High 2000).
http://purl.obolibrary.org/obo/STATO_0000200
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000200
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000200
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000200
adapted from wikipedia (http://en.wikipedia.org/wiki/Statistical_power), polled June 10th, 2013
http://purl.obolibrary.org/obo/STATO_0000200
http://purl.obolibrary.org/obo/STATO_0000200
statistical test power
http://purl.obolibrary.org/obo/STATO_0000201
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000201
Spearman's rank correlation coefficient is a correlation coefficient which is a nonparametric measure of statistical dependence between two ranked variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other.
Spearman's coefficient may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) but may require a ranking transformation of the variables
http://purl.obolibrary.org/obo/STATO_0000201
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000201
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000201
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000201
Spearman's rho
http://purl.obolibrary.org/obo/STATO_0000201
http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
http://purl.obolibrary.org/obo/STATO_0000201
http://purl.obolibrary.org/obo/STATO_0000201
cor(x, y = NULL, use = "everything",method = c("spearman"))
http://purl.obolibrary.org/obo/STATO_0000201
scipy.stats.spearmanr(a, b=None, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2643
http://purl.obolibrary.org/obo/STATO_0000201
Spearman's rank correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000202
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000202
within subject comparison statistical test is a kind of statistical test which evaluates if a change occurs within one experimental unit over time following a treatment or an event
http://purl.obolibrary.org/obo/STATO_0000202
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000202
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000202
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000202
STATO
http://purl.obolibrary.org/obo/STATO_0000202
http://purl.obolibrary.org/obo/STATO_0000202
within subject comparison statistical test
http://purl.obolibrary.org/obo/STATO_0000203
http://purl.obolibrary.org/obo/STATO_0000203
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000203
a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design
http://purl.obolibrary.org/obo/STATO_0000203
possibly submit to 'Population and Community Ontology'
http://purl.obolibrary.org/obo/STATO_0000203
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000203
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000203
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000203
STATO
http://purl.obolibrary.org/obo/STATO_0000203
http://purl.obolibrary.org/obo/STATO_0000203
cohort
http://purl.obolibrary.org/obo/STATO_0000204
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000204
the F-distribution is a continuous probability distribution which arises in the testing of whether two observed samples have the same variance.
http://purl.obolibrary.org/obo/STATO_0000204
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000204
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000204
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000204
Fisher distribution
http://purl.obolibrary.org/obo/STATO_0000204
Snedecor Fisher distribution
http://purl.obolibrary.org/obo/STATO_0000204
http://mathworld.wolfram.com/F-Distribution.html
http://purl.obolibrary.org/obo/STATO_0000204
http://purl.obolibrary.org/obo/STATO_0000204
df(x, df1, df2, ncp, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Fdist.html
http://purl.obolibrary.org/obo/STATO_0000204
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f.html#scipy.stats.f
http://purl.obolibrary.org/obo/STATO_0000204
F-distribution
http://purl.obolibrary.org/obo/STATO_0000205
Inverse relation of 'denotes', where denotation is what happens when someone creates an information content entity E in order to specifically refer to something (from 'denotes' definition).
http://purl.obolibrary.org/obo/STATO_0000205
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000205
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000205
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000205
is denoted by
http://purl.obolibrary.org/obo/STATO_0000206
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000206
RPKM is a kind of count which numbers the sequence reads found per kilobase of transcript reported to million of sequence reads. RPKM is a metric generated by ERANGE software tool as reported by Mortazi et al, in 2008.
The metric has been enhanced and replaced by FPKM to better take into account splice variant. FKPM uses a statistical model to perform the computation.
http://purl.obolibrary.org/obo/STATO_0000206
Alejandra Gonzalez Beltran
http://purl.obolibrary.org/obo/STATO_0000206
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000206
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000206
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000206
RPKM
http://purl.obolibrary.org/obo/STATO_0000206
http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html
http://purl.obolibrary.org/obo/STATO_0000206
reads per kilobase of transcript per million fragments mapped
http://purl.obolibrary.org/obo/STATO_0000207
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000207
a planned process which etablishes and states the different hypothesis to be evaluated during a null hypothesis statistical test
http://purl.obolibrary.org/obo/STATO_0000207
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000207
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000207
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000207
STATO
http://purl.obolibrary.org/obo/STATO_0000207
specifying null and alternate hypothesis
http://purl.obolibrary.org/obo/STATO_0000208
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000208
An alternative hypothesis is an hypothesis defined in a statistical test that is the opposite of the null hypothesis.
http://purl.obolibrary.org/obo/STATO_0000208
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000208
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000208
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000208
STATO
http://purl.obolibrary.org/obo/STATO_0000208
http://purl.obolibrary.org/obo/STATO_0000208
alternative hypothesis
http://purl.obolibrary.org/obo/STATO_0000209
PMID:12892658
"Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change."
http://purl.obolibrary.org/obo/STATO_0000209
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000209
area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph
http://purl.obolibrary.org/obo/STATO_0000209
PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch
http://purl.obolibrary.org/obo/STATO_0000209
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000209
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000209
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000209
area under curve
http://purl.obolibrary.org/obo/STATO_0000210
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000210
is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes.
http://purl.obolibrary.org/obo/STATO_0000210
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000210
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000210
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000210
STATO
http://purl.obolibrary.org/obo/STATO_0000210
channel1/channel2 fluorescence intensity ratio
http://purl.obolibrary.org/obo/STATO_0000210
channel1/channel2 fluorescence intensity ratio
http://purl.obolibrary.org/obo/STATO_0000211
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000211
odds ratio homogeneity hypothesis is a null hypothesis stating that all odds ratio are homogenous, that is remain within the same range
http://purl.obolibrary.org/obo/STATO_0000211
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000211
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000211
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000211
STATO
http://purl.obolibrary.org/obo/STATO_0000211
odds ratio homogeneity hypothesis
http://purl.obolibrary.org/obo/STATO_0000211
odds ratio homogeneity hypothesis
http://purl.obolibrary.org/obo/STATO_0000212
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000212
a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables.
http://purl.obolibrary.org/obo/STATO_0000212
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000212
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000212
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000212
adapted from:
http://www.rasch.org/rmt/rmt193c.htm
and
http://en.wikipedia.org/wiki/Polychoric_correlation
http://purl.obolibrary.org/obo/STATO_0000212
tetrachoric correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000213
http://purl.obolibrary.org/obo/STATO_0000213
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000213
discretization as a processing converting a continuous variable into a polychotomous variable by concretizing a set of discretization rules
http://purl.obolibrary.org/obo/STATO_0000213
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000213
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000213
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000213
AGB,PRS adapted from wikipedia (http://en.wikipedia.org/wiki/Discretization)
http://purl.obolibrary.org/obo/STATO_0000213
http://purl.obolibrary.org/obo/STATO_0000213
http://cran.r-project.org/web/packages/discretization/index.html
http://purl.obolibrary.org/obo/STATO_0000213
continuous variable discretization
http://purl.obolibrary.org/obo/STATO_0000214
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
http://purl.obolibrary.org/obo/STATO_0000214
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000214
a confidence interval which covers 50% of the sampling distribution, meaning that there is a 50% risk of false positive (type I error)
http://purl.obolibrary.org/obo/STATO_0000214
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000214
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000214
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000214
confidence interval at 10% of type I error rate
http://purl.obolibrary.org/obo/STATO_0000214
STATO
http://purl.obolibrary.org/obo/STATO_0000214
http://purl.obolibrary.org/obo/STATO_0000214
50% confidence interval
http://purl.obolibrary.org/obo/STATO_0000215
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000215
probit regression model is a model which attempts to explain data distribution associated with *ordinal* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the ordered probit function.
http://purl.obolibrary.org/obo/STATO_0000215
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000215
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000215
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000215
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013
http://purl.obolibrary.org/obo/STATO_0000215
http://purl.obolibrary.org/obo/STATO_0000215
http://purl.obolibrary.org/obo/STATO_0000215
ordered probit regression for analysis of ordinal dependent variable
http://purl.obolibrary.org/obo/STATO_0000216
http://purl.obolibrary.org/obo/STATO_0000216
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000216
a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria
http://purl.obolibrary.org/obo/STATO_0000216
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000216
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000216
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000216
STATO
http://purl.obolibrary.org/obo/STATO_0000216
http://purl.obolibrary.org/obo/STATO_0000216
stratum population
http://purl.obolibrary.org/obo/STATO_0000217
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000217
a null hypothesis which states that a given matrix is proportional to a Wishart-distributed covariance matrix
http://purl.obolibrary.org/obo/STATO_0000217
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000217
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000217
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000217
STATO
http://purl.obolibrary.org/obo/STATO_0000217
hypothesis of sphericity
http://purl.obolibrary.org/obo/STATO_0000217
sphericity hypothesis
http://purl.obolibrary.org/obo/STATO_0000218
http://purl.obolibrary.org/obo/STATO_0000218
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000218
Model fitting is a data transformation process which evaluates if a model appropriately represents a dataset. A model fitting process tests the goodness of fit of the model to the data
http://purl.obolibrary.org/obo/STATO_0000218
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000218
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000218
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000218
model fitting
http://purl.obolibrary.org/obo/STATO_0000219
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000219
a real time pcr standard curve is a line graph which plots the fluorescence intensity signal as a function of the concentration of a sample used as reference and used to determine relative abundance of test samples
http://purl.obolibrary.org/obo/STATO_0000219
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000219
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000219
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000219
adapted from:
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/qpcr_technical_guide.pdf
and
http://www.lifetechnologies.com/uk/en/home/life-science/pcr/real-time-pcr/qpcr-education/absolute-vs-relative-quantification-for-qpcr.html
http://purl.obolibrary.org/obo/STATO_0000219
RT-PCR standard curve
http://purl.obolibrary.org/obo/STATO_0000220
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000220
the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria
http://purl.obolibrary.org/obo/STATO_0000220
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000220
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000220
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000220
STATO, adapted from
http://purl.obolibrary.org/obo/STATO_0000220
type II error rate
http://purl.obolibrary.org/obo/STATO_0000220
β
http://purl.obolibrary.org/obo/STATO_0000220
false negative rate
http://purl.obolibrary.org/obo/STATO_0000221
http://purl.obolibrary.org/obo/STATO_0000221
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000221
a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense)
http://purl.obolibrary.org/obo/STATO_0000221
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000221
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000221
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000221
aleatory variable
http://purl.obolibrary.org/obo/STATO_0000221
stochastic variable
http://purl.obolibrary.org/obo/STATO_0000221
wikipedia:
http://en.wikipedia.org/wiki/Random_variable
http://purl.obolibrary.org/obo/STATO_0000221
random variable
http://purl.obolibrary.org/obo/STATO_0000222
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000222
graeco-latin square design is_a study design which allows in its simpler form controlling 3 levels of nuisance variables (also known as blocking variables). The 3 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
http://purl.obolibrary.org/obo/STATO_0000222
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000222
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000222
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000222
http://purl.obolibrary.org/obo/STATO_0000222
graeco-latin square design
http://purl.obolibrary.org/obo/STATO_0000223
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000223
group assignment based on blocking variable specification is a kind of group assignment process which takes into account the levels assumed by a blocking variable to allocate subjects or experimental units to a treatment group
http://purl.obolibrary.org/obo/STATO_0000223
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000223
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000223
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000223
STATO
http://purl.obolibrary.org/obo/STATO_0000223
group assignment based on blocking variable specification
http://purl.obolibrary.org/obo/STATO_0000224
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000224
A testing objective to ensure that the sample used in a statistical test actually follows a normal distribution.
http://purl.obolibrary.org/obo/STATO_0000224
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000224
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000224
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000224
STATO
http://purl.obolibrary.org/obo/STATO_0000224
http://purl.obolibrary.org/obo/STATO_0000224
goodness of fit testing objective
http://purl.obolibrary.org/obo/STATO_0000225
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000225
A probability distribution is a information content entity that specifies the probability of the value of a random variable.
For a discrete random variable, a mathematical formula that gives the probability of each value of the variable.
For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.
http://purl.obolibrary.org/obo/STATO_0000225
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000225
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000225
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000225
probability distribution
http://purl.obolibrary.org/obo/STATO_0000226
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000226
It is a testing objective to ensure the variances of the different groups used in a statistical test are similar (i.e. not too different).
http://purl.obolibrary.org/obo/STATO_0000226
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000226
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000226
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000226
homoschedacity testing objective
http://purl.obolibrary.org/obo/STATO_0000226
STATO
http://purl.obolibrary.org/obo/STATO_0000226
http://purl.obolibrary.org/obo/STATO_0000226
equal variance testing objective
http://purl.obolibrary.org/obo/STATO_0000227
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000227
a normal distribution is a continuous probability distribution described by a probability distribution function described here:
http://mathworld.wolfram.com/NormalDistribution.html
http://purl.obolibrary.org/obo/STATO_0000227
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000227
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000227
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000227
Gaussian distribution
http://purl.obolibrary.org/obo/STATO_0000227
http://mathworld.wolfram.com/NormalDistribution.html
http://purl.obolibrary.org/obo/STATO_0000227
http://purl.obolibrary.org/obo/STATO_0000227
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.norm.html#scipy.stats.norm
http://purl.obolibrary.org/obo/STATO_0000227
normal distribution
http://purl.obolibrary.org/obo/STATO_0000228
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000228
ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking
http://purl.obolibrary.org/obo/STATO_0000228
Alejandra Gonzalez-Beltan
http://purl.obolibrary.org/obo/STATO_0000228
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000228
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000228
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000228
ranked variable
http://purl.obolibrary.org/obo/STATO_0000228
http://udel.edu/~mcdonald/statvartypes.html
http://purl.obolibrary.org/obo/STATO_0000228
http://purl.obolibrary.org/obo/STATO_0000228
ordinal variable
http://purl.obolibrary.org/obo/STATO_0000229
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000229
Chi-square probability distribution with k degrees of freedom is a theoretical probability distribution which corresponds to the distribution of a sum of the squares of k independent standard normal random variables.
http://purl.obolibrary.org/obo/STATO_0000229
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000229
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000229
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000229
http://purl.obolibrary.org/obo/STATO_0000229
dchisq(x, df, ncp = 0, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Chisquare.html
http://purl.obolibrary.org/obo/STATO_0000229
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chi2.html#scipy.stats.chi2
http://purl.obolibrary.org/obo/STATO_0000229
Chi-square probability distribution
http://purl.obolibrary.org/obo/STATO_0000230
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000230
the expected value (or expectation, mathematical expectation, EV, mean, or the first moment) of a random variable is a data item which corresponds to the weighted average of all possible values that this random variable can take on. The weights used in computing this average correspond to the probabilities in case of a discrete random variable, or densities in case of a continuous random variable. From a rigorous theoretical standpoint, the expected value is the integral of the random variable with respect to its probability measure.
http://purl.obolibrary.org/obo/STATO_0000230
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000230
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000230
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000230
first moment
http://purl.obolibrary.org/obo/STATO_0000230
mean
http://purl.obolibrary.org/obo/STATO_0000230
μ
http://purl.obolibrary.org/obo/STATO_0000230
http://en.wikipedia.org/wiki/Expected_value
http://purl.obolibrary.org/obo/STATO_0000230
http://purl.obolibrary.org/obo/STATO_0000230
expected value
http://purl.obolibrary.org/obo/STATO_0000231
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
http://purl.obolibrary.org/obo/STATO_0000231
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000231
a confidence interval which covers 95% of the sampling distribution, meaning that there is a 5% risk of false positive (type I error). If the number of observations made is large enough, the sampling distribution can be assumed to be normal, which entails that 95% of the sampling distributions falls within roughly2 (1.96) standard deviations from the mean.
http://purl.obolibrary.org/obo/STATO_0000231
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000231
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000231
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000231
confidence interval at 5% of type I error rate
http://purl.obolibrary.org/obo/STATO_0000231
STATO
http://purl.obolibrary.org/obo/STATO_0000231
http://purl.obolibrary.org/obo/STATO_0000231
95% confidence interval
http://purl.obolibrary.org/obo/STATO_0000232
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000232
number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR.
http://purl.obolibrary.org/obo/STATO_0000232
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000232
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000232
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000232
adapted from various sources including:
http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml
http://purl.obolibrary.org/obo/STATO_0000232
number of PCR cycle
http://purl.obolibrary.org/obo/STATO_0000233
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000233
sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1
http://purl.obolibrary.org/obo/STATO_0000233
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000233
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000233
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000233
recall
http://purl.obolibrary.org/obo/STATO_0000233
sensitivity
http://purl.obolibrary.org/obo/STATO_0000233
adapted from:
http://en.wikipedia.org/wiki/Sensitivity_and_specificity
and
http://mathworld.wolfram.com/Sensitivity.html
http://purl.obolibrary.org/obo/STATO_0000233
http://purl.obolibrary.org/obo/STATO_0000233
true positive rate
http://purl.obolibrary.org/obo/STATO_0000234
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000234
a residual is a data item which is the output of an error estimate or model fitting process and which is an observable estimate of the unobservable error
http://purl.obolibrary.org/obo/STATO_0000234
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000234
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000234
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000234
residual
http://purl.obolibrary.org/obo/STATO_0000235
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000235
A genetic association study is a kind of study whose objective is to detect associations between phenotypes, between a phenotype and a genetic polymorphism or between two genetic polymorphisms.
http://purl.obolibrary.org/obo/STATO_0000235
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000235
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000235
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000235
http://en.wikipedia.org/wiki/Genetic_association
http://purl.obolibrary.org/obo/STATO_0000235
genetic association study
http://purl.obolibrary.org/obo/STATO_0000236
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000236
the coefficient of variation is a normalized measure fo dispersion of a probability distribution of frequency distribution.
http://purl.obolibrary.org/obo/STATO_0000236
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000236
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000236
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000236
http://en.wikipedia.org/wiki/Coefficient_of_variation
last accessed: 2013-10-18
http://purl.obolibrary.org/obo/STATO_0000236
scipy.stats.variation(a, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.variation.html#scipy.stats.variation
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L951
http://purl.obolibrary.org/obo/STATO_0000236
coefficient of variation
http://purl.obolibrary.org/obo/STATO_0000237
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000237
The standard deviation of a random variable, statistical population, data set, or probability distribution is a measure of variation which correspond to the average distance from the mean of the data set to any given point of that dataset. It also corresponds to the square root of its variance.
http://purl.obolibrary.org/obo/STATO_0000237
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000237
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000237
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000237
σ
http://purl.obolibrary.org/obo/STATO_0000237
http://en.wikipedia.org/wiki/Standard_deviation
http://purl.obolibrary.org/obo/STATO_0000237
http://purl.obolibrary.org/obo/STATO_0000237
sd(x, na.rm = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/sd.html
http://purl.obolibrary.org/obo/STATO_0000237
standard deviation
http://purl.obolibrary.org/obo/STATO_0000238
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000238
high content screening is a kind of investigation which uses a standardized cellular assays to test the effect of substances (RNAi or small molecules) held in libraries on a cellular phenotype. it relies on microscopy imaging and or flow-cytometry, robotic handling to ensure fast and high-throughput.
http://purl.obolibrary.org/obo/STATO_0000238
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000238
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000238
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000238
high throughput screening
http://purl.obolibrary.org/obo/STATO_0000238
adapted from:
http://en.wikipedia.org/wiki/High-content_screening
http://purl.obolibrary.org/obo/STATO_0000238
http://purl.obolibrary.org/obo/STATO_0000238
high-content screening
http://purl.obolibrary.org/obo/STATO_0000239
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000239
high throughput screening is a kind of investigation which uses a standardized assays (cell based, enzymatic or chemometric) to test the effect of substances (RNAi or small molecules) held in libraries on a very specific and measureable outcome (e.g fluorence intensity). it relies on robotic handling to ensure fast and high-throughput in assay performance, data acquisition and hit selection.
http://purl.obolibrary.org/obo/STATO_0000239
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000239
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000239
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000239
AGB,PRS
http://purl.obolibrary.org/obo/STATO_0000239
http://purl.obolibrary.org/obo/STATO_0000239
high throughput screening
http://purl.obolibrary.org/obo/STATO_0000240
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000240
Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables)
http://purl.obolibrary.org/obo/STATO_0000240
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000240
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000240
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000240
Kendall rank correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000240
Kendall's tau (τ) coefficient
http://purl.obolibrary.org/obo/STATO_0000240
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient), polled in june 2013
and from:
http://stamash.org/pearsons-correlation-coefficient/
http://stamash.org/kendalls-tau-correlation/
http://purl.obolibrary.org/obo/STATO_0000240
http://purl.obolibrary.org/obo/STATO_0000240
cor(x, y = NULL, use = "everything",method = c("kendall"))
http://purl.obolibrary.org/obo/STATO_0000240
scipy.stats.kendalltau(x, y, initial_lexsort=True)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kendalltau.html#scipy.stats.kendalltau
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2827
http://purl.obolibrary.org/obo/STATO_0000240
Kendall's correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000241
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000241
Q-Q plot or quantile-quantile plot is the output of a graphical method for comparing two probability distributions by plotting their quantiles against each other
http://purl.obolibrary.org/obo/STATO_0000241
PRS,AGB: need to add the notion of quantile
http://purl.obolibrary.org/obo/STATO_0000241
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000241
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000241
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000241
STATO
http://purl.obolibrary.org/obo/STATO_0000241
quantile-quantile plot
http://purl.obolibrary.org/obo/STATO_0000241
qqplot(x, y, plot.it = TRUE, xlab = deparse(substitute(x)),
ylab = deparse(substitute(y)), ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/qqnorm.html
http://purl.obolibrary.org/obo/STATO_0000241
Q-Q plot
http://purl.obolibrary.org/obo/STATO_0000242
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000242
statistical error is an data item denoting the amount by which an observation differs from the expected value, being based on the whole statistical population from which the statistical unit was chosen randomly
http://purl.obolibrary.org/obo/STATO_0000242
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000242
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000242
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000242
adapted from wikipedia:
http://en.wikipedia.org/wiki/Errors_and_residuals_in_statistics
last accessed: 18-11-2013
http://purl.obolibrary.org/obo/STATO_0000242
disturbance
http://purl.obolibrary.org/obo/STATO_0000242
statistical error
http://purl.obolibrary.org/obo/STATO_0000243
A box and whisker plot is appropriate to represent the characteristics oc a distribution.
http://purl.obolibrary.org/obo/STATO_0000243
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000243
a box plot is a graph which plots datasets relying on their quartiles and the interquartile range to create the box and the whiskers
http://purl.obolibrary.org/obo/STATO_0000243
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000243
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000243
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000243
Tukey box and whisker plot
http://purl.obolibrary.org/obo/STATO_0000243
box plot
http://purl.obolibrary.org/obo/STATO_0000243
Tukey, J. W. "Box-and-Whisker Plots." §2C in Exploratory Data Analysis. Reading, MA: Addison-Wesley, pp. 39-43, 1977.
http://purl.obolibrary.org/obo/STATO_0000243
boxplot
http://purl.obolibrary.org/obo/STATO_0000243
boxplot(x, ...)
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/boxplot.html
http://purl.obolibrary.org/obo/STATO_0000243
box and whisker plot
http://purl.obolibrary.org/obo/STATO_0000244
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000244
(Rn +) − (Rn −), where Rn + = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR with template and Rn − = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR without template or early cycles of a real-time reaction. Ct = threshold cycle, i.e., cycle at which a statistically significant increase in ΔRn is first detected
http://purl.obolibrary.org/obo/STATO_0000244
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000244
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000244
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000244
http://jcm.asm.org/content/38/7/2516.figures-only
http://purl.obolibrary.org/obo/STATO_0000244
ΔRn
http://purl.obolibrary.org/obo/STATO_0000245
Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group.
http://purl.obolibrary.org/obo/STATO_0000245
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000245
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000245
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000245
risk ratio
http://purl.obolibrary.org/obo/STATO_0000245
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000245
http://purl.obolibrary.org/obo/STATO_0000245
relative risk
http://purl.obolibrary.org/obo/STATO_0000246
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000246
Woolf's test is a statistical test which evaluates the null hypothesis that odds ratio are the same accross all strata of population under investigation
http://purl.obolibrary.org/obo/STATO_0000246
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000246
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000246
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000246
http://people.umass.edu/biep640w/pdf/4.%20%20Categorical%20Data%20Analysis%202012.pdf
http://purl.obolibrary.org/obo/STATO_0000246
http://purl.obolibrary.org/obo/STATO_0000246
woolf_test(x) where x is 2 x 2 x k contingency table
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vcd/html/woolf_test.html
http://purl.obolibrary.org/obo/STATO_0000246
Woolf's test
http://purl.obolibrary.org/obo/STATO_0000247
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000247
odds ratio homogeneity test is a statistical test which aims to evaluate that null the hypothesis of consistency odds ratio accross different strata of population is true or not
http://purl.obolibrary.org/obo/STATO_0000247
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000247
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000247
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000247
STATO
http://purl.obolibrary.org/obo/STATO_0000247
http://purl.obolibrary.org/obo/STATO_0000247
odds ratio homogeneity test
http://purl.obolibrary.org/obo/STATO_0000248
https://onlinecourses.science.psu.edu/stat503/node/19
Often in medical studies, the blocking factor used is the type of institution. This provides a very useful blocking factor, hopefully removing institutionally related factors such as size of the institution, types of populations served, hospitals versus clinics, etc., that would influence the overall results of the experiment.
http://purl.obolibrary.org/obo/STATO_0000248
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000248
a blocking variable is a independent variable which is used in a blocking process part of an experiment with the purpose of maximizing the signal coming from the main variable.
http://purl.obolibrary.org/obo/STATO_0000248
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000248
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000248
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000248
nuisance variable
http://purl.obolibrary.org/obo/STATO_0000248
https://onlinecourses.science.psu.edu/stat503/node/18
http://purl.obolibrary.org/obo/STATO_0000248
http://purl.obolibrary.org/obo/STATO_0000248
blocking variable
http://purl.obolibrary.org/obo/STATO_0000249
a DNA microarray hybridization is an assay relying on nucleic acid hybridization , which uses a DNA microarray device and a nucleic acid as input. It precedes a data acquisition process
http://purl.obolibrary.org/obo/STATO_0000249
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000249
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000249
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000249
DNA microarray hybridization
http://purl.obolibrary.org/obo/STATO_0000250
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000250
group comparison objective is a data transformation objective which aims to determine if 2 or more study group differ with respect to the signal of a response variable
http://purl.obolibrary.org/obo/STATO_0000250
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000250
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000250
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000250
STATO
http://purl.obolibrary.org/obo/STATO_0000250
group comparison objective
http://purl.obolibrary.org/obo/STATO_0000251
"Time to solve an anagram problem" is continuous since it could take 2 minutes, 2.13 minutes etc. to finish a problem
http://purl.obolibrary.org/obo/STATO_0000251
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000251
A continuous variable is one for which, within the limits the variable ranges, any value is possible.
http://purl.obolibrary.org/obo/STATO_0000251
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000251
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000251
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000251
http://davidmlane.com/hyperstat/A97418.html
http://purl.obolibrary.org/obo/STATO_0000251
http://udel.edu/~mcdonald/statvartypes.html
http://purl.obolibrary.org/obo/STATO_0000251
http://purl.obolibrary.org/obo/STATO_0000251
continuous variable
http://purl.obolibrary.org/obo/STATO_0000252
http://purl.obolibrary.org/obo/STATO_0000252
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000252
a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories
http://purl.obolibrary.org/obo/STATO_0000252
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000252
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000252
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000252
discrete variable
http://purl.obolibrary.org/obo/STATO_0000252
nominal variable
http://purl.obolibrary.org/obo/STATO_0000252
qualitative factor
http://purl.obolibrary.org/obo/STATO_0000252
http://udel.edu/~mcdonald/statvartypes.html
http://purl.obolibrary.org/obo/STATO_0000252
http://purl.obolibrary.org/obo/STATO_0000252
https://onlinecourses.science.psu.edu/stat503/node/7
http://purl.obolibrary.org/obo/STATO_0000252
categorical variable
http://purl.obolibrary.org/obo/STATO_0000253
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000253
the objective of a data transformation to test a null hypothesis of absence of difference within subject holds.
http://purl.obolibrary.org/obo/STATO_0000253
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000253
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000253
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000253
STATO
http://purl.obolibrary.org/obo/STATO_0000253
http://purl.obolibrary.org/obo/STATO_0000253
within subject comparison objective
http://purl.obolibrary.org/obo/STATO_0000254
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000254
The allele frequency is a data item which denotes the incidence of a gene variant in a population. It is calculated as a ratio, by dividing the number of copies of a particular allele by the number of copies of all alleles at the genetic place (locus) in a population.
http://purl.obolibrary.org/obo/STATO_0000254
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000254
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000254
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000254
http://www.nature.com/scitable/definition/allele-frequency-298
http://purl.obolibrary.org/obo/STATO_0000254
http://purl.obolibrary.org/obo/STATO_0000254
allele frequency
http://purl.obolibrary.org/obo/STATO_0000255
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000255
the objective of a data transformation to test a null hypothesis of absence of difference withing subject holds.
http://purl.obolibrary.org/obo/STATO_0000255
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000255
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000255
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000255
STATO
http://purl.obolibrary.org/obo/STATO_0000255
http://purl.obolibrary.org/obo/STATO_0000255
between group comparison objective
http://purl.obolibrary.org/obo/STATO_0000256
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000256
a manhattan plot for gwas is a kind of scatter plot used to facilitate presentation of genome-wide association study (GWAS) data. Genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism displayed on the Y-axis.
http://purl.obolibrary.org/obo/STATO_0000256
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000256
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000256
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000256
http://en.wikipedia.org/wiki/Manhattan_plot
http://purl.obolibrary.org/obo/STATO_0000256
http://purl.obolibrary.org/obo/STATO_0000256
plotGrandLinear(obj, ..., facets, space.skip = 0.01, geom = NULL,
cutoff = NULL, cutoff.color = "red", cutoff.size = 1,
legend = FALSE, xlim, ylim, xlab, ylab, main)
http://www.tengfei.name/ggbio/docs/man/plotGrandLinear.html
http://purl.obolibrary.org/obo/STATO_0000256
manhattan plot for gwas
http://purl.obolibrary.org/obo/STATO_0000257
A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
http://purl.obolibrary.org/obo/STATO_0000257
import from Population and Community Ontology:
http://www.ontobee.org/browser/rdf.php?o=PCO&iri=http://purl.obolibrary.org/obo/PCO_0000020
http://purl.obolibrary.org/obo/STATO_0000257
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000257
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000257
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000257
http://purl.obolibrary.org/obo/PCO_0000020
http://purl.obolibrary.org/obo/STATO_0000257
family
http://purl.obolibrary.org/obo/STATO_0000258
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000258
a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.
http://purl.obolibrary.org/obo/STATO_0000258
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000258
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000258
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000258
STATO
http://purl.obolibrary.org/obo/STATO_0000258
adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2.
and from Oxford English Dictionary:
http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1
http://purl.obolibrary.org/obo/STATO_0000258
http://purl.obolibrary.org/obo/STATO_0000258
variable
http://purl.obolibrary.org/obo/STATO_0000259
the relationship between a fraction and the number below the line (or divisor)
http://purl.obolibrary.org/obo/STATO_0000259
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000259
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000259
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000259
AGB
http://purl.obolibrary.org/obo/STATO_0000259
has denominator
http://purl.obolibrary.org/obo/STATO_0000260
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000260
repeated measure ANOVA is a kind of ANOVA specifically developed for non-independent observations as found when repeated measurements on the sample experimental unit.
repeated measure ANOVA is sensitive to departure from normality (evaluation using Bartlett's test), more so in the case of unbalanced groups (i.e. different sizes of sample populations).
Departure from sphericity (evaluation using Mauchly'test) used to be an issue which is now handled robustly by modern tools such as R's lme4 or nlme, which accommodate dependence assumptions other than sphericity.
http://purl.obolibrary.org/obo/STATO_0000260
discussion in https://github.com/ISA-tools/stato/issues/28
http://purl.obolibrary.org/obo/STATO_0000260
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000260
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000260
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000260
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000260
ANOVA for correlated samples
http://purl.obolibrary.org/obo/STATO_0000260
adapted from wikipedia and https://statistics.laerd.com/statistical-guides/repeated-measures-anova-statistical-guide-3.php
http://purl.obolibrary.org/obo/STATO_0000260
http://www.ats.ucla.edu/stat/sas/library/repeated_ut.htm
http://purl.obolibrary.org/obo/STATO_0000260
ANOVA for correlated samples
http://purl.obolibrary.org/obo/STATO_0000260
http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html
http://purl.obolibrary.org/obo/STATO_0000260
repeated measure ANOVA
http://purl.obolibrary.org/obo/STATO_0000261
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000261
The Newman–Keuls or Student–Newman–Keuls (SNK) method is a stepwise multiple comparisons procedure used to identify sample means that are significantly different from each other. It was named after Student (1927), D. Newman, and M. Keuls. This procedure is often used as a post-hoc test whenever a significant difference between three or more sample means has been revealed by an analysis of variance (ANOVA). The Newman–Keuls method is similar to Tukey's range test as both procedures use Studentized range statistics.Compared to Tukey's range test, the Newman–Keuls method is more powerful but less conservative.
http://purl.obolibrary.org/obo/STATO_0000261
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000261
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000261
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000261
adapted from wikipedia:
last accessed: 2013-11-15
http://purl.obolibrary.org/obo/STATO_0000261
SNK.test(y, trt, DFerror, MSerror, alpha = 0.05, group=TRUE, main = NULL)
http://artax.karlin.mff.cuni.cz/r-help/library/agricolae/html/SNK.test.html
http://purl.obolibrary.org/obo/STATO_0000261
Newman-Keuls test post-hoc analysis
http://purl.obolibrary.org/obo/STATO_0000262
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000262
Bernoulli distribution is a binomial distribution where the number of trials is equal to 1.
notation: B(1,p)
The mean is p
The variance is p*q
http://purl.obolibrary.org/obo/STATO_0000262
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000262
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000262
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000262
http://purl.obolibrary.org/obo/STATO_0000262
Bernoulli distribution
http://purl.obolibrary.org/obo/STATO_0000263
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000263
Galbraith (Radial) plot is a scatter plot which can be used in the meta-analytic context to examine the data for heterogeneity. For a fixed-effects model, the plot shows the inverse of the standard errors on the horizontal axis against the individual observed effect sizes or outcomes standardized by their corresponding standard errors on the vertical axis.
Radial plots were introduced by Rex Galbraith (1988a, 1988b, 1994).
http://purl.obolibrary.org/obo/STATO_0000263
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000263
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000263
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000263
Galbraith, Rex (1988). "Graphical display of estimates having differing standard errors". Technometrics (Technometrics, Vol. 30, No. 3) 30 (3): 271–281. doi:10.2307/1270081. JSTOR 1270081
http://purl.obolibrary.org/obo/STATO_0000263
radial Galbraith plot
http://purl.obolibrary.org/obo/STATO_0000263
http://www.inside-r.org/packages/cran/Luminescence/docs/plot_RadialPlot
plot_RadialPlot(data, na.exclude = TRUE, negatives = "remove",
log.z = TRUE, central.value, centrality = "mean.weighted",
plot.ratio, bar.col, grid.col, legend.text, summary = FALSE,
stats, line, line.col, line.label, output = FALSE, ...)
http://purl.obolibrary.org/obo/STATO_0000263
http://www.metafor-project.org/doku.php/plots:radial_plot
http://purl.obolibrary.org/obo/STATO_0000263
Galbraith plot
http://purl.obolibrary.org/obo/STATO_0000264
http://isogenic.info/html/9__treatments.html#factorial
http://purl.obolibrary.org/obo/STATO_0000264
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000264
a factor level combination is one a possible sets of factor levels resulting from the cartesian product of sets of factor and their levels as defined in a factorial design
http://purl.obolibrary.org/obo/STATO_0000264
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000264
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000264
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000264
treatment combination
http://purl.obolibrary.org/obo/STATO_0000264
STATO
http://purl.obolibrary.org/obo/STATO_0000264
http://purl.obolibrary.org/obo/STATO_0000264
factor level combination
http://purl.obolibrary.org/obo/STATO_0000265
http://isogenic.info/html/9__treatments.html#factorial
http://purl.obolibrary.org/obo/STATO_0000265
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000265
A factor level is data item which corresponds to one of the value assumed by a factor or independent variable manipulated and set by the experimentalist. In the context of factorial design, a factor level is assumed to be or treated as a category in a categorical variable
http://purl.obolibrary.org/obo/STATO_0000265
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000265
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000265
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000265
treatment
http://purl.obolibrary.org/obo/STATO_0000265
AGB-PRS
http://purl.obolibrary.org/obo/STATO_0000265
https://onlinecourses.science.psu.edu/stat503/node/7
http://purl.obolibrary.org/obo/STATO_0000265
http://purl.obolibrary.org/obo/STATO_0000265
factor level
http://purl.obolibrary.org/obo/STATO_0000266
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000266
Bayes factor is a ratio between 2 probabilities of observing data according 2 distinct models. It is used in Bayes model selection to evaluate which model best explains the data. if K<0, the model used in the denominator term is supported, if K>1, the model used in the numerator term is supported.
The Bayes factor is about the plausibility of 2 different models
http://purl.obolibrary.org/obo/STATO_0000266
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000266
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000266
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000266
adapted from Wikipedia
last accessed 2013-11-13
http://purl.obolibrary.org/obo/STATO_0000266
http://purl.obolibrary.org/obo/STATO_0000266
Bayes factor
http://purl.obolibrary.org/obo/STATO_0000267
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000267
grouped bar chart is a kind of bar chart which juxtaposes the discrete values for each of the possible value of a given categorical variable, thus providing within group comparison. Grouped bar charts are good for comparing between each element in the categories, and comparing elements across categories. However, the grouping can make it harder to tell the difference between the total of each group.
http://purl.obolibrary.org/obo/STATO_0000267
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000267
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000267
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000267
adapter from
http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts
and
http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/
[last accessed: 2014-03-04]
http://purl.obolibrary.org/obo/STATO_0000267
barplot(height....)
set argument " beside = TRUE "
http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html
http://purl.obolibrary.org/obo/STATO_0000267
grouped bar chart
http://purl.obolibrary.org/obo/STATO_0000268
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000268
A gamma distribution is a general type of continous statistical distribution (related to the beta distribution) that arises naturally in processes for which the waiting times between Poisson distributed events are relevant. Gamma distributions have two free parameters shape k and scale denoted theta .
http://purl.obolibrary.org/obo/STATO_0000268
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000268
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000268
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000268
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000268
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000268
http://mathworld.wolfram.com/GammaDistribution.html
http://purl.obolibrary.org/obo/STATO_0000268
http://purl.obolibrary.org/obo/STATO_0000268
dgamma(x, shape, rate = 1, scale = 1/rate, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html
http://purl.obolibrary.org/obo/STATO_0000268
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gamma.html#scipy.stats.gamma
http://purl.obolibrary.org/obo/STATO_0000268
Gamma distribution
http://purl.obolibrary.org/obo/STATO_0000269
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000269
polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed.
http://purl.obolibrary.org/obo/STATO_0000269
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000269
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000269
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000269
adapted from:
http://www.rasch.org/rmt/rmt193c.htm
and
http://en.wikipedia.org/wiki/Polychoric_correlation
http://purl.obolibrary.org/obo/STATO_0000269
http://cran.r-project.org/web/packages/polycor/
polychor(x, y, ML = FALSE, control = list(), std.err = FALSE, maxcor=.9999)
http://purl.obolibrary.org/obo/STATO_0000269
polychoric correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000270
a full factorial design is a factorial design which ensures that all possible factor level combinations are defined and used so all between group differences can be explored
http://purl.obolibrary.org/obo/STATO_0000270
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000270
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000270
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000270
http://purl.obolibrary.org/obo/STATO_0000270
full factorial design
http://purl.obolibrary.org/obo/STATO_0000271
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000271
permutation numbering is a data tranformation allowing to count the number of possible permutations of elements in a set of size n, each element occurring exactly once. This number is factorial n.
http://purl.obolibrary.org/obo/STATO_0000271
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000271
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000271
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000271
STATO
http://purl.obolibrary.org/obo/STATO_0000271
http://purl.obolibrary.org/obo/STATO_0000271
permutation numbering
http://purl.obolibrary.org/obo/STATO_0000272
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000272
The Michaelis constant is the substrate concentration at which the reaction rate is at half-maximum, and is an inverse measure of the substrate's affinity for the enzyme—as a small indicates high affinity, meaning that the rate will approach more quickly.[5] The value of is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH.
http://purl.obolibrary.org/obo/STATO_0000272
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000272
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000272
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000272
adapted from wikipedia:
http://en.wikipedia.org/wiki/Michaelis–Menten_constant
last accessed: 22-11-2013
http://purl.obolibrary.org/obo/STATO_0000272
half maximal reaction rate substrate concentration (Km)
http://purl.obolibrary.org/obo/STATO_0000272
Michaelis-Menten constant
http://purl.obolibrary.org/obo/STATO_0000273
A population of two parents and a child.
http://purl.obolibrary.org/obo/STATO_0000273
possibly submit to 'Population and Community Ontology'
http://purl.obolibrary.org/obo/STATO_0000273
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000273
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000273
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000273
child-parent trio
http://purl.obolibrary.org/obo/STATO_0000273
parent-child trio
http://purl.obolibrary.org/obo/STATO_0000273
parents-child trio
http://purl.obolibrary.org/obo/STATO_0000273
child-parents trio
http://purl.obolibrary.org/obo/STATO_0000274
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000274
receiver operational characteristics curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold (aka cut-off point) is varied by plotting sensitivity vs (1 − specificity)
http://purl.obolibrary.org/obo/STATO_0000274
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000274
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000274
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000274
http://en.wikipedia.org/wiki/Receiver_operating_characteristic
http://purl.obolibrary.org/obo/STATO_0000274
roc.from.table(table, graph = TRUE, add = FALSE, title = FALSE,
line.col = "red", auc.coords = NULL, ...)
http://rss.acs.unt.edu/Rdoc/library/epicalc/html/roc.html
http://purl.obolibrary.org/obo/STATO_0000274
receiver operational characteristics curve
http://purl.obolibrary.org/obo/STATO_0000275
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000275
The transmission disequilibrium test is a statistical test for genetic linkage between genetic marker and a trait in families. The test is robust to population structure.
http://purl.obolibrary.org/obo/STATO_0000275
TODO: need to modify restrictions to include family and trio
http://purl.obolibrary.org/obo/STATO_0000275
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000275
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000275
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000275
TDT
http://purl.obolibrary.org/obo/STATO_0000275
STATO , adapted wikipedia (from http://en.wikipedia.org/wiki/Transmission_disequilibrium_test), polled on June,2013
http://purl.obolibrary.org/obo/STATO_0000275
http://purl.obolibrary.org/obo/STATO_0000275
transmission disequilibrium test
http://purl.obolibrary.org/obo/STATO_0000276
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000276
The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N.
The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N.
The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p )
notation: B(n,p)
The mean is N*p
The variance is N*p*q
http://purl.obolibrary.org/obo/STATO_0000276
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000276
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000276
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000276
http://en.wikipedia.org/wiki/Binomial_distribution
http://purl.obolibrary.org/obo/STATO_0000276
http://purl.obolibrary.org/obo/STATO_0000276
dbinom(x, size, prob, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html
http://purl.obolibrary.org/obo/STATO_0000276
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binom.html#scipy.stats.binom
http://purl.obolibrary.org/obo/STATO_0000276
binomial distribution
http://purl.obolibrary.org/obo/STATO_0000277
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000277
hit selection is a planned process which in screening processes such as high-throughput screening, lead to the identification of perturbing agent which cause the typical signal generated by a standardized assay to significantly differ from the negative control. The selection hitself results from meeting or exceeding selection threshold (for instance 6 sigma from the mean or SSMD value beyond 5 when compared to positive controls or below -5 when compared to negative controls
http://purl.obolibrary.org/obo/STATO_0000277
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000277
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000277
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000277
AGB, PRS
http://purl.obolibrary.org/obo/STATO_0000277
adapted from:
http://en.wikipedia.org/wiki/SSMD
http://purl.obolibrary.org/obo/STATO_0000277
adapted from:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/
http://purl.obolibrary.org/obo/STATO_0000277
http://purl.obolibrary.org/obo/STATO_0000277
hit selection
http://purl.obolibrary.org/obo/STATO_0000278
TODO
http://purl.obolibrary.org/obo/STATO_0000278
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000278
pairing rule is a rule which is specifies the criteria for deciding on how to associated any 2 entities.
http://purl.obolibrary.org/obo/STATO_0000278
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000278
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000278
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000278
STATO
http://purl.obolibrary.org/obo/STATO_0000278
http://purl.obolibrary.org/obo/STATO_0000278
pairing rule
http://purl.obolibrary.org/obo/STATO_0000279
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000279
between group comparison statistical test is a statistical test which aims to detect difference between the means computing for each of the study group populations
http://purl.obolibrary.org/obo/STATO_0000279
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000279
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000279
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000279
http://purl.obolibrary.org/obo/STATO_0000279
between group comparison statistical test
http://purl.obolibrary.org/obo/STATO_0000280
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000280
The Pearson's correlation coefficient is a correlation coefficient which evaluates two continuous variables for association strength in a data sample. It assumes that both variables are normally distributed and linearity exists.
The coefficient is calculated by dividing their covariance with the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
http://purl.obolibrary.org/obo/STATO_0000280
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000280
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000280
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000280
Pearson product-moment correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000280
Pearson's r
http://purl.obolibrary.org/obo/STATO_0000280
r statistics
http://purl.obolibrary.org/obo/STATO_0000280
STATO, adapted from
http://www.r-tutor.com/elementary-statistics/numerical-measures/correlation-coefficient
and from:
http://stamash.org/pearsons-correlation-coefficient/
http://stamash.org/kendalls-tau-correlation/
http://purl.obolibrary.org/obo/STATO_0000280
http://purl.obolibrary.org/obo/STATO_0000280
cor(x, y = NULL, use = "everything",method = c("pearson"))
http://purl.obolibrary.org/obo/STATO_0000280
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html
http://purl.obolibrary.org/obo/STATO_0000280
scipy.stats.pearsonr(x, y)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2427
http://purl.obolibrary.org/obo/STATO_0000280
Pearson's correlation coefficient
http://purl.obolibrary.org/obo/STATO_0000281
a false positive rate whose value is 1 per cent
http://purl.obolibrary.org/obo/STATO_0000281
Following discussion with OBCS, deprecated of class STATO_0000281 and creation of instance
http://purl.obolibrary.org/obo/STATO_0000281
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000281
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000281
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000281
STATO
http://purl.obolibrary.org/obo/STATO_0000281
1 % false positive rate
http://purl.obolibrary.org/obo/STATO_0000282
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000282
F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability
http://purl.obolibrary.org/obo/STATO_0000282
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000282
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000282
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000282
STATO
http://purl.obolibrary.org/obo/STATO_0000282
F
http://purl.obolibrary.org/obo/STATO_0000282
F-statistic
http://purl.obolibrary.org/obo/STATO_0000283
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000283
negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur.
The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial.
http://purl.obolibrary.org/obo/STATO_0000283
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000283
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000283
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000283
Pascal distribution
http://purl.obolibrary.org/obo/STATO_0000283
Pólya distribution
http://purl.obolibrary.org/obo/STATO_0000283
http://mathworld.wolfram.com/NegativeBinomialDistribution.html
http://purl.obolibrary.org/obo/STATO_0000283
http://purl.obolibrary.org/obo/STATO_0000283
dnbinom(x, size, prob, mu, log = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/NegBinomial.html
http://purl.obolibrary.org/obo/STATO_0000283
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.nbinom.html#scipy.stats.nbinom
http://purl.obolibrary.org/obo/STATO_0000283
negative binomial distribution
http://purl.obolibrary.org/obo/STATO_0000284
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000284
Breusch-Pagan test is a statistical test which computes a score test of the hypothesis of constant error variance against the alternative that the error variance changes with the level of the response (fitted values), or with a linear combination of predictors.
http://purl.obolibrary.org/obo/STATO_0000284
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000284
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000284
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000284
Breusch, T. S. and Pagan, A. R. (1979) A simple test for heteroscedasticity and random coefficient variation. Econometrica 47, 1287--1294.
and adapted from:
http://www.inside-r.org/packages/cran/car/docs/ncvTest
last accessed [2014-03-15]
http://purl.obolibrary.org/obo/STATO_0000284
http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/bptest.html
bptest(formula, varformula = NULL, studentize = TRUE, data = list())
or
http://www.inside-r.org/packages/cran/car/docs/ncvTest
http://purl.obolibrary.org/obo/STATO_0000284
Breusch-Pagan test
http://purl.obolibrary.org/obo/STATO_0000285
http://www.ncbi.nlm.nih.gov/pubmed/?term=17182697
Bioinformatics. 2007 Feb 15;23(4):401-7.
Enrichment or depletion of a GO category within a class of genes: which test?
Rivals I1, Personnaz L, Taing L, Potier MC.
http://purl.obolibrary.org/obo/STATO_0000285
hypergeometric test is a null hypothesis test which evaluates if a random variable follows a hypergeometric distribution. It is a test of goodness of fit to that distribution. The test is suited for situation aimed at assessing cases of sampling from a finite set without replacements. For instance, testing for enrichment or depletion of elements (e.g GO categories, genes)
http://purl.obolibrary.org/obo/STATO_0000285
Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6
http://purl.obolibrary.org/obo/STATO_0000285
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000285
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000285
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000285
phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE)
lower.tail
logical; if TRUE (default), probabilities are P[X ≤ x], otherwise, P[X > x].
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html
http://purl.obolibrary.org/obo/STATO_0000285
hypergeometric test
http://purl.obolibrary.org/obo/STATO_0000286
http://purl.obolibrary.org/obo/STATO_0000286
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000286
a one-tailed test is a statistical test which, assuming an unskewed probability distribution, allocates all of the significance level to evaluate only one hypothesis to explain a difference.
The one-tailed test provides more power to detect an effect in one direction by not testing the effect in the other direction.
one-tailed test should be preceded by two-tailed test in order to avoid missing out on detecting alternate effect explaining an observed difference.
http://purl.obolibrary.org/obo/STATO_0000286
Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6
http://purl.obolibrary.org/obo/STATO_0000286
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000286
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000286
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000286
one sided test
http://purl.obolibrary.org/obo/STATO_0000286
adapted from:
http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm
http://purl.obolibrary.org/obo/STATO_0000286
http://purl.obolibrary.org/obo/STATO_0000286
one tailed test
http://purl.obolibrary.org/obo/STATO_0000287
For example, we may wish to compare the mean of a sample to a given value x using a t-test. Our null hypothesis is that the mean is equal to x. A two-tailed test will test both if the mean is significantly greater than x and if the mean significantly less than x. The mean is considered significantly different from x if the test statistic is in the top 2.5% or bottom 2.5% of its probability distribution, resulting in a p-value less than 0.05.
http://purl.obolibrary.org/obo/STATO_0000287
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000287
a two tailed test is a statistical test which assess the null hypothesis of absence of difference assuming a symmetric (not skewed) underlying probability distribution by allocating half of the significance level selected to each of the direction of change which could explain a difference (for example, a difference can be an excess or a loss).
http://purl.obolibrary.org/obo/STATO_0000287
Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6
http://purl.obolibrary.org/obo/STATO_0000287
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000287
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000287
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000287
two sided test
http://purl.obolibrary.org/obo/STATO_0000287
adapted from:
http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm
http://purl.obolibrary.org/obo/STATO_0000287
http://purl.obolibrary.org/obo/STATO_0000287
two tailed test
http://purl.obolibrary.org/obo/STATO_0000288
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000288
A null hypothesis which states that no difference exists between 2 or more groups being considered.
http://purl.obolibrary.org/obo/STATO_0000288
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000288
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000288
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000288
STATO
http://purl.obolibrary.org/obo/STATO_0000288
absence of difference hypothesis
http://purl.obolibrary.org/obo/STATO_0000289
let's consider an experiment evaluating 2 compounds (aspirin & ibuprofen) at 3 distinct dose levels (low, medium, high) and 4 time points post exposure (0h, 6h, 12h, 24h). Assuming the treatments are applied only once (no replication), the number of observation in a full factorial design is 2 x 3 x 4 = 24 so the design matrix would have 24 rows and 3 columns (1 per factor (independent variable).
http://purl.obolibrary.org/obo/STATO_0000289
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000289
a design matrix is an information content entity which denotes a study design. The design matrix is a n by m matrix where n the number of rows, corresponds to the number of observations (4 rows if quadruplicates) and where m, the number of columns corresponds to the number of independent variables. Each element in the matrix correspond to a discretized value representing one of the factor levels for a given factor.
A design matrix can be used as input to statistical modeling or statistical analysis.
The design matrix contains data on the independent variables (also called explanatory variables) in statistical models which attempt to explain observed data on a response variable (often called a dependent variable) in terms of the explanatory variables. The theory relating to such models makes substantial use of matrix manipulations involving the design matrix: see for example linear regression. A notable feature of the concept of a design matrix is that it is able to represent a number of different experimental designs and statistical models, e.g., ANOVA, ANCOVA, and linear regression
http://purl.obolibrary.org/obo/STATO_0000289
Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/9
http://purl.obolibrary.org/obo/STATO_0000289
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000289
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000289
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000289
model matrix
http://purl.obolibrary.org/obo/STATO_0000289
adapted from:
Design of Experiments: Principles and Applications
edited by Lennart Eriksson, 1999-2008 Umetrics. ISBN-13:978-91-973730-4-3
and
http://en.wikipedia.org/wiki/Design_matrix
[last accessed: 22-05-2014]
http://purl.obolibrary.org/obo/STATO_0000289
model.matrix(object, data = environment(object),
contrasts.arg = NULL, xlev = NULL, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/model.matrix.html
http://purl.obolibrary.org/obo/STATO_0000289
design matrix
http://purl.obolibrary.org/obo/STATO_0000290
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000290
A contrast is the weighted sum of group means, the c_j coefficients represent the assigned weights of the means (these must sum to 0 for orthogonal contrasts)
http://purl.obolibrary.org/obo/STATO_0000290
Term request by Nolan Nichols via https://github.com/ISA-tools/stato/issues/9
http://purl.obolibrary.org/obo/STATO_0000290
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000290
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000290
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000290
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000290
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000290
http://en.wikipedia.org/wiki/Contrast_%28statistics%29
http://purl.obolibrary.org/obo/STATO_0000290
contrasts(x, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrasts.html
http://purl.obolibrary.org/obo/STATO_0000290
contrast
http://purl.obolibrary.org/obo/STATO_0000291
http://purl.obolibrary.org/obo/STATO_0000291
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000291
a quantile is a data item which corresponds to specific elements x in the range of a variate X.
the k-th n-tile P_k is that value of x, say x_k, which corresponds to a cumulative frequency of Nk/n (Kenney and Keeping 1962). If n=4, the quantity is called a quartile, and if n=100, it is called a percentile.
http://purl.obolibrary.org/obo/STATO_0000291
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000291
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000291
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000291
Evans, M.; Hastings, N.; and Peacock, B. Statistical Distributions, 3rd ed. New York: Wiley, 2000.
http://purl.obolibrary.org/obo/STATO_0000291
http://mathworld.wolfram.com/Quantile.html
http://purl.obolibrary.org/obo/STATO_0000291
quantile
http://purl.obolibrary.org/obo/STATO_0000292
http://purl.obolibrary.org/obo/STATO_0000292
a decile is a quantile where n=10 and which splits data into sections accrued of 10% of data, so the first decile delineates 10% of the data, the second decile delineates 20% of the data and the nineth decile, 90 % of the data
http://purl.obolibrary.org/obo/STATO_0000292
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000292
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000292
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000292
STATO
http://purl.obolibrary.org/obo/STATO_0000292
decile
http://purl.obolibrary.org/obo/STATO_0000293
http://purl.obolibrary.org/obo/STATO_0000293
a percentile is a quantile which splits data into sections accrued of 1% of data, so the first percentile delineates 1% of the data, the second quartile delineates 2% of the data and the 99th percentile, 99 % of the data
http://purl.obolibrary.org/obo/STATO_0000293
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000293
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000293
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000293
STATO
http://purl.obolibrary.org/obo/STATO_0000293
percentile
http://purl.obolibrary.org/obo/STATO_0000294
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000294
absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly less than a threshold does not exist.
http://purl.obolibrary.org/obo/STATO_0000294
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000294
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000294
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000294
STATO
http://purl.obolibrary.org/obo/STATO_0000294
absence of negative difference hypothesis
http://purl.obolibrary.org/obo/STATO_0000295
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000295
absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly greater than a threshold does not exist.
http://purl.obolibrary.org/obo/STATO_0000295
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000295
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000295
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000295
STATO
http://purl.obolibrary.org/obo/STATO_0000295
absence of positive difference hypothesis
http://purl.obolibrary.org/obo/STATO_0000296
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000296
absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly greater than a threshold does not exist.
http://purl.obolibrary.org/obo/STATO_0000296
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000296
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000296
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000296
absence of over representation hypothesis
http://purl.obolibrary.org/obo/STATO_0000296
STATO
http://purl.obolibrary.org/obo/STATO_0000296
absence of enrichment hypothesis
http://purl.obolibrary.org/obo/STATO_0000297
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000297
absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly less than a threshold does not exist.
http://purl.obolibrary.org/obo/STATO_0000297
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000297
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000297
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000297
absence of under representation hypothesis
http://purl.obolibrary.org/obo/STATO_0000297
STATO
http://purl.obolibrary.org/obo/STATO_0000297
absence of depletion hypothesis
http://purl.obolibrary.org/obo/STATO_0000298
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000298
a binomial test is a statistical hypothesis test which evaluates if the observations made about a Bernoulli experiment , that is an experiment which tests the statistical significance of deviations from a theoretically expected distribution (the binomial distribution) of observations into 2 categories. It is a goodness of fit test.
http://purl.obolibrary.org/obo/STATO_0000298
Added following a term request by Chris Mungall:
https://github.com/ISA-tools/stato/issues/6
http://purl.obolibrary.org/obo/STATO_0000298
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000298
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000298
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000298
adapted from:
http://en.wikipedia.org/wiki/Binomial_test
http://purl.obolibrary.org/obo/STATO_0000298
binomial test
http://purl.obolibrary.org/obo/STATO_0000298
binom.test(x, n, p = 0.5,
alternative = c("two.sided", "less", "greater"),
conf.level = 0.95)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/binom.test.html
http://purl.obolibrary.org/obo/STATO_0000298
scipy.stats.binom_test(x, n=None, p=0.5)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binom_test.html#scipy.stats.binom_test
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1605
http://purl.obolibrary.org/obo/STATO_0000298
exact binomial test
http://purl.obolibrary.org/obo/STATO_0000299
Evaluation of statistical inference on empirical resting state fMRI.
IEEE Trans Biomed Eng. 2014 Apr;61(4):1091-9. doi: 10.1109/TBME.2013.2294013.
http://www.ncbi.nlm.nih.gov/pubmed/24658234
http://purl.obolibrary.org/obo/STATO_0000299
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000299
statistical inference is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis
http://purl.obolibrary.org/obo/STATO_0000299
Added following a term request by Nolan Nichols:
https://github.com/ISA-tools/stato/issues/12
http://purl.obolibrary.org/obo/STATO_0000299
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000299
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000299
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000299
STATO
http://purl.obolibrary.org/obo/STATO_0000299
statistical inference
http://purl.obolibrary.org/obo/STATO_0000300
A ratio where the numerator and denominator are expressed in the same unit.
http://purl.obolibrary.org/obo/STATO_0000300
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000300
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000300
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000300
STATO
http://purl.obolibrary.org/obo/STATO_0000300
dimensionless ratio
http://purl.obolibrary.org/obo/STATO_0000300
dimensionless ratio
http://purl.obolibrary.org/obo/STATO_0000301
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000301
The covariance is a measurement data item about the strength of correlation between a set (2 or more) of random variables.
The covariance is obtained by forming:
cov(X,Y)=E([X-E(X)][Y-E(Y)] where E(X), E(Y) is the expected value (mean) of variable X and Y respectively.
covariance is symmetric so cov(X,Y)=cov(Y,X).
The covariance is usefull when looking at the variance of the sum of the 2 random variables since:
var(X+Y) = var(X) +var(Y) +2cov(X,Y)
The covariance cov(x,y) is used to obtain the coefficient of correlation cor(x,y) by normalizing (dividing) cov(x,y) but the product of the standard deviations of x and y.
http://purl.obolibrary.org/obo/STATO_0000301
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000301
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000301
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000301
adapted from:
http://mathworld.wolfram.com/Covariance.html
http://purl.obolibrary.org/obo/STATO_0000301
covariance
http://purl.obolibrary.org/obo/STATO_0000301
cov(x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman"))
from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html
http://purl.obolibrary.org/obo/STATO_0000301
covariance
http://purl.obolibrary.org/obo/STATO_0000302
one sample t-test is a kind of Student's t-test which evaluates if a given sample can be reasonably assumed to be taken from the population.
The test compares the sample statistic (m) to the population parameter (M).
The one sample t-test is the small sample analog of the z test, which is suitable for large samples.
http://purl.obolibrary.org/obo/STATO_0000302
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000302
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000302
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000302
adapted from various sources, including:
Practical Statistics for Medical Research by D.Altman.
ISBN: 0-412-27630-5
http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tone.htm
http://purl.obolibrary.org/obo/STATO_0000302
one sample t-test
http://purl.obolibrary.org/obo/STATO_0000302
t.test(x = NULL,
alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = FALSE,
conf.level = 0.95, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
http://purl.obolibrary.org/obo/STATO_0000302
scipy.stats.ttest_1samp(a, popmean, axis=0)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_1samp.html#scipy.stats.ttest_1samp
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3194
http://purl.obolibrary.org/obo/STATO_0000302
one sample t-test
http://purl.obolibrary.org/obo/STATO_0000303
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000303
two sample t-test is a null hypothesis statistical test which is used to reject or accept the hypothesis of absence of difference between the means over 2 randomly sampled populations.
It uses a t-distribution for the test and assumes that the variables in the population are normally distributed and with equal variances.
http://purl.obolibrary.org/obo/STATO_0000303
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000303
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000303
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000303
two sample t-test
http://purl.obolibrary.org/obo/STATO_0000303
adapted from:
http://en.wikipedia.org/wiki/Student's_t-test#Independent_.28unpaired.29_samples
and from:
http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tind.htm
http://purl.obolibrary.org/obo/STATO_0000303
t-test for independent means assuming equal variance
http://purl.obolibrary.org/obo/STATO_0000303
t.test(x, y = NULL,
alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = TRUE,
conf.level = 0.95, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
http://purl.obolibrary.org/obo/STATO_0000303
scipy.stats.ttest_ind(a, b, axis=0, equal_var=True)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3271
http://purl.obolibrary.org/obo/STATO_0000303
two sample t-test with equal variance
http://purl.obolibrary.org/obo/STATO_0000304
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000304
Welch t-test is a two sample t-test used when the variances of the 2 populations/samples are thought to be unequal (homoskedasticity hypothesis not verified). In this version of the two-sample t-test, the denominator used to form the t-statistics, does not rely on a 'pooled variance' estimate.
http://purl.obolibrary.org/obo/STATO_0000304
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000304
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000304
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000304
Welsh t-test
http://purl.obolibrary.org/obo/STATO_0000304
Welch, B. L. (1947). "The generalization of "Student's" problem when several different population variances are involved". Biometrika 34 (1–2): 28–35. doi:10.1093/biomet/34.1-2.28
http://purl.obolibrary.org/obo/STATO_0000304
adapted from wikipedia:
http://en.wikipedia.org/wiki/Welch's_t_test
last accessed: 2014-05-06
http://purl.obolibrary.org/obo/STATO_0000304
t-test for independent means assuming unequal variance
http://purl.obolibrary.org/obo/STATO_0000304
t.test(x, y = NULL,
alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = FALSE,
conf.level = 0.95, ...)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
http://purl.obolibrary.org/obo/STATO_0000304
scipy.stats.ttest_ind(a, b, axis=0, equal_var=False)
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind
source:
https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3271
http://purl.obolibrary.org/obo/STATO_0000304
two sample t-test with unequal variance
http://purl.obolibrary.org/obo/STATO_0000305
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000305
A Helmert contrast is a contrast in which the coefficients for the Helmert regressors compare each level with the average of the “preceding” ones
http://purl.obolibrary.org/obo/STATO_0000305
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000305
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000305
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000305
http://www.clayford.net/statistics/tag/helmert-contrasts/
An R and S-Plus Companion to Applied Regression. John Fox
ISBN-13: 978-0761922803
http://purl.obolibrary.org/obo/STATO_0000305
contr.helmert(n, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
http://purl.obolibrary.org/obo/STATO_0000305
Helmert contrast
http://purl.obolibrary.org/obo/STATO_0000306
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000306
a polynomial contrast is a contrast which...
http://purl.obolibrary.org/obo/STATO_0000306
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000306
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000306
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000306
http://purl.obolibrary.org/obo/STATO_0000306
contr.poly(n, scores = 1:n, contrasts = TRUE, sparse = FALSE)
from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
http://purl.obolibrary.org/obo/STATO_0000306
polynomial contrast
http://purl.obolibrary.org/obo/STATO_0000307
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000307
treatment contrast is a contrast which allows to test how linear model coefficients of categorical variables are interpreted in case where the “first” level (aka, the baseline) is included into the intercept and all subsequent levels have a coefficient that represents their difference from the baseline.
http://purl.obolibrary.org/obo/STATO_0000307
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000307
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000307
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000307
adapted from multiple sources:
http://pic.dhe.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Fidh_idd_genlin_emmeans.htm
http://www.clayford.net/statistics/tag/helmert-contrasts/
http://www.aliquote.org/articles/tech/contrasts.html
http://purl.obolibrary.org/obo/STATO_0000307
contr.treatment(n, base = 1, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
http://purl.obolibrary.org/obo/STATO_0000307
treatment contrast
http://purl.obolibrary.org/obo/STATO_0000308
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000308
the sum contrast is a contrast in which each coefficient compares the corresponding level of the factor to the average of the other levels
http://purl.obolibrary.org/obo/STATO_0000308
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000308
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000308
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000308
http://www.clayford.net/statistics/tag/helmert-contrasts/
An R and S-Plus Companion to Applied Regression. John Fox
ISBN-13: 978-0761922803
http://purl.obolibrary.org/obo/STATO_0000308
contr.sum(n, contrasts = TRUE, sparse = FALSE)
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html
http://purl.obolibrary.org/obo/STATO_0000308
sum contrast
http://purl.obolibrary.org/obo/STATO_0000309
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000309
Pearson's Chi-Squared test for goodnes of fit is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution
http://purl.obolibrary.org/obo/STATO_0000309
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000309
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000309
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000309
Chi2 test for goodness of fit
http://purl.obolibrary.org/obo/STATO_0000309
adapted from:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
and
http://en.wikipedia.org/wiki/Pearson's_chi-squared_test
http://purl.obolibrary.org/obo/STATO_0000309
http://purl.obolibrary.org/obo/STATO_0000309
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html
chisq.test(x = NULL, correct = FALSE,
p = rep(1/length(x), length(x)), rescale.p = FALSE,
simulate.p.value = FALSE, B = 2000)
http://purl.obolibrary.org/obo/STATO_0000309
Pearson's Chi square test of goodness of fit
http://purl.obolibrary.org/obo/STATO_0000310
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000310
Barnard's test is an exact statistical test used to determine if there are nonrandom associations between two categorical variables. It was developed in 1949 by Barnard and is a test which is, most times, more powerfull that the Fisher exact test
http://purl.obolibrary.org/obo/STATO_0000310
duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI
http://purl.obolibrary.org/obo/STATO_0000310
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000310
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000310
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000310
http://en.wikipedia.org/wiki/Barnard's_test
and
G A Barnard (1945) "A New Test for 2X2 Tables", Nature, 156, 177 & 783.
http://purl.obolibrary.org/obo/STATO_0000310
Barnard's test
http://purl.obolibrary.org/obo/STATO_0000310
barnardw.test(n1, n2, n3, n4, dp = 0.001, verbose = FALSE)
from
http://www.inside-r.org/packages/cran/Barnard/docs/barnardw.test
http://purl.obolibrary.org/obo/STATO_0000310
Barnard's test
http://purl.obolibrary.org/obo/STATO_0000311
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000311
a central composite design is a study design which contains an imbedded factorial or fractional factorial design with center points that is augmented with a group of so-called 'star points' that allow estimation of curvature.
A CCD design with k factors has 2k star points.
http://purl.obolibrary.org/obo/STATO_0000311
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000311
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000311
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000311
http://www.itl.nist.gov/div898/handbook/pri/section3/pri3361.htm
http://purl.obolibrary.org/obo/STATO_0000311
Box-Wilson Central Composite Design
http://purl.obolibrary.org/obo/STATO_0000311
cd(basis, generators, blocks = "Block", n0 = 4, alpha = "orthogonal",
wbreps = 1, bbreps = 1, randomize = TRUE, inscribed = FALSE, coding)
http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/ccd.html
http://purl.obolibrary.org/obo/STATO_0000311
central composite design
http://purl.obolibrary.org/obo/STATO_0000312
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000312
The Box-Behnken design is an independent quadratic design in that it does not contain an embedded factorial or fractional factorial design. In this design the treatment combinations are at the midpoints of edges of the process space and at the center. These designs are rotatable (or near rotatable) and require 3 levels of each factor. The designs have limited capability for orthogonal blocking compared to the central composite designs.
http://purl.obolibrary.org/obo/STATO_0000312
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000312
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000312
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000312
http://www.itl.nist.gov/div898/handbook/pri/section3/pri3362.htm
http://purl.obolibrary.org/obo/STATO_0000312
bbd(k, n0 = 4, block = (k == 4 | k == 5), randomize = TRUE, coding)
from:
http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/bbd.html
http://purl.obolibrary.org/obo/STATO_0000312
Box–Behnkens design
http://purl.obolibrary.org/obo/STATO_0000313
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000313
Plackett-Burman design is a type of study design optimizing multifactorial experiments characterized by their parsimony and economy with the run number a multiple of 4 (rather than a power of 2).
Plackett-Burman design is often used for screening experiments where the main effect is often heavily confounded with two-factor interactions.
This type of design is very useful for economically detecting large main effects, assuming all interactions are negligible when compared with the few important main effects.
http://purl.obolibrary.org/obo/STATO_0000313
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000313
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000313
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000313
http://www.itl.nist.gov/div898/handbook/pri/section3/pri335.htm
http://purl.obolibrary.org/obo/STATO_0000313
pb(nruns, nfactors = nruns - 1, factor.names = if (nfactors <= 50)
Letters[1:nfactors] else paste("F", 1:nfactors, sep = ""),
default.levels = c(-1, 1), ncenter=0, center.distribute=NULL,
boxtyssedal = TRUE, n12.taguchi = FALSE,
replications = 1, repeat.only = FALSE,
randomize = TRUE, seed = NULL, oldver = FALSE, ...)
from:
http://www.inside-r.org/packages/cran/FrF2/docs/pb
http://purl.obolibrary.org/obo/STATO_0000313
Plackett-Burman design
http://purl.obolibrary.org/obo/STATO_0000314
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000314
upper confidence limit is a data item which is a largest value bounding a confidence interval
http://purl.obolibrary.org/obo/STATO_0000314
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000314
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000314
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000314
STATO
http://purl.obolibrary.org/obo/STATO_0000314
upper confidence limit
http://purl.obolibrary.org/obo/STATO_0000315
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000315
lower confidence limit is a data item which is a lowest value bounding a confidence interval
http://purl.obolibrary.org/obo/STATO_0000315
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000315
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000315
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000315
STATO
http://purl.obolibrary.org/obo/STATO_0000315
lower confidence limit
http://purl.obolibrary.org/obo/STATO_0000316
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000316
root-mean-square standardized effect is a data item which denotes effect size in the context of analysis of variance and corresponds to the square root of the arithmetic average of p standardized effects (effects normalized to be expressed in standard deviation units).
http://purl.obolibrary.org/obo/STATO_0000316
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000316
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000316
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000316
Ψ
http://purl.obolibrary.org/obo/STATO_0000316
http://www.statpower.net/Steiger%20Biblio/Steiger04.pdf
http://purl.obolibrary.org/obo/STATO_0000316
RMSSE
http://purl.obolibrary.org/obo/STATO_0000316
root-mean-square standardized effect
http://purl.obolibrary.org/obo/STATO_0000317
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000317
Eta-squared is a biased estimator of the variance explained by the model in the population (it estimates only the effect size in the sample). Eta-squared describes the ratio of variance explained in the dependent variable by a predictor while controlling for other predictors, making it analogous to the r2. This estimate shares the weakness with r2 that each additional variable will automatically increase the value of η2. In addition, it measures the variance explained of the sample, not the population, meaning that it will always overestimate the effect size, although the bias grows smaller as the sample grows larger.
http://purl.obolibrary.org/obo/STATO_0000317
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000317
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000317
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000317
http://en.wikipedia.org/wiki/Effect_size#Eta-squared.2C_.CE.B72
http://purl.obolibrary.org/obo/STATO_0000317
η2
http://purl.obolibrary.org/obo/STATO_0000317
eta-squared
http://purl.obolibrary.org/obo/STATO_0000318
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000318
omega-squared is a effect size estimate for variance explained which is less biased than the eta-squared coefficient.
http://purl.obolibrary.org/obo/STATO_0000318
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000318
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000318
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000318
adapted from:
http://en.wikipedia.org/wiki/Effect_size#Omega-squared.2C_.CF.892
http://purl.obolibrary.org/obo/STATO_0000318
ω2
http://purl.obolibrary.org/obo/STATO_0000318
omega-squared
http://purl.obolibrary.org/obo/STATO_0000319
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000319
Hedges's g is an estimator of effect size, which is similar to Cohen's d and is a measure based on a standardized difference. However, the denominator, corresponding to a pooled standard deviation, is computed differently from Cohen's d coefficient, by applying a correction factor (which involves a Gamma function).
http://purl.obolibrary.org/obo/STATO_0000319
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000319
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000319
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000319
adapted from :
http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d
and
http://blog.stata.com/tag/cohens-d/
http://purl.obolibrary.org/obo/STATO_0000319
Hedges's g
http://purl.obolibrary.org/obo/STATO_0000320
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000320
Glass's delta is an estimator of effect size which is similar to Cohen's d but where the denominator corresponds only to the standard deviation of the control group (or second group). It is considered less biais than the Cohen's d for estimating effect sizes based on means and distances between means.
http://purl.obolibrary.org/obo/STATO_0000320
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000320
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000320
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000320
adapted from :
http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d
and
http://blog.stata.com/tag/cohens-d/
http://purl.obolibrary.org/obo/STATO_0000320
Glass's delta
http://purl.obolibrary.org/obo/STATO_0000321
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000321
Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.
http://purl.obolibrary.org/obo/STATO_0000321
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000321
Karl Helmer
http://purl.obolibrary.org/obo/STATO_0000321
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000321
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000321
Initially discussed at https://github.com/incf-nidash/nidm/pull/191
http://purl.obolibrary.org/obo/STATO_0000321
non-parametric distribution
http://purl.obolibrary.org/obo/STATO_0000322
http://artax.karlin.mff.cuni.cz/r-help/library/nparcomp/html/weight.matrix.html
http://purl.obolibrary.org/obo/STATO_0000322
a contrast weight is a coefficient which multiplies a group mean, part of a linear combinaison defining a constrast as a weighted sum of group means, giving a 'weight' to a specific group mean hence the name.
http://purl.obolibrary.org/obo/STATO_0000322
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000322
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000322
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000322
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000322
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000322
adapted from wikipedia:
http://en.wikipedia.org/wiki/Contrast_%28statistics%29
http://purl.obolibrary.org/obo/STATO_0000322
contrast coefficient
http://purl.obolibrary.org/obo/STATO_0000322
contrast weight
http://purl.obolibrary.org/obo/STATO_0000323
[1,0,0]
http://purl.obolibrary.org/obo/STATO_0000323
a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast
http://purl.obolibrary.org/obo/STATO_0000323
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000323
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000323
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000323
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000323
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000323
STATO
http://purl.obolibrary.org/obo/STATO_0000323
contrast weights
http://purl.obolibrary.org/obo/STATO_0000323
contrast weight matrix
http://purl.obolibrary.org/obo/STATO_0000324
contrast weight estimate is a model parameter estimate which results from the computation from the data and that is used as input to a model fitting process
http://purl.obolibrary.org/obo/STATO_0000324
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000324
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000324
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000324
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000324
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000324
STATO
http://purl.obolibrary.org/obo/STATO_0000324
contrast weight estimate
http://purl.obolibrary.org/obo/STATO_0000325
http://www.ncbi.nlm.nih.gov/pubmed/7791040
http://purl.obolibrary.org/obo/STATO_0000325
The Akaike information criterion (AIC) is a measure of the relative quality of a statistical model for a given set of data. As such, AIC provides a means for model selection. AIC is defined as:
AIC = 2K - 2log(L)
where K is the number of predictors and L is the maximized likelihood value.
AIC deals with the trade-off between the goodness of fit of the model and the complexity of the model. It is founded on information theory: it offers a relative estimate of the information lost when a given model is used to represent the process that generates the data. AIC does not provide a test of a model in the sense of testing a null hypothesis; i.e. AIC can tell nothing about the quality of the model in an absolute sense. If all the candidate models fit poorly, AIC will not give any warning of that.
http://purl.obolibrary.org/obo/STATO_0000325
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000325
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000325
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000325
http://en.wikipedia.org/wiki/Akaike_information_criterion
and
http://users.ecs.soton.ac.uk/jn2/teaching/aic.pdf
http://purl.obolibrary.org/obo/STATO_0000325
AIC
http://purl.obolibrary.org/obo/STATO_0000325
AIC(object, ..., k = 2)
from:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/AIC.html
http://purl.obolibrary.org/obo/STATO_0000325
Akaike information criterion
http://purl.obolibrary.org/obo/STATO_0000326
http://www.ncbi.nlm.nih.gov/pubmed/19761098
http://purl.obolibrary.org/obo/STATO_0000326
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000326
corrected Akaike information criteria is a modified version of the Akaike information criterion
http://purl.obolibrary.org/obo/STATO_0000326
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000326
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000326
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000326
CAIC
http://purl.obolibrary.org/obo/STATO_0000326
http://purl.obolibrary.org/obo/STATO_0000326
corrected Akaike information criterion
http://purl.obolibrary.org/obo/STATO_0000327
http://www.ncbi.nlm.nih.gov/pubmed/7791040
http://purl.obolibrary.org/obo/STATO_0000327
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000327
Bayesian information criterion or Schwartz's Bayesian information criterion is a criterion for model selection among a finite set of models. It is based, in part, on the likelihood function and it is closely related to the Akaike information criterion (AIC).
Given any two estimated models, the model with the lower value of BIC is the one to be preferred. The BIC is an increasing function of sigma_e^2 and an increasing function of k. That is, unexplained variation in the dependent variable and the number of explanatory variables increase the value of BIC. Hence, lower BIC implies either fewer explanatory variables, better fit, or both.
http://purl.obolibrary.org/obo/STATO_0000327
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000327
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000327
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000327
Schwarz, Gideon E. (1978). "Estimating the dimension of a model". Annals of Statistics 6 (2): 461–464. doi:10.1214/aos/1176344136.
http://purl.obolibrary.org/obo/STATO_0000327
http://en.wikipedia.org/wiki/Bayesian_information_criterion
http://purl.obolibrary.org/obo/STATO_0000327
BIC
http://purl.obolibrary.org/obo/STATO_0000327
SBIC
http://purl.obolibrary.org/obo/STATO_0000327
Schwartz's Baeysian information criterion
http://purl.obolibrary.org/obo/STATO_0000327
http://purl.obolibrary.org/obo/STATO_0000327
Bayesian information criterion
http://purl.obolibrary.org/obo/STATO_0000328
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000328
a statistical model selection is a data transformation which is based on computing a relative quality value in order to evaluate and select which model best explains data.
http://purl.obolibrary.org/obo/STATO_0000328
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000328
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000328
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000328
STATO
http://purl.obolibrary.org/obo/STATO_0000328
statistical model selection
http://purl.obolibrary.org/obo/STATO_0000329
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000329
Probability distribution which has no skew so its skewness=0
http://purl.obolibrary.org/obo/STATO_0000329
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000329
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000329
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000329
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000329
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000329
STATO
http://purl.obolibrary.org/obo/STATO_0000329
symmetric distribution
http://purl.obolibrary.org/obo/STATO_0000330
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000330
Probability distribution estimated empirically from all acquired data
http://purl.obolibrary.org/obo/STATO_0000330
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000330
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000330
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000330
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000330
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000330
http://reference.wolfram.com/language/ref/EmpiricalDistribution.html
http://purl.obolibrary.org/obo/STATO_0000330
empirical distribution
http://purl.obolibrary.org/obo/STATO_0000331
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000331
Probability distribution estimated empirically on the data following a binning process
http://purl.obolibrary.org/obo/STATO_0000331
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000331
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000331
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000331
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000331
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000331
histogram distribution
http://purl.obolibrary.org/obo/STATO_0000332
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000332
Probability distribution estimated using a smooth kernel function to avoid making assumptions about the distribution of the data. The kernel density estimator is the estimated probability density function (pdf) of the random variable.
http://purl.obolibrary.org/obo/STATO_0000332
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000332
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000332
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000332
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000332
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000332
http://uk.mathworks.com/help/stats/kernel-distribution.html
and
http://reference.wolfram.com/language/ref/SmoothKernelDistribution.html
http://purl.obolibrary.org/obo/STATO_0000332
smooth kernel distribution
http://purl.obolibrary.org/obo/STATO_0000333
http://purl.obolibrary.org/obo/IAO_0000428
http://purl.obolibrary.org/obo/STATO_0000333
kernel density estimation (KDE) is a non-parametric way to estimate the probability density function of a random variable
http://purl.obolibrary.org/obo/STATO_0000333
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000333
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000333
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000333
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000333
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000333
https://en.wikipedia.org/wiki/Kernel_density_estimation
http://purl.obolibrary.org/obo/STATO_0000333
https://reference.wolfram.com/language/ref/KernelMixtureDistribution.html
http://purl.obolibrary.org/obo/STATO_0000333
kernel mixture distribution
http://purl.obolibrary.org/obo/STATO_0000334
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000334
Mixture distribution is the probability distribution of a random variable that is derived from a collection of other random variables as follows: first, a random variable is selected by chance from the collection according to given probabilities of selection, and then the value of the selected random variable is realized.
http://purl.obolibrary.org/obo/STATO_0000334
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000334
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000334
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000334
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000334
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000334
http://en.wikipedia.org/wiki/Mixture_distribution
http://purl.obolibrary.org/obo/STATO_0000334
mixture distribution
http://purl.obolibrary.org/obo/STATO_0000335
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000335
Probability distribution estimated empirically from a censored lifetime data
http://purl.obolibrary.org/obo/STATO_0000335
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000335
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000335
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000335
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000335
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000335
http://reference.wolfram.com/language/ref/SurvivalDistribution.html
http://purl.obolibrary.org/obo/STATO_0000335
survival distribution
http://purl.obolibrary.org/obo/STATO_0000346
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000346
a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suiteable model
http://purl.obolibrary.org/obo/STATO_0000346
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000346
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000346
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000346
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000346
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000346
http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf
http://purl.obolibrary.org/obo/STATO_0000346
covariance structure
http://purl.obolibrary.org/obo/STATO_0000347
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000347
http://purl.obolibrary.org/obo/STATO_0000347
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000347
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000347
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000347
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000347
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000347
http://purl.obolibrary.org/obo/STATO_0000347
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000347
http://purl.obolibrary.org/obo/STATO_0000347
Matern function anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000348
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000348
http://purl.obolibrary.org/obo/STATO_0000348
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000348
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000348
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000348
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000348
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000348
http://purl.obolibrary.org/obo/STATO_0000348
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000348
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corRatio.html
http://purl.obolibrary.org/obo/STATO_0000348
rational quadratic anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000349
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000349
http://purl.obolibrary.org/obo/STATO_0000349
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000349
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000349
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000349
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000349
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000349
SP(LINGA)
http://purl.obolibrary.org/obo/STATO_0000349
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000349
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corLin.html
http://purl.obolibrary.org/obo/STATO_0000349
spatial linear geometric anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000350
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000350
http://purl.obolibrary.org/obo/STATO_0000350
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000350
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000350
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000350
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000350
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000350
SP(SPHGA)
http://purl.obolibrary.org/obo/STATO_0000350
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000350
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corSpher.html
http://purl.obolibrary.org/obo/STATO_0000350
spatial spherical geometric anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000351
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000351
http://purl.obolibrary.org/obo/STATO_0000351
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000351
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000351
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000351
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000351
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000351
SP(GAUGA)
http://purl.obolibrary.org/obo/STATO_0000351
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000351
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corGaus.html
http://purl.obolibrary.org/obo/STATO_0000351
spatial gaussian geometric anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000352
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000352
http://purl.obolibrary.org/obo/STATO_0000352
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000352
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000352
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000352
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000352
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000352
SP(EXPGA)
http://purl.obolibrary.org/obo/STATO_0000352
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000352
http://purl.obolibrary.org/obo/STATO_0000352
spatial exponential geometric anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000353
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000353
http://purl.obolibrary.org/obo/STATO_0000353
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000353
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000353
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000353
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000353
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000353
SP(EXPA)(c-list)
http://purl.obolibrary.org/obo/STATO_0000353
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Sacks et al. (1989)
http://purl.obolibrary.org/obo/STATO_0000353
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corExp.html
http://purl.obolibrary.org/obo/STATO_0000353
spatial exponential anisotropic covariance structure
http://purl.obolibrary.org/obo/STATO_0000354
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000354
http://purl.obolibrary.org/obo/STATO_0000354
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000354
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000354
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000354
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000354
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000354
TOEPH(q)
http://purl.obolibrary.org/obo/STATO_0000354
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000354
http://purl.obolibrary.org/obo/STATO_0000354
banded heterogeneous Toeplitz covariance structure
http://purl.obolibrary.org/obo/STATO_0000355
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000355
http://purl.obolibrary.org/obo/STATO_0000355
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000355
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000355
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000355
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000355
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000355
TOEPH
http://purl.obolibrary.org/obo/STATO_0000355
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000355
http://purl.obolibrary.org/obo/STATO_0000355
heterogeneous Toeplitz covariance structure
http://purl.obolibrary.org/obo/STATO_0000356
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000356
http://purl.obolibrary.org/obo/STATO_0000356
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000356
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000356
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000356
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000356
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000356
TOEP(q)
http://purl.obolibrary.org/obo/STATO_0000356
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000356
http://purl.obolibrary.org/obo/STATO_0000356
banded Toeplitz covariance structure
http://purl.obolibrary.org/obo/STATO_0000357
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000357
http://purl.obolibrary.org/obo/STATO_0000357
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000357
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000357
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000357
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000357
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000357
TOEP
http://purl.obolibrary.org/obo/STATO_0000357
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000357
http://purl.obolibrary.org/obo/STATO_0000357
Toeplitz covariance structure
http://purl.obolibrary.org/obo/STATO_0000358
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000358
http://purl.obolibrary.org/obo/STATO_0000358
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000358
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000358
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000358
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000358
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000358
HF
http://purl.obolibrary.org/obo/STATO_0000358
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Huynh and Feldt 1970
http://purl.obolibrary.org/obo/STATO_0000358
http://purl.obolibrary.org/obo/STATO_0000358
Huynh-Feldt covariance structure
http://purl.obolibrary.org/obo/STATO_0000359
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000359
factor-analytic structure is a covariance structure which is specified for q factors
http://purl.obolibrary.org/obo/STATO_0000359
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000359
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000359
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000359
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000359
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000359
FA1(q)
http://purl.obolibrary.org/obo/STATO_0000359
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000359
http://purl.obolibrary.org/obo/STATO_0000359
equal diagonal Factor Analytic covariance structure
http://purl.obolibrary.org/obo/STATO_0000360
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000360
factor-analytic structure is a covariance structure which is specified for q factors
http://purl.obolibrary.org/obo/STATO_0000360
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000360
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000360
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000360
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000360
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000360
FA0(q)
http://purl.obolibrary.org/obo/STATO_0000360
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000360
http://purl.obolibrary.org/obo/STATO_0000360
no diagonal Factor Analytic covariance structure
http://purl.obolibrary.org/obo/STATO_0000361
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000361
factor-analytic structure is a covariance structure which is specified for q factors
http://purl.obolibrary.org/obo/STATO_0000361
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000361
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000361
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000361
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000361
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000361
FA(q)
http://purl.obolibrary.org/obo/STATO_0000361
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
Jennrich and Schluchter 1986
http://purl.obolibrary.org/obo/STATO_0000361
http://purl.obolibrary.org/obo/STATO_0000361
Factor Analytic covariance structure
http://purl.obolibrary.org/obo/STATO_0000362
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000362
compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal.
http://purl.obolibrary.org/obo/STATO_0000362
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000362
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000362
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000362
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000362
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000362
CS
http://purl.obolibrary.org/obo/STATO_0000362
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000362
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html
http://purl.obolibrary.org/obo/STATO_0000362
compound symmetry covariance structure
http://purl.obolibrary.org/obo/STATO_0000363
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000363
heterogenous compound symmetry structure is a compound symmetry covariance structure which has a different variance parameter for each diagonal element, and it uses the square roots of these parameters in the off-diagonal entries.
http://purl.obolibrary.org/obo/STATO_0000363
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000363
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000363
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000363
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000363
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000363
CSH
http://purl.obolibrary.org/obo/STATO_0000363
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000363
http://purl.obolibrary.org/obo/STATO_0000363
heterogeneous compound symmetry covariance structure
http://purl.obolibrary.org/obo/STATO_0000364
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000364
http://purl.obolibrary.org/obo/STATO_0000364
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000364
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000364
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000364
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000364
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000364
ARMA(1,1)
http://purl.obolibrary.org/obo/STATO_0000364
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000364
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corARMA.html
http://purl.obolibrary.org/obo/STATO_0000364
first order autoregressive moving average covariance structure
http://purl.obolibrary.org/obo/STATO_0000365
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000365
first order autoregressive covariance structure is a covariance structure where correlations among errors decline exponentially with distance
http://purl.obolibrary.org/obo/STATO_0000365
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000365
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000365
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000365
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000365
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000365
AR(1)
http://purl.obolibrary.org/obo/STATO_0000365
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000365
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corAR1.html
http://purl.obolibrary.org/obo/STATO_0000365
first order autoregressive covariance structure
http://purl.obolibrary.org/obo/STATO_0000366
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000366
http://purl.obolibrary.org/obo/STATO_0000366
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000366
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000366
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000366
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000366
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000366
ARH(1)
http://purl.obolibrary.org/obo/STATO_0000366
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000366
http://purl.obolibrary.org/obo/STATO_0000366
heterogeneous first-order autoregressive covariance structure
http://purl.obolibrary.org/obo/STATO_0000367
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000367
Ante-dependence covariance structure is a covariance structure which specifies that the covariance between two time points is a function of the product of variances at both points (hence allowing hetrogenity of error variance across measures to affect the correlation) and the product of the correlations at the distances up to the one chosen.
http://purl.obolibrary.org/obo/STATO_0000367
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000367
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000367
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000367
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000367
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000367
ANTE(1)
http://purl.obolibrary.org/obo/STATO_0000367
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
http://purl.obolibrary.org/obo/STATO_0000367
http://purl.obolibrary.org/obo/STATO_0000367
Ante-dependence covariance structure
http://purl.obolibrary.org/obo/STATO_0000368
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000368
Mallows' Cp is a data item which compares the precision and bias of the full model to models with a subset of the predictors thus helping to choose between multiple regression models.
the mallows cp is a function of the number of parameter used in the model relying on the residuals sum of squares to compute a score.
the smaller Cp is, the better the model fit is.
http://purl.obolibrary.org/obo/STATO_0000368
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000368
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000368
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000368
http://support.minitab.com/en-us/minitab/17/topic-library/modeling-statistics/regression-and-correlation/goodness-of-fit-statistics/what-is-mallows-cp/
http://purl.obolibrary.org/obo/STATO_0000368
http://ugrad.stat.ubc.ca/R/library/locfit/html/cp.html
http://purl.obolibrary.org/obo/STATO_0000368
Mallows' Cp
http://purl.obolibrary.org/obo/STATO_0000369
http://purl.obolibrary.org/obo/IAO_0000125
http://purl.obolibrary.org/obo/STATO_0000369
repeated measure analysis is a kind of data transformation which deals with signals measured in the same experimental units at different times and, possibly, under different conditions over a period of time. Data produced by longitudinal studies qualify for such analysis. Since measurements are made on the same experimental units a number of times, they are likely to be correlated. Repeated measure analysis usually takes into consideration the possibility of correlation with time. It does so by specifying covariance structure in the analysis
http://purl.obolibrary.org/obo/STATO_0000369
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000369
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000369
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000369
adapted from https://ciser.cornell.edu/sasdoc/saspdf/analyst/chap16.pdf
http://purl.obolibrary.org/obo/STATO_0000369
repeated measure analysis
http://purl.obolibrary.org/obo/STATO_0000369
repeated measure analysis
http://purl.obolibrary.org/obo/STATO_0000370
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000370
the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
http://purl.obolibrary.org/obo/STATO_0000370
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000370
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000370
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000370
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000370
http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000370
OLS estimation
http://purl.obolibrary.org/obo/STATO_0000370
http://purl.obolibrary.org/obo/STATO_0000370
https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html
http://purl.obolibrary.org/obo/STATO_0000370
ordinary least squares estimation
http://purl.obolibrary.org/obo/STATO_0000371
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000371
the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
http://purl.obolibrary.org/obo/STATO_0000371
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000371
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000371
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000371
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000371
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000371
http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000371
WLS estimation
http://purl.obolibrary.org/obo/STATO_0000371
https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html
http://purl.obolibrary.org/obo/STATO_0000371
weighted least squares estimation
http://purl.obolibrary.org/obo/STATO_0000372
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000372
the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to "whiten" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
http://purl.obolibrary.org/obo/STATO_0000372
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000372
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000372
http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000372
GLS estimation
http://purl.obolibrary.org/obo/STATO_0000372
http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html
http://purl.obolibrary.org/obo/STATO_0000372
generalized least squares estimation
http://purl.obolibrary.org/obo/STATO_0000373
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000373
the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights
http://purl.obolibrary.org/obo/STATO_0000373
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000373
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000373
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000373
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000373
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000373
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000373
http://purl.obolibrary.org/obo/STATO_0000373
iteratively reweighted least squares estimation
http://purl.obolibrary.org/obo/STATO_0000374
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000374
the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix.
http://purl.obolibrary.org/obo/STATO_0000374
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000374
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000374
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000374
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000374
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000374
Tom Nichols
http://purl.obolibrary.org/obo/STATO_0000374
feasible generalized least squares estimation
http://purl.obolibrary.org/obo/STATO_0000375
used as an unbiased estimator of teh variance for a regression model
http://purl.obolibrary.org/obo/STATO_0000375
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000375
a residual mean square is a data item which is obtained by dividing the sum of squared residuals (SSR) by the number of degrees of freedom
http://purl.obolibrary.org/obo/STATO_0000375
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000375
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000375
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000375
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000375
http://en.wikipedia.org/wiki/Mean_squared_error#Regression
http://purl.obolibrary.org/obo/STATO_0000375
http://support.minitab.com/en-us/minitab/17/topic-library/modeling-statistics/anova/anova-statistics/understanding-mean-squares/
http://purl.obolibrary.org/obo/STATO_0000375
https://github.com/ISA-tools/stato/issues/35
http://purl.obolibrary.org/obo/STATO_0000375
MSE
http://purl.obolibrary.org/obo/STATO_0000375
error mean square
http://purl.obolibrary.org/obo/STATO_0000375
residual mean square
http://purl.obolibrary.org/obo/STATO_0000376
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000376
Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test.
http://purl.obolibrary.org/obo/STATO_0000376
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000376
Camille Maument
http://purl.obolibrary.org/obo/STATO_0000376
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000376
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000376
http://en.wikipedia.org/wiki/Z-test
http://purl.obolibrary.org/obo/STATO_0000376
Z-statistic
http://purl.obolibrary.org/obo/STATO_0000377
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000377
Deviance is an indicator of fit and can be estimated by computing -2 times the log-likelihood ratio of the fitted model compared to a saturated(full) model.
It is a generalization of the idea of using the sum of squares of residuals in ordinary least squares to cases where model-fitting is achieved by maximum likelihood.
http://purl.obolibrary.org/obo/STATO_0000377
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000377
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000377
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000377
http://en.wikipedia.org/wiki/Deviance_%28statistics%29
http://purl.obolibrary.org/obo/STATO_0000377
deviance
http://purl.obolibrary.org/obo/STATO_0000377
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/deviance.html
http://purl.obolibrary.org/obo/STATO_0000377
deviance
http://purl.obolibrary.org/obo/STATO_0000378
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682718/
http://purl.obolibrary.org/obo/STATO_0000378
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000378
The deviance information criterion (DIC) is a hierarchical modeling generalization of the AIC (Akaike information criterion) and BIC (Bayesian information criterion, also known as the Schwarz criterion). It is particularly useful in Bayesian model selection problems where the posterior distributions of the models have been obtained by Markov chain Monte Carlo (MCMC) simulation. Like AIC and BIC it is an asymptotic approximation as the sample size becomes large. It is only valid when the posterior distribution is approximately multivariate normal.
The deviance information criterion was published in 2002 by Spiegelhalter et al.
Spiegelhalter, D. J., N. G. Best, B. P. Carlin, and A. van der Linde, 2002. Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society, B, 64, 583-639.
http://purl.obolibrary.org/obo/STATO_0000378
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000378
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000378
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000378
http://en.wikipedia.org/wiki/Deviance_information_criterion
http://purl.obolibrary.org/obo/STATO_0000378
DIC
http://purl.obolibrary.org/obo/STATO_0000378
http://artax.karlin.mff.cuni.cz/r-help/library/SpatialExtremes/html/DIC.html
http://purl.obolibrary.org/obo/STATO_0000378
deviance information criterion
http://purl.obolibrary.org/obo/STATO_0000379
http://purl.obolibrary.org/obo/IAO_0000120
http://purl.obolibrary.org/obo/STATO_0000379
The focused information criterion is a measurement data item which aims at facilitating model selection. It was published in 2003 by Claeskens, G. and Hjort, N.L. (2003). "The focused information criterion". Journal of the American Statistical Association, volume 98, pp. 879–899. doi:10.1198/016214503000000819
http://purl.obolibrary.org/obo/STATO_0000379
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000379
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000379
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000379
Journal of the American Statistical Association, volume 98, pp. 879–899. doi:10.1198/016214503000000819
http://purl.obolibrary.org/obo/STATO_0000379
FIC
http://purl.obolibrary.org/obo/STATO_0000379
focused information criterion
http://purl.obolibrary.org/obo/STATO_0000383
a data transformation that finds a contrast value (the contrast estimate) by computing the weighted sum of model parameter estimates using a set of contrast weights.
http://purl.obolibrary.org/obo/STATO_0000383
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000383
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000383
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000383
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000383
https://github.com/ISA-tools/stato/pull/37
http://purl.obolibrary.org/obo/STATO_0000383
contrast estimation
http://purl.obolibrary.org/obo/STATO_0000384
estimate of a contrast obtained by computing the weighted sum of model parameter estimates using a set of contrast weights.
http://purl.obolibrary.org/obo/STATO_0000384
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000384
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000384
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000384
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000384
https://github.com/ISA-tools/stato/pull/37
http://purl.obolibrary.org/obo/STATO_0000384
contrast estimate
http://purl.obolibrary.org/obo/STATO_0000385
an estimate of the standard deviation of a contrast estimate sampling distribution.
http://purl.obolibrary.org/obo/STATO_0000385
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000385
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000385
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000385
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000385
https://github.com/ISA-tools/stato/pull/37
http://purl.obolibrary.org/obo/STATO_0000385
standard error of a contrast estimate
http://purl.obolibrary.org/obo/STATO_0000386
A scree plot is a graphical display of the variance of each component in the dataset which is used to determine how many components should be retained in order to explain a high percentage of the variation in the data
http://purl.obolibrary.org/obo/STATO_0000386
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000386
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000386
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000386
http://www.stats.gla.ac.uk/glossary/?q=node/451
http://purl.obolibrary.org/obo/STATO_0000386
Cattell scree test plot
http://purl.obolibrary.org/obo/STATO_0000386
scree plot
http://purl.obolibrary.org/obo/STATO_0000387
A scatterplot matrix contains all the pairwise scatter plots of a set of variables on a single page in a matrix format.
http://purl.obolibrary.org/obo/STATO_0000387
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000387
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000387
Adapted from http://itl.nist.gov/div898/handbook/eda/section3/eda33qb.htm
http://purl.obolibrary.org/obo/STATO_0000387
scatterplot matrix
http://purl.obolibrary.org/obo/STATO_0000388
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000388
http://purl.obolibrary.org/obo/STATO_0000388
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000388
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000388
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000388
http://purl.obolibrary.org/obo/STATO_0000388
http://purl.obolibrary.org/obo/STATO_0000388
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.alpha.html#scipy.stats.alpha
http://purl.obolibrary.org/obo/STATO_0000388
alpha distribution
http://purl.obolibrary.org/obo/STATO_0000389
a power-law probability distribution is a probability distribution whose density function (or mass function in the discrete case) has the form
p(x) = L(x) . x^{-alpha}
where alpha is a parameter >1 and L(x) is a slowly varying function.
http://purl.obolibrary.org/obo/STATO_0000389
adapted from wikipedia and wolfram alpha:
https://en.wikipedia.org/wiki/Power_law#Power-law_probability_distributions
last accessed: 2015-11-03
http://purl.obolibrary.org/obo/STATO_0000389
http://purl.obolibrary.org/obo/STATO_0000389
http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.powerlaw.html#scipy.stats.powerlaw
http://purl.obolibrary.org/obo/STATO_0000389
power law distribution
http://purl.obolibrary.org/obo/STATO_0000390
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000390
A regression model is a statistical model used in a type of analysis knowns as regression analysis, whereby a function is used to determine the relation between a response variable and an independent variable , with a set of unknown parameters.
http://purl.obolibrary.org/obo/STATO_0000390
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000390
adapted from wikipedia:
https://en.wikipedia.org/wiki/Regression_analysis#Regression_models
last accessed: 2015-11-03
http://purl.obolibrary.org/obo/STATO_0000390
regression model
http://purl.obolibrary.org/obo/STATO_0000391
an annotation property to provide a canonical command to invoke a method implementation using Python programming language
http://purl.obolibrary.org/obo/STATO_0000391
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000391
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000391
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000391
Python command
http://purl.obolibrary.org/obo/STATO_0000392
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000392
The Pareto distribution is a continuous probability distribution, which is defined by the follwoing probability density (1) function and distribution function (2)
(1): P(x)=(ab^a)/(x^(a+1))
(2): D(x)=1-(b/x)^a
defined over the interval x>=b.
http://purl.obolibrary.org/obo/STATO_0000392
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000392
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000392
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000392
adapter from:
http://mathworld.wolfram.com/ParetoDistribution.html
last accessed: 2015-11-04
http://purl.obolibrary.org/obo/STATO_0000392
http://artax.karlin.mff.cuni.cz/r-help/library/LaplacesDemon/html/dist.Pareto.html
last accessed: 2015-11-04
Usage
>dpareto(x, alpha, log=FALSE)
>ppareto(q, alpha)
>qpareto(p, alpha)
>rpareto(n, alpha)
Arguments
x,q
These are each a vector of quantiles.
p
This is a vector of probabilities.
n
This is the number of observations, which must be a positive integer that has length 1.
alpha
This is the shape parameter alpha, which must be positive.
log
Logical. If log=TRUE, then the logarithm of the density or result is returned.
http://purl.obolibrary.org/obo/STATO_0000392
Pareto type-I probability distribution
http://purl.obolibrary.org/obo/STATO_0000393
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000393
the Pareto type-II probability distribution is a continuous probability distribution which is defined by a probability density function characterized by 2 parameters, alpha and lambda, 2 real, strictly positive numbers. alpha is known as the shape parameter while lambda is known as the scale parameter.
the function defines the probably of a continous random variable according to the following:
p(x) = {\alpha \over \lambda} \left[{1+ {x \over \lambda}}\right]^{-(\alpha+1)}, \qquad x \geq 0,
http://purl.obolibrary.org/obo/STATO_0000393
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000393
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000393
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000393
https://en.wikipedia.org/wiki/Lomax_distribution
http://purl.obolibrary.org/obo/STATO_0000393
Lomax distribution
http://purl.obolibrary.org/obo/STATO_0000393
http://www.inside-r.org/packages/cran/actuar/docs/Pareto
dpareto(x, shape, scale, log = FALSE)
http://purl.obolibrary.org/obo/STATO_0000393
Pareto type-II probability distribution
http://purl.obolibrary.org/obo/STATO_0000394
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000394
The Pareto(III) distribution is a continous probability distribution which is described with a cumulative distribution function of the following form:
F(x) = 1 − [1 + ((x − mu)/sigma)1/gamma]−1
for x > mu, sigma > 0, gamma > 0 and s =1.
a is the location parameter,
b is the scale parameter,
g is the inequality parameter
s is the shape parameter of value 1
The Pareto III distribution corresponds to a Pareto Type IV distribution where the shape parameter has a value of 1.
http://purl.obolibrary.org/obo/STATO_0000394
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000394
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000394
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000394
adapted from wikipedia:
https://en.wikipedia.org/wiki/Pareto_distribution#Pareto_types_I.E2.80.93IV
last accessed: 2015-11-04
http://purl.obolibrary.org/obo/STATO_0000394
Pareto type-III probability distribution
http://purl.obolibrary.org/obo/STATO_0000395
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000395
The Pareto(IV) distribution is a continous probability distribution which is described with a cumulative distribution function of the following form:
F(y) = 1 − [1 + ((y − a)/b)1/g]−s
for y > a, b > 0, g > 0 and s > 0.
a is the location parameter,
b is the scale parameter,
g is the inequality parameter
s is the shape parameter
The distribution is used in actuarial science, economics, finance and telecommunications, but not restricted to those fields.
http://purl.obolibrary.org/obo/STATO_0000395
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000395
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000395
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000395
https://cran.r-project.org/web/packages/VGAM/VGAM.pdf
page 517
http://purl.obolibrary.org/obo/STATO_0000395
dparetoIV(x, location = 0, scale = 1, inequality = 1, shape = 1, log = FALSE)
https://cran.r-project.org/web/packages/VGAM/VGAM.pdf
http://purl.obolibrary.org/obo/STATO_0000395
Pareto type-IV probability distribution
http://purl.obolibrary.org/obo/STATO_0000396
The geometric mean of two numbers, say 2 and 8, is just the square root of their product; that is sqrt(2 x 8)=4
http://purl.obolibrary.org/obo/STATO_0000396
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000396
The geometric mean is defined as the nth root of the product of n numbers, i.e., for a set of numbers \{x_i\}_{i=1}^N, the geometric mean is defined as \left(\prod_{i=1}^N x_i\right)^{1/N}.
http://purl.obolibrary.org/obo/STATO_0000396
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000396
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000396
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000396
https://en.wikipedia.org/wiki/Mean#Geometric_mean_.28GM.29
https://en.wikipedia.org/wiki/Geometric_mean
http://purl.obolibrary.org/obo/STATO_0000396
http://personality-project.org/r/html/geometric.mean.html
Usage: >geometric.mean(x,na.rm=TRUE)
Arguments: x , a vector or data.frame
http://purl.obolibrary.org/obo/STATO_0000396
http://docs.scipy.org/doc/scipy-0.13.0/reference/generated/scipy.stats.mstats.gmean.html
http://purl.obolibrary.org/obo/STATO_0000396
geometric mean
http://purl.obolibrary.org/obo/STATO_0000397
The harmonic mean is a kind of mean which is calculated by dividing the total number of observations by the reciprocal of each number in a series.
Harmonic Mean = N/(1/a1+1/a2+1/a3+1/a4+.......+1/aN)
where a(i)= Individual score and N = Sample size (Number of scores)
http://purl.obolibrary.org/obo/STATO_0000397
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000397
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000397
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000397
adapted from wikipedia and
https://www.easycalculation.com/statistics/learn-harmonic-mean.php
last accessed: 2015-11-04
http://purl.obolibrary.org/obo/STATO_0000397
https://en.wikipedia.org/wiki/Harmonic_mean
http://purl.obolibrary.org/obo/STATO_0000397
https://en.wikipedia.org/wiki/Mean#Harmonic_mean_.28HM.29
http://purl.obolibrary.org/obo/STATO_0000397
http://personality-project.org/r/html/harmonic.mean.html
Usage: > harmonic.mean(x,na.rm=TRUE)
Arguments:
x, a vector, matrix, or data.frame
na.rm, na.rm=TRUE remove NA values before processing
http://purl.obolibrary.org/obo/STATO_0000397
http://docs.scipy.org/doc/scipy-0.13.0/reference/generated/scipy.stats.mstats.hmean.html
http://purl.obolibrary.org/obo/STATO_0000397
harmonic mean
http://purl.obolibrary.org/obo/STATO_0000398
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000398
The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points contribute more than others.
The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes.
http://purl.obolibrary.org/obo/STATO_0000398
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000398
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000398
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000398
https://en.wikipedia.org/wiki/Weighted_arithmetic_mean
http://purl.obolibrary.org/obo/STATO_0000398
http://purl.obolibrary.org/obo/STATO_0000398
weighted arithmetic mean
http://purl.obolibrary.org/obo/STATO_0000399
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000399
The interquartile mean (IQM) (or midmean) is a statistical measure of central tendency based on the truncated mean of the interquartile range.
In the calculation of the IQM, only the data in the second and third quartiles is used (as in the interquartile range), and the lowest 25% and the highest 25% of the scores are discarded. These points are called the first and third quartiles, hence the name of the IQM.
http://purl.obolibrary.org/obo/STATO_0000399
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000399
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000399
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000399
IQM
http://purl.obolibrary.org/obo/STATO_0000399
https://en.wikipedia.org/wiki/Mean#Interquartile_mean
http://purl.obolibrary.org/obo/STATO_0000399
interquartile mean
http://purl.obolibrary.org/obo/STATO_0000400
http://purl.obolibrary.org/obo/IAO_0000122
http://purl.obolibrary.org/obo/STATO_0000400
The root mean square (abbreviated RMS or rms), also known as the quadratic mean, in statistics is a statistical measure of central tendency defined as the square root of the mean of the squares of a sample.
( To find the root mean square of a set of numbers, square all the numbers in the set and then find the arithmetic mean of the squares. Take the square root of the result. This is the root mean square.)
http://purl.obolibrary.org/obo/STATO_0000400
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000400
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000400
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000400
RMS
http://purl.obolibrary.org/obo/STATO_0000400
root mean square
http://purl.obolibrary.org/obo/STATO_0000400
https://en.wikipedia.org/wiki/Root_mean_square
and
http://www.mathwords.com/r/root_mean_square.htm
last accessed: 2015-11-04
http://purl.obolibrary.org/obo/STATO_0000400
quadratic mean
http://purl.obolibrary.org/obo/STATO_0000401
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000401
the sample mean of sample of size n with n observations is an arithmetic mean computed over n number of observations on a statistical sample.
The sample mean, denoted x¯ and read “x-bar,” is simply the average of the n data points x1, x2, ..., xn:
x¯=x1+x2+⋯+xnn=1n∑i=1nxi
The sample mean summarizes the "location" or "center" of the data.
the sample mean is a measure of dispersion of the observations made on the sample and provides an unbias estimate of the population mean
http://purl.obolibrary.org/obo/STATO_0000401
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000401
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000401
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000401
adapted from:
https://onlinecourses.science.psu.edu/stat414/node/66
and
http://mathworld.wolfram.com/SampleMean.html
last accessed: 2015-11-05
http://purl.obolibrary.org/obo/STATO_0000401
sample mean
http://purl.obolibrary.org/obo/STATO_0000402
http://purl.obolibrary.org/obo/IAO_0000123
http://purl.obolibrary.org/obo/STATO_0000402
the population mean or distribution mean is a parameter of a probability distribution or population indicative of the data dispersion. For continous probabibility distribution, the population mean is computed using the probability density function, for discrete probability distributions, a mass density function is used instead.
A population mean can be estimated by computing a sample mean
http://purl.obolibrary.org/obo/STATO_0000402
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000402
Orlaith Burke
http://purl.obolibrary.org/obo/STATO_0000402
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000402
adapted from:
http://mathworld.wolfram.com/PopulationMean.html
last accessed: 2015-11-05
http://purl.obolibrary.org/obo/STATO_0000402
population mean
http://purl.obolibrary.org/obo/STATO_0000403
Relationship between a quantity and a parameter, where the quantity used or evaluated as an estimate of the value of a parameter.
http://purl.obolibrary.org/obo/STATO_0000403
estimator of
http://purl.obolibrary.org/obo/STATO_0000404
the most common series or system of written mathematical symbols used to represent the entity
http://purl.obolibrary.org/obo/STATO_0000404
AGB
http://purl.obolibrary.org/obo/STATO_0000404
preferred mathematical notation
http://purl.obolibrary.org/obo/STATO_0000405
A covariance structure where no restrictions are made on the covariance between any pair of measurements.
http://purl.obolibrary.org/obo/STATO_0000405
Alejandra Gonzalez-Beltran
http://purl.obolibrary.org/obo/STATO_0000405
Camille Maumet
http://purl.obolibrary.org/obo/STATO_0000405
Philippe Rocca-Serra
http://purl.obolibrary.org/obo/STATO_0000405
Thomas Nichols
http://purl.obolibrary.org/obo/STATO_0000405
http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm#statug.mixed.mixedcovstruct
http://purl.obolibrary.org/obo/STATO_0000405
unstructured covariance structure
http://purl.obolibrary.org/obo/UO_0000001
length unit
http://purl.obolibrary.org/obo/UO_0000001
A unit which is a standard measure of the distance between two points.
http://purl.obolibrary.org/obo/UO_0000001
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/UO_0000001
http://purl.obolibrary.org/obo/uo.owl
http://purl.obolibrary.org/obo/UO_0000001
length unit
http://purl.obolibrary.org/obo/UO_0000003
time unit
http://purl.obolibrary.org/obo/UO_0000003
A unit which is a standard measure of the dimension in which events occur in sequence.
http://purl.obolibrary.org/obo/UO_0000003
http://purl.obolibrary.org/obo/obi.owl
http://purl.obolibrary.org/obo/UO_0000003
http://purl.obolibrary.org/obo/uo.owl
http://purl.obolibrary.org/obo/UO_0000003
time unit
http://purl.org/dc/elements/1.1/contributor
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/contributor
Contributor
http://purl.org/dc/elements/1.1/contributor
Contributor
http://purl.org/dc/elements/1.1/creator
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/creator
Creator
http://purl.org/dc/elements/1.1/creator
Creator
http://purl.org/dc/elements/1.1/date
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/date
Date
http://purl.org/dc/elements/1.1/date
Date
http://purl.org/dc/elements/1.1/description
An account of the content of the resource.
http://purl.org/dc/elements/1.1/description
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/description
Description
http://purl.org/dc/elements/1.1/description
Description
http://purl.org/dc/elements/1.1/format
The physical or digital manifestation of the resource.
http://purl.org/dc/elements/1.1/format
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/format
Format
http://purl.org/dc/elements/1.1/format
Format
http://purl.org/dc/elements/1.1/subject
The topic of the content of the resource.
http://purl.org/dc/elements/1.1/subject
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/subject
Subject and Keywords
http://purl.org/dc/elements/1.1/subject
Subject and Keywords
http://purl.org/dc/elements/1.1/title
A name given to the resource.
http://purl.org/dc/elements/1.1/title
http://purl.org/dc/elements/1.1/
http://purl.org/dc/elements/1.1/title
Title
http://purl.org/dc/elements/1.1/title
Title