Alan Ruttenberg
Albert Goldfain
Barry Smith
Bill Duncan
Bjoern Peters
Chris Mungall
David Osumi-Sutherland
Fabian Neuhaus
James A. Overton
Janna Hastings
Jie Zheng
Jonathan Bona
Larry Hunter
Leonard Jacuzzo
Ludger Jansen
Mark Ressler
Mathias Brochhausen
Mauricio Almeida
Melanie Courtot
Pierre Grenon
Randall Dipert
Robert Rovetto
Ron Rudnicki
Stefan Schulz
Thomas Bittner
Werner Ceusters
Yongqun "Oliver" He
Karl Hammar, Patrick Lambrix, Noel Kennedy, Victor Oliveira, Crawford Revie, Ann Lindberg, Eva Blomqvist
Fernanda Dórea (nanda
An ontology to support semantic interoperability among domains involved in health surveillance (animal health, public health and food safety). More details at http://datadrivensurveillance.org.
Health Surveillance Ontology (HSO)
The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl.
If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies.
See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1.
This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif
This is an ontology to support (one) health surveillance, focused on "surveillance system level data", hat is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc.
0.1.0
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
The user interface label is the label that should be placed on a datum when presented on a form or report
Damion Dooley
user interface label
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
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
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
definition
textual definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
editor note
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
definition source
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
true
curator_notes
curator note
curator notes
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
Person: Alejandra Gonzalez-Beltran
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
temporal interpretation
https://github.com/oborel/obo-relations/wiki/ROAndTime
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
RO:0002174
uberon
dubious_for_taxon
true
true
dubious_for_taxon
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
dubious_for_taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
RO:0002175
applicable for taxon
uberon
present_in_taxon
true
true
present_in_taxon
present_in_taxon
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
UBPROP:0000001
uberon
external_definition
true
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
A textual description of an axiom loss in this ontology compared to an external ontology.
UBPROP:0000002
uberon
axiom_lost_from_external_ontology
true
axiom_lost_from_external_ontology
This annotation property may be replaced with an annotation property from an external ontology such as IAO
axiom_lost_from_external_ontology
Notes on the homology status of this class.
UBPROP:0000003
uberon
homology_notes
true
homology_notes
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_notes
UBPROP:0000006
uberon
implements_design_pattern
true
implements_design_pattern
implements_design_pattern
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
UBPROP:0000007
uberon
has_relational_adjective
true
has_relational_adjective
has_relational_adjective
Notes on the how instances of this class vary across species.
UBPROP:0000008
uberon
taxon_notes
true
taxon_notes
taxon_notes
Notes on the evolved function of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000009
uberon
function_notes
true
function_notes
function_notes
Notes on the structure, composition or histology of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000010
uberon
structure_notes
true
structure_notes
structure_notes
Notes on the ontogenic development of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000011
uberon
development_notes
true
development_notes
development_notes
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000012
uberon
external_ontology_notes
true
external_ontology_notes
external_ontology_notes
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000013
uberon
terminology_notes
true
terminology_notes
terminology_notes
UBPROP:0000100
uberon
is_count_of
true
is_count_of
is count of
A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)
UBPROP:0000101
uberon
preceding_element_is
true
preceding_element_is
preceding element is
x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
gill arch N = PA N-2. the term branchial_arch is ambiguous.
UBPROP:0000103
uberon
pharyngeal_arch_number
true
pharyngeal_arch_number
pharyngeal arch number
FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
UBPROP:0000202
uberon
fma_set_term
true
fma_set_term
fma_set_term
A metadata relation between a class and its taxonomic rank (eg species, family)
ncbi_taxonomy
has_rank
Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.
uberon
dc-contributor
true
dc-contributor
An entity responsible for making contributions to the
content of the resource.
Contributor
Contributor
contributor
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
uberon
dc-creator
true
dc-creator
An entity primarily responsible for making the content
of the resource.
Creator
Creator
creator
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the
resource.
Date
Date
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
uberon
dc-description
true
dc-description
An account of the content of the resource.
Description
Description
description
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
Format
uberon
dc-publisher
true
dc-publisher
publisher
uberon
dc-rights
true
dc-rights
rights
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
uberon
dc-source
true
dc-source
A reference to a resource from which the present resource
is derived.
Source
Source
derived from resource
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
The topic of the content of the resource.
Subject and Keywords
Subject and Keywords
uberon
dc-title
true
dc-title
title
uberon
dcterms-isReferencedBy
true
dcterms-isReferencedBy
is referenced by
Mark Miller
2018-05-11T13:47:29Z
uberon
doap-GitRepository
true
doap-GitRepository
Git repository
uberon
doap-SVNRepository
true
doap-SVNRepository
SVN repository
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_namespace
has_related_synonym
has synonym
in_subset
shorthand
label
label
uberon
foaf-homepage
true
foaf-homepage
homepage
From the European Food Safety Agency (EFSA):
https://zenodo.org/record/344473#.WzvvyvkzYkV
The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research.
DCF_catalogues file contains all the valid catalogues published in the DCF.
The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives.
This annotation points to the specific catalague, within SSD2, form which terms were imported.
SSD_catalogue
"This annotation gives the specific code for the concept include din the ontology. Look for this code in the specific catalogue via the annotation property ""SSD_catalogue"".
Full names are stored in the property ""SSD_termExtendedName""."
SSD_termCode
This annotation gives the specific term name for the concept include din the ontology. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode".
SSD_temExtendedName
This annotation gives any additional notes. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode".
SSD_termScopeNote
an annotation created specifically for the NLP work of recognizing entities automatically from published/printed reports.
synonyms_NLP
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
uberon
part_of
part_of
part of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
uberon
has_part
has_part
has part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
BFO:0000062
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded_by
BFO:0000063
uberon
precedes
precedes
precedes
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior_to
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
BSPO:0000097
uberon
distal_to
distal_to
distal_to
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal_to
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
BSPO:0000099
caudal_to
uberon
posterior_to
posterior_to
posterior_to
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral_to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
uberon
deep_to
deep_to
deep_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in_left_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in_right_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in_anterior_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
BSPO:0001108
uberon
distalmost_part_of
distalmost_part_of
distalmost_part_of
has measurement unit label
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
m is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
Alan Ruttenberg
is quality measurement of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
is quality measured as
has_specified_input
has_specified_input
see is_input_of example_of_usage
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
is_specified_input_of
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
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
has_specified_output
has_specified_output
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_specified_output_of
is_specified_output_of
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
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.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
OBI
OBI
objective_achieved_by
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
has value specification
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
derives from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
RO:0001015
uberon
location_of
location_of
location_of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
uberon
located_in
located_in
located in
located in
located_in
located_in (type level)
aligned with
RO:0002002
uberon
has_boundary
has_boundary
has boundary
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
Relation between occurrents, shares start and end boundaries.
RO:0002082
coincides_with
is_equal_to
uberon
simultaneous_with
simultaneous_with
simultaneous_with
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
immediately_preceded_by
RO:0002150
uberon
continuous_with
continuous_with
continuous_with
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
RO:0002176
uberon
connects
connects
connects
relation between an artery and the structure is supplies with blood.
RO:0002178
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
RO:0002202
uberon
develops_from
develops_from
develops_from
RO:0002203
uberon
develops_into
develops_into
develops_into
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded_by
x adjacent_to y iff: x and y share a boundary
RO:0002220
uberon
adjacent_to
adjacent_to
adjacent_to
inverse of surrounded_by
RO:0002221
uberon
surrounds
surrounds
surrounds
Relation between occurrents, shares a start boundary with.
RO:0002223
uberon
starts
starts
starts
RO:0002224
uberon
starts_with
starts_with
starts with
Relation between occurrents, shares an end boundary with.
RO:0002229
finishes
uberon
ends
ends
ends
RO:0002230
uberon
ends_with
ends_with
ends with
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally_induced_by
RO:0002258
uberon
developmentally_preceded_by
developmentally_preceded_by
developmentally preceded by
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally_replaces
RO:0002351
uberon
has_member
has_member
has member
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
RO:0002473
uberon
composed_primarily_of
composed_primarily_of
composed primarily of
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
RO:0002488
begins_to_exist_during
uberon
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant and occurrent, such that c comes into existence at the start of p.
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
RO:0002492
ceases_to_exist_during
uberon
existence_ends_during
existence_ends_during
existence ends during
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
RO:0002493
uberon
existence_ends_with
existence_ends_with
existence ends with
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
existence starts during or after
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
existence ends during or before
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
RO:0003000
uberon
produces
produces
produces
RO:0003001
uberon
produced_by
produced_by
produced_by
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
uberon
existence_starts_and_ends_during
existence starts and ends during
uberon
extends_fibers_into
extends_fibers_into
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
uberon
filtered_through
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
filtered through
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
uberon
in_central_side_of
in_central_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
uberon
protects
protects
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
uberon
proximally_connected_to
proximally connected to
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
uberon
transitively_connected_to
transitively_connected to
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
isSubSpeciesOf
isSerotypeOf
hasDatum
hasSpecimenDatum
hasMatrixType
hasReportItem
SAspecimen
SAmatrixtype
SAcontext
SAsampler
reportLang
reportCountry
SAsampledArea
SAproductionType
SAepiUnit
SAsamplingStrategy
SAestablishment
SAdiagnTest
SAtestType
sampled from
sampled from anatomical entity
sampled from organism
hasSpecimenFromOrganismType
follows surveillance protocol
executed in surveillance activity
has legal basis
is legal basis of
has surveillance objective
has surveillance purpose
has surveillance actions
has sampling design
has reporting protocol
has sample collection protocol
has diagnostic protocol
has surveillance context
target population
target geographical area
target country
target host species
target host sector
target pathogen
susceptible species
applies sampling strategy
has sampling unit
has sampler type
sampling stage
sampled specimen
employs assay
has diagnostic test type
has assay datum
realized in surveillance activity
realizes surveillance system
has measurement value
surveillance history item
surveillance activity start date
surveillance activity end date
has dateTime measurement value
has integer measurement value
has decimal measurement value
number of units tested
number of PSU tested
number of SSU tested
number of units positive
number of PSU positive
number of SSU positive
number of units negative
number of PSU negative
number of SSU negative
number of specimen tested
Number of specimen negative
calculated sample size
calculated number of PSU
calculated number of SSU
Number of specimen positive
0.0
100.0
has percentage measurement value
0.0
100.0
percentage of units positive
0.0
100.0
percentage of PSU positive
0.0
100.0
percentage of SSU positive
0.0
100.0
percentage of specimen positive
surveillance aggregated results
surveillance activity year
has mass measurement
has mass measurement in grams
year started
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
Continuant
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
independent continuant
spatial region
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
spatiotemporal region
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
disposition
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
zero-dimensional spatial region
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
fiat object part
an edge of a cube-shaped portion of space.
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
object
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
function
the boundary between the 2nd and 3rd year of your life.
process boundary
the temporal region during which a process occurs.
one-dimensional temporal region
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
material entity
continuant fiat boundary
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
process profile
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
a marriage bond, an instance of love, an obligation between one person and another.
relational quality
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
zero-dimensional temporal region
history
FTT:1242
FTT:1252
FTT:15
FTT:16
FTT:18
FTT:19
FTT:21
FTT:22
FTT:23
FTT:24
FTT:25
FTT:26
FTT:27
FTT:28
FTT:29
FTT:37
SWEETRealm:AdministrativeRegion
TGN:80001
TGN:81099
TGN:81123
https://en.wikipedia.org/wiki/Administrative_region
administrative area
administrative region
state / province / territory / region
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A primary administrative division of a country, such as a state in the United States.
A primary administrative division of a country, such as a state in the United States.
FTT:414
FTT:569
Geonames:A.ADM1
TGN:81100
first-order administrative region
first-order administrative region
A political association with effective dominion over a geographic area.
FTT:424
FTT:566
FTT:567
FTT:571
SWEETRealm:Country
SWEETRealm:State
TGN:80006
TGN:81010
TGN:81011
TGN:81102
https://en.wikipedia.org/wiki/Nation
http://purl.obolibrary.org/obo/NCIT_C25464
nation
independent nation
independent political entity
independent sovereign nation
national geopolitical entity
A geographical region whose affairs and population are administered by an authority.
FTT:1093
Geonames:A.PCL
TGN:80002
political entity
A reference to a place on the Earth, by its name or by its geographical location.
GAZ:00000467
geographic region {alternative name}
geographic location
region
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A subnational region is a type of subnational entity similar to a nation's state, province, or territory.
Damion Dooley
subnational region
This is a catch-all category for listing specimen related terms
Damion Dooley
specimen datum
http://purl.obolibrary.org/obo/GENEPIO_0002105
http://purl.obolibrary.org/obo/OBI_0001616
A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time.
Damion Dooley
designated area on Earth
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term.
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
datum label
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is 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 which reliably tends to produce (approximately) truthful statements.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".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.
2013-05-30 Alan Ruttenberg: 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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information entity
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
OBI_0000042
group:OBI
data set
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
plan specification
measurement datum
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,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
http://www.ebi.ac.uk/efo/EFO_0001444
measurement datum
1
A scalar measurement datum that is the result of measurement of mass quality
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
mass measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards
time measurement datum
Proteobacteria
purple bacteria
purple bacteria and relatives
purple non-sulfur bacteria
purple photosynthetic bacteria
purple photosynthetic bacteria and relatives
Proteobacteria
GC_ID:1
PMID:11743200
PMID:11791233
ncbi_taxonomy
Boreotheria
Boreoeutheria
Campylobacter
Campylobacter
PARAM
RF-00000042-MCG
Bacteria
eubacteria
Bacteria
GC_ID:1
PMID:23020233
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
eukaryotes
Eukaryota
GC_ID:1
amniotes
ncbi_taxonomy
Amniota
Enterobacteriaceae
Enterobacteriaceae
Salmonella
Salmonella
PARAM
RF-00000304-MCG
GC_ID:1
whales, hippos, ruminants, pigs, camels etc.
ncbi_taxonomy
even-toed ungulates
Cetartiodactyla
A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states.
Country
http://purl.obolibrary.org/obo/GEO_000000396
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A region, district or division of a country; a tract; a portion a state, especially one remote from the capital.
Province
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A political unit, such as a city, town, or village, incorporated for local self-government.
Municipality
http://semanticscience.org/resource/SIO_000665
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A constituent administrative district of a nation.
Damion's note: Placing or "multihoming" state (a governmental region) under various classes means that the entity can be interpreted within the respective class, and can inherit properties/axioms of that class
State under "categorical" yeilds a uri enabling reference to the state as a unique entity.
State under "area" references the polygon region bounding the state.
State under "geopolitical region" references concepts of governance and law.
State under "name" references its name, a string.
Complications arise: a state can change names, boundaries, laws, etc. over time.
On a data entry form we're primarily intersted in state as categorical item (= pulldown list). In cases of countries where we don't have lists of states or provinces, then we could accept "state name" - a string - in form input?
One could create "state name" as an ontology term, etc. Organizing state concept as a compendium of "state name" ,"state area" , "state boundary" etc. accomplishes the same goal of defining aspects of state-ness, but adds alot of compound-term complexity.
State
lookup:http://purl.obolibrary.org/obo/GAZ_00000448
A geographical area under the jurisdiction of a sovereign state and marked off for administrative or other purposes.
Territory
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'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.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
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)
planned process
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
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.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
study assay
any method
assay
specimen role
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.
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
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.
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.
blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.
parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.
GROUP: Role Branch
OBI
specimen role
organization
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.
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.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
GROUP: OBI
organization
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
AR, BP, JM, MC, PRS
branch derived
plan
hospital
human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
A medical organization at which sick or injured people are given clinical care
Person:Alan Ruttenberg
Person:Helen Parkinson
http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
modified from the wording of the wordnet definition
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
hospital
SAMPNT
E210A
value specification
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
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.
PERSON:Bjoern Peters
value specification
organism
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.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
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.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
specimen
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
mass
An organ that is capable of transducing sensory stimulus to the nervous system.
AEO:0000094
BSA:0000121
BTO:0000202
CALOHA:TS-2043
EHDAA2:0001824
EHDAA:500
EMAPA:35955
FBbt:00005155
GAID:63
HAO:0000930
MA:0000017
MESH:D012679
NCIT:C33224
UMLS:C0935626
VHOG:0001407
WBbt:0006929
organ of sense organ system
organ of sensory organ system
organ of sensory system
sense organ system organ
sensory organ
sensory organ system organ
sensory system organ
sensillum
uberon
Sinnesorgan
sensor
UBERON:0000020
sense organ
cjm
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
organ
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
AAO:0011124
EFO:0000635
FMA:82472
cardinal organ part
uberon
regional part of organ
UBERON:0000064
organ part
A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]
zona pellucida - vitelline membrane
BTO:0003135
EHDAA2:0002220
EHDAA:31
EHDAA:62
EMAPA:16035
FMA:18674
GAID:410
MA:0001715
MESH:D015044
NCIT:C33896
TAO:0001111
UMLS:C0043519
VHOG:0000720
ZFA:0001111
uberon
oolemma
pellucid zone
striated membrane
vitelline envelope
vitelline membrane
zona radiata
zona striata
UBERON:0000086
zona pellucida
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
cjm
2009-07-30T05:19:13Z
membrane
FMA:7145
membrane of organ
uberon
UBERON:0000094
membrane organ
cjm
1
1
1
1
The pair of anatomical structures comprised of a left lung and right lung.
FMA:68877
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
lungs
lungs pair
pulmones
set of lungs
uberon
UBERON:0000170
pair of lungs
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
EMAPA:17607
SPD:0000428
TGMA:0001247
apparatus respiratorius organ
breathing organ
organ of apparatus respiratorius
organ of respiratory system
respiratory organ
respiratory system organ
uberon
gas exchange organ
UBERON:0000171
respiration organ
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
UBERON:0000324
UBERON:0007550
AEO:0000184
BTO:0000491
EHDAA2_RETIRED:0003184
ENVO:02000022
FMA:9674
galen:Excretion
excreted substance
portion of excreted substance
waste substance
uberon
excretion
UBERON:0000174
excreta
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
cjm
2009-04-08T04:38:19Z
CARO:0000081
uberon
blood or blood analog
circulating fluid
UBERON:0000179
haemolymphatic fluid
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
BTO:0000503
EMAPA:27181
FMA:14919
uberon
UBERON:0000325
gastric gland
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
BTO:0001837
EMAPA:37950
FMA:62889
uberon
UBERON:0000409
serous gland
A gland in which the principal secretory cells are mucus secreting cells.
In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
AAO:0010601
BTO:0001979
EMAPA:37913
FMA:62888
glandula mucosa
uberon
muciparous gland
mucous secreting gland
mucus gland
mucus-secreting gland
UBERON:0000414
mucous gland
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
UBERON:0006540
secretion
AEO:0001005
BTO:0002977
BTO:0002979
EMAPA:36535
FMA:9675
MA:0002504
MESH:D012634
NCIT:C34062
UMLS:C1516992
galen:Secretion
bodily secretion
exocrine gland fluid/secretion
secreted substance
uberon
exocrine gland fluid
exocrine gland fluid or secretion
exocrine gland secretion
external secretion
UBERON:0000456
secretion of exocrine gland
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
AAO:0010839
AEO:0000004
BILA:0000004
CALOHA:TS-2101
CARO:0000004
EHDAA2:0003004
EMAPA:35178
FBbt:00007019
FMA:9669
HAO:0000004
MA:0002450
NCIT:C13236
SPD:0000008
TAO:0001487
TGMA:0001824
VHOG:0001726
XAO:0004001
ZFA:0001487
galen:BodySubstance
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
uberon
UBERON:0000463
organism substance
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
system
AAO:0000007
AEO:0000011
BILA:0000011
BSA:0000049
CALOHA:TS-2088
CARO:0000011
EHDAA2:0003011
EHDAA:392
EMAPA:16103
EV:0100000
FBbt:00004856
FMA:7149
HAO:0000011
MA:0000003
NCIT:C12919
OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
TAO:0001439
TGMA:0001831
UMLS:C0460002
VHOG:0001725
WBbt:0005746
WBbt:0005763
XAO:0003002
ZFA:0001439
galen:AnatomicalSystem
body system
connected anatomical system
organ system
uberon
anatomical systems
UBERON:0000467
anatomical system
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
organismal
organism
AAO:0010026
AEO:0000191
BILA:0000012
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
NCIT:C13041
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
animal
uberon
Koerper
body
whole body
whole organism
UBERON:0000468
multicellular organism
The organs and associated structures associated with bearing offspring in a female animal.
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
BTO:0000083
CALOHA:TS-1303
EFO:0000969
EHDAA2:0000506
EHDAA:8116
EMAPA:17959
EV:0100110
FBbt:00004864
FMA:45663
GAID:364
HAO:0000324
MA:0000381
MESH:D005836
MIAA:0000028
NCIT:C12402
OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA
TGMA:0000635
UMLS:C0700038
VHOG:0000726
WBbt:0006748
WikipediaCategory:Female_reproductive_system
XAO:0000156
female organism genitalia
female organism reproductive system
genitalia of female organism
reproductive system of female organism
uberon
female genital system
female genital tract
female genitalia
female genitals
female reproductive tract
gynaecological tissue
systema genitale femininum
UBERON:0000474
female reproductive system
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
AAO:0010268
AEO:0000040
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
XAO:0003162
ZFA:0000382
uberon
acellular anatomical structures
UBERON:0000476
acellular anatomical structure
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
NCIT:C12801
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
tissue
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
AAO:0010048
AEO:0000055
BILA:0000055
CARO:0000055
EHDAA2:0003055
FBbt:00007010
HAO:0000055
TAO:0001488
TGMA:0001847
VHOG:0001762
XAO:0003037
ZFA:0001488
uberon
multi-tissue structures
UBERON:0000481
multi-tissue structure
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
AAO:0010016
AEO:0000072
BILA:0000072
CARO:0000072
EHDAA2:0003072
FMA:55671
HAO:0000072
TAO:0001490
TGMA:0001857
VHOG:0001730
XAO:0003165
ZFA:0001490
cavitated organ
uberon
cavitated compound organs
UBERON:0000489
cavitated compound organ
Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid.
ENVO:02000042
FMA:9673
NCIT:C120839
intercellular fluid
tissue fluid
uberon
UBERON:0000913
interstitial fluid
cjm
cjm
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
endocrine
AAO:0010279
CALOHA:TS-1301
EFO:0002969
EHDAA2:0002224
EMAPA:35306
EV:0100128
FBbt:00005068
FMA:9668
GAID:439
MA:0000012
MESH:D004703
NCIT:C12705
TAO:0001158
UMLS:C0014136
VHOG:0000098
XAO:0000158
ZFA:0001158
endocrine glandular system
endocrine system
systema endocrinum
uberon
UBERON:0000949
endocrine system
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
AAO:0010258
BILA:0000103
BTO:0000081
CALOHA:TS-1318
EFO:0000809
EHDAA2:0001603
EHDAA:5923
EMAPA:17381
EV:0100100
FBbt:00004857
FMA:7160
GAID:363
HAO:0000374
HAO:0000895
MA:0000326
MIAA:0000305
NCIT:C12841
OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA
TAO:0000632
UMLS:C1261210
VHOG:0000182
WBbt:0005747
XAO:0000142
ZFA:0000632
uberon
Geschlechtsorgan
animal reproductive system
genital system
genital tract
genitalia
organa genitalia
reproductive tissue
reproductive tract
systemata genitalia
UBERON:0000990
reproductive system
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
AAO:0000541
BTO:0000203
CALOHA:TS-1319
EFO:0000804
EHDAA2:0001604
EHDAA:2203
EMAPA:16727
EV:0100036
FMA:7158
GAID:78
MA:0000327
MAT:0000030
MESH:D012137
MIAA:0000030
NCIT:C12779
OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA
TAO:0000272
UMLS:C0035237
VHOG:0000202
XAO:0000117
ZFA:0000272
apparatus respiratorius
respiratory system
uberon
Atmungssystem
apparatus respiratorius
systema respiratorium
UBERON:0001004
respiratory system
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
digestive
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
AAO:0000129
BILA:0000082
BTO:0000058
CALOHA:TS-1293
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MA:0002431
MAT:0000018
MESH:D004064
MIAA:0000018
TADS:0000170
TAO:0000339
WBbt:0005748
XAO:0000125
ZFA:0000339
galen:DigestiveSystem
ncithesaurus:Digestive_System
uberon
alimentary system
alimentary tract
gastrointestinal system
gut
UBERON:0001007
digestive system
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
AAO:0010257
BILA:0000015
BTO:0001244
BTO:0003092
CALOHA:TS-1323
EFO:0000803
EHDAA2:0001601
EHDAA:5901
EMAPA:17366
EV:0100095
FBbt:00005056
FMA:7159
GAID:391
MA:0000325
MAT:0000027
MESH:D014551
MIAA:0000027
NCIT:C12413
TADS:0000162
TAO:0000163
UMLS:C1508753
VHOG:0000723
WBbt:0005736
XAO:0000143
ZFA:0000163
galen:UrinaryTract
excretory system
renal system
systema urinaria
systema urinarium
urinary system
urinary tract
uberon
renal or urinary system
renal/urinary system
UBERON:0001008
renal system
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
AAO:0000959
CALOHA:TS-2103
FBbt:00005057
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
VHOG:0001248
uberon
systema cardiovasculare
UBERON:0001009
circulatory system
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
nervous
neural
AAO:0000324
BILA:0000079
BTO:0001484
CALOHA:TS-1313
EFO:0000802
EHDAA2:0001246
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMA:7157
GAID:466
MA:0000016
MAT:0000026
MESH:D009420
MIAA:0000026
NCIT:C12755
OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
TAO:0000396
UMLS:C0027763
VHOG:0000402
WBbt:0005735
XAO:0000177
ZFA:0000396
neurological system
nerve net
uberon
systema nervosum
UBERON:0001016
nervous system
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
AAO:0000555
BAMS:SEN
BILA:0000099
EFO:0000805
EHDAA2:0003094
EMAPA:16192
FBbt:00007692
FMA:75259
MA:0002442
MAT:0000031
MIAA:0000031
TAO:0000282
VHOG:0001674
XAO:0003194
ZFA:0000282
organa sensuum
sense organ subsystem
sense organs
sense organs set
sensory subsystem
sensory systems
uberon
organa sensuum
sensory organ system
set of sense organs
UBERON:0001032
sensory system
4
cjm
MA
ISBN10:0073040584
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
EHDAA2
3
cjm
FMA
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
in FMA embryo is_a embryonic structure
AAO:0000138
BILA:0000034
BTO:0000174
CALOHA:TS-2110
EFO:0000461
FBbt:00004208
FMA:69067
GAID:407
MESH:D004628
NCIT:C13229
RETIRED_EHDAA2:0003169
TAO:0001105
UMLS:C0013948
VSAO:0000178
XAO:0003042
ZFA:0001105
developing embryonic structure
embryonic anatomical structure
uberon
developing structure
embryonale Struktur
embryonic structures
UBERON:0002050
embryonic structure
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
AAO:0010386
BTO:0001491
EHDAA:512
EMAPA:16245
FMA:7085
MA:0000019
MESH:D014781
NCIT:C28287
RETIRED_EHDAA2:0002201
UMLS:C0042779
XAO:0003034
visceral organ
visceral organ system
uberon
Organsystem@de
splanchnic tissue
viscera
visceral tissue
UBERON:0002075
viscus
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
AAO:0000631
EMAPA:36002
EMAPA:37985
FMA:78500
TAO:0001138
XAO:0003195
ZFA:0001138
auditory organ system
vestibuloauditory system
uberon
auditory system
auditory/vestibular system
vestibuloauditory system
UBERON:0002105
vestibulo-auditory system
2
cjm
3
cjm
3
cjm
3
cjm
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EHDAA2:0001730
EHDAA:4969
EMAPA:17661
FMA:7309
MA:0000426
NCIT:C33483
OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0225706
VHOG:0000301
uberon
UBERON:0002167
right lung
Lung which consists of the left upper lobe and left lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
EHDAA2:0000943
EHDAA:4947
EMAPA:17653
FMA:7310
MA:0000425
NCIT:C32967
OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA
UMLS:C0225730
VHOG:0000618
uberon
UBERON:0002168
left lung
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
CALOHA:TS-2018
EHDAA2:0004615
EMAPA:18765
FMA:74562
MA:0000013
hematolymphoid system
lymphomyeloid complex
uberon
haemolymphoid system
UBERON:0002193
hemolymphoid system
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
musculoskeletal
AAO:0010546
CALOHA:TS-1311
EMAPA:32714
EV:0100139
FMA:7482
GAID:98
MA:0002418
MESH:D009141
NCIT:C12754
OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g
UMLS:C0026860
VHOG:0001275
VSAO:0000031
XAO:0000168
musculo-skeletal system
uberon
UBERON:0002204
musculoskeletal system
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
AAO:0010180
BTO:0001772
FBbt:00005158
FMA:77659
VHOG:0000287
XAO:0000273
olfactory organ
olfactory sense organ
olfactory sensory organ
main olfactory organ
primary olfactory organ
uberon
olfactory neuroepithelium
organ olfactus
organum olfactorium
UBERON:0002268
olfactory organ
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
CALOHA:TS-2057
EHDAA2:0002225
EMAPA:35329
FMA:85539
MA:0002411
NCIT:C12957
UMLS:C1516995
WikipediaCategory:Exocrine_system
exocrine glandular system
uberon
UBERON:0002330
exocrine system
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
AEO:0000097
BTO:0000765
CALOHA:TS-2012
EHDAA2:0003097
EMAPA:35327
FMA:9596
GAID:34
MA:0002564
MESH:D005088
NCIT:C12712
UMLS:C0015282
ducted gland
glandula exocrina
uberon
UBERON:0002365
exocrine gland
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
AEO:0000098
BTO:0001488
CALOHA:TS-1300
EHDAA2:0003098
EMAPA:35999
FMA:9602
GAID:335
MA:0002563
MESH:D004702
NCIT:C12704
OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA
UMLS:C0014133
ductless gland
glandula endocrina
uberon
ductless gland
glandulae endocrinae
UBERON:0002368
endocrine gland
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
hematopoietic
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
AAO:0011002
BTO:0000570
CALOHA:TS-0449
EFO:0000798
EMAPA:35402
EV:0100045
FMA:9667
GAID:1008
MA:0002434
MAT:0000022
MESH:D006413
MIAA:0000022
NCIT:C12909
TAO:0005023
UMLS:C0018957
VHOG:0001624
XAO:0000122
ZFA:0005023
haematological system
haemopoietic system
organa haemopoietica
uberon
Blutbildungssystem
haematopoietic system
hematological system
hematolymphoid system
hemopoietic system
UBERON:0002390
hematopoietic system
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
AAO:0011003
BILA:0000104
BTO:0005810
FMA:9825
GAID:328
MA:0002711
MESH:D007107
NCIT:C12735
OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
TAO:0001159
UMLS:C0020962
VHOG:0001247
XAO:0003152
ZFA:0001159
uberon
UBERON:0002405
immune system
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
UBERON:0007029
AEO:0000154
BILA:0000118
CALOHA:TS-1299
CARO:0002001
EFO:0000807
EHDAA2:0000836
EHDAA2_RETIRED:0003154
EHDAA:6520
EMAPA:17524
EV:0100151
FBbt:00004969
FMA:72979
HAO:0000421
MA:0000014
MAT:0000033
MESH:D034582
MIAA:0000033
NCIT:C12907
TADS:0000108
UMLS:C0037267
VHOG:0000403
XAO:0000176
galen:Surface
integumentary system
uberon
body surface
dermal system
external covering of organism
integumentum commune
organism surface
surface
UBERON:0002416
integumental system
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
lymphoid
The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]
The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]
We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
UBERON:0002096
EHDAA2:0001043
EHDAA:8677
EMAPA:37664
FMA:74594
GAID:931
MA:0002435
MAT:0000197
MIAA:0000197
NCIT:C12746
OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA
TAO:0000385
UMLS:C0024235
VHOG:0000842
XAO:0003199
ZFA:0000385
lymphatic system
uberon
lymphatic circulatory system
lymphatic drainage system
systema lymphoideum
UBERON:0002465
lymphoid system
an organ that functions as a secretory or excretory organ
glandular
UBERON:MIAA_0000021
AAO:0000212
AEO:0000096
BTO:0000522
EFO:0000797
EHDAA2:0003096
EHDAA:2161
EHDAA:4475
EHDAA:6522
EMAPA:18425
FBbt:00100317
FMA:7146
FMA:86294
HAO:0000375
MA:0003038
MAT:0000021
MIAA:0000021
NCIT:C13319
OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
UMLS:C1285092
WikipediaCategory:Glands
galen:Gland
glandular organ
uberon
Druese
glandula
UBERON:0002530
gland
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
AAO:0010015
AEO:0000024
BILA:0000024
CARO:0000024
EHDAA2:0003024
HAO:0000024
TADS:0000598
TAO:0000496
TGMA:0001837
VHOG:0001723
XAO:0003041
ZFA:0000496
uberon
organ
UBERON:0003103
compound organ
An organ involved in reproduction
GO uses genitalia for the singular organ
EMAPA:17381
EMAPA:37731
MA:0001752
MESH:D005835
NCIT:C25177
OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
TGMA:0000591
UMLS:C0017420
WBbt:0008422
genital organ
reproductive system organ
sex organ
uberon
genitalia
UBERON:0003133
reproductive organ
A gland that is part of a foregut [Automatically generated definition].
EHDAA2:0000567
EHDAA:950
EMAPA:16557
VHOG:0000650
foregut gland
uberon
UBERON:0003294
gland of foregut
A gland that is part of a integumental system [Automatically generated definition].
EHDAA2:0000837
EHDAA:6522
EMAPA:17758
MA:0000144
VHOG:0000654
integumental gland
integumental system gland
integumentary gland
uberon
UBERON:0003297
gland of integumental system
A gland that is part of a digestive tract [Automatically generated definition].
EMAPA:18815
MA:0003202
digestive tract gland
gland of digestive tract
gland of lower gastrointestinal tract
gut gland
lower gastrointestinal tract gland
uberon
UBERON:0003408
gland of digestive tract
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
AEO:0000080
EHDAA2:0003080
FMA:242873
foramen
foramina
uberon
opening
ostia
ostium
UBERON:0004111
anatomical conduit
An anatomical structure that develops (entirely or partially) from the endoderm.
Grouping term for query purposes
uberon
UBERON:0004119
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
Grouping term for query purposes
FBbt:00025998
mesodermal derivative
uberon
UBERON:0004120
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
Grouping term for query purposes
FBbt:00025990
ectodermal deriviative
uberon
UBERON:0004121
ectoderm-derived structure
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
genitourinary
urogenital
AAO:0000624
BILA:0000122
BTO:0003091
EFO:0003864
EHDAA:1013
EMAPA:16367
EV:0100094
FMA:280610
GAID:362
MESH:D014566
NCIT:C12810
OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g
UMLS:C0042066
VHOG:0000286
XAO:0000140
galen:GenitoUrinarySystem
urogenital system
uberon
GU tract
UG tract
Urogenitalsystem
genito-urinary system
genitourinary tract
urogenital tract
UBERON:0004122
genitourinary system
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
skeletal
AEO:0000168
EHDAA2:0001843
EHDAA:5047
EMAPA:17213
FMA:23875
GAID:177
MA:0003006
MAT:0000032
MESH:D012863
MIAA:0000032
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
VSAO:0000026
XAO:0004053
galen:Skeleton
set of all bones
set of bones of body
uberon
UBERON:0004288
skeleton
https://github.com/obophenotype/uberon/wiki/The-skeletal-system
Sum of all sensory systems in an organism.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
FMA:78499
sense organ system
uberon
UBERON:0004456
entire sense organ system
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
AAO:0011001
BILA:0000016
BTO:0000088
CALOHA:TS-1297
EFO:0000791
EHDAA2:0000216
EHDAA:394
EMAPA:16104
EMAPA:16370
EV:0100017
FMA:7161
GAID:467
MA:0000010
MAT:0000016
MESH:D002319
MIAA:0000016
NCIT:C12686
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
TAO:0000010
UMLS:C0007226
VHOG:0000302
WikipediaCategory:Cardiovascular_system
XAO:0000100
XAO:0001010
ZFA:0000010
uberon
CV system
Herz und Gefaesssystem
UBERON:0004535
cardiovascular system
The part of the cardiovascular system consisting of all arteries.
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
BTO:0004690
EHDAA2:0000143
EHDAA:396
EMAPA:16201
EMAPA:16371
MA:0002719
VHOG:0000273
uberon
UBERON:0004572
arterial system
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
BTO:0004692
EHDAA2:0002171
EHDAA:486
EMAPA:16240
MA:0002720
NCIT:C33858
UMLS:C1267406
VHOG:0000277
vein system
uberon
UBERON:0004582
venous system
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
AAO:0011129
TAO:0001890
VSAO:0000128
XAO:0004012
ZFA:0005494
galen:SkeletalStructure
uberon
UBERON:0004765
skeletal element
Anatomical system that consists of all the joints of the body.
EMAPA:35150
FMA:23878
MA:0003007
VSAO:0000181
joint system
set of all joints of body
uberon
set of all joints
set of joints of body
UBERON:0004770
articular system
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
FBbt:00100315
FMA:71131
uberon
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
UBERON:0004921
subdivision of digestive tract
A proximal-distal subdivision of the digestive tract.
alimentary system subdivision
FMA:71131
subdivision of alimentary system
FMA:71131
An organ that is part of a immune system [Automatically generated definition].
immune system organ
uberon
UBERON:0005057
immune organ
Any anatomical structure that is part of the reproductive system.
reproductive system element
reproductive system structure
uberon
UBERON:0005156
reproductive structure
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
MA:0000522
abdomen organ
uberon
UBERON:0005172
abdomen element
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
EMAPA:37062
MA:0000529
abdominal segment organ
uberon
UBERON:0005173
abdominal segment element
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
EMAPA:37274
MA:0001901
back organ
dorsal region organ
uberon
UBERON:0005174
dorsal region element
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
EMAPA:37270
MA:0000516
trunk organ
uberon
UBERON:0005177
trunk region element
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
EMAPA:37273
MA:0000557
thoracic cavity organ
uberon
UBERON:0005178
thoracic cavity element
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
EMAPA:37271
MA:0000563
uberon
upper body organ
UBERON:0005181
thoracic segment organ
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
BTO:0000058
CALOHA:TS-0407
EHDAA2:0000110
EHDAA:514
EMAPA:16246
EV:0100056
FMA:71132
GAID:294
MA:0000323
MESH:A03.492
NCIT:C12378
UMLS:C0012240
VHOG:0000412
galen:GastrointestinalTract
uberon
GI tract
alimentary system
alimentary tract
gastro-intestinal system
gastroenterological system
gastrointestinal (GI) tract
gastrointestinal system
gastrointestinal tract
UBERON:0005409
alimentary part of gastrointestinal system
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
FMA:292313
MIAA:0000019
uberon
developing structure
developmental structure
developmental tissue
UBERON:0005423
developing anatomical structure
A acellular anatomical structure that is the bounding layer of a anatomical structure.
FMA:63871
uberon
UBERON:0005764
acellular membrane
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
AAO:0010596
FMA:63872
GAID:915
NCIT:C13191
UMLS:C0004799
basement membrane of connective tissue
membrana basalis
uberon
basement membrane
UBERON:0005769
basement membrane of epithelium
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
fluid
EMAPA:37441
FMA:280556
GAID:266
MESH:D001826
galen:BodyFluid
body fluid
uberon
UBERON:0006314
bodily fluid
A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards.
EMAPA:36538
MA:0002505
uberon
lactiferous gland fluid
lactiferous gland secretion
mammary gland fluid
mammary gland secreted fluid
mammary gland secretion
secretion of mammary gland
UBERON:0006539
mammary gland fluid/secretion
Any gland that is part of the digestive system.
AAO:0000130
BTO:0000345
uberon
digestive gland
UBERON:0006925
digestive system gland
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
FBbt:00003154
SPD:0000130
TADS:0000147
dorsal tube
heart
uberon
adult heart
UBERON:0007100
Gene notes: Bmp, Nkx, Gata
primary circulatory organ
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
transudative
characteristically low in protein and cellular content (unless there has been secondary concentration)
FMA:12276
GAID:1195
MESH:D005122
ncithesaurus:Transudate
uberon
plasma ultrafiltrate
UBERON:0007779
transudate
Any fluid produced by a serous gland.
serous fluid
serosal fluid
serous gland fluid
uberon
UBERON:0007794
secretion of serous gland
Anatomical system that consists of all blood and lymph vessels.
consider merging with vasculature
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
BTO:0001085
CALOHA:TS-2053
EHDAA2:0004520
EMAPA:35905
MA:0002718
NCIT:C33854
UMLS:C0489903
uberon
Gefaesssystem@de
UBERON:0007798
vascular system
Branch or outpocketing of the digestive tract.
FBbt:00100316
uberon
diverticulum of gut
intestinal pouch
UBERON:0009854
digestive tract diverticulum
Branch or outpocketing of the digestive tract.
diverticulum of gut
FBbt:00100316
galen:Diverticulum
pouch
uberon
diverticulum
UBERON:0009856
sac
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
An organ of the digestive tract that is capable of retaining and storing food
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
BSA:0000123
TADS:0000172
TGMA:0001041
uberon
UBERON:0010039
food storage organ
the FMA class specifically refers to ureter
FMA:63212
MESH:D024022
NCIT:C32339
NIF_Subcellular:sao7547390221
uberon
UBERON:0011860
collection of collagen fibrils
A blood that is part of a vein.
FMA:83067
blood in vein
portion of venous blood
venous blood
uberon
UBERON:0013756
venous blood
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
digestive organ
digestive system organ
uberon
UBERON:0013765
digestive system element
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
uberon
UBERON:0015212
lateral structure
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
heart
SPD:0000130
cardiac pump
heart or heart like organ
circulatory vessel
uberon
cardiac structure
UBERON:0015228
circulatory organ
EMAPA:37597
MA:0002449
heart/pericardium
uberon
UBERON:0015410
heart plus pericardium
A viscus that is part of a abdomen.
FMA:32413
FMA:67355
abdominal viscera
abdominal viscera set
set of abdominal viscera
uberon
UBERON:0017672
abdominal viscera
An exocrine gland that is part of a integumental system.
integumental exocrine gland
integumental system exocrine gland
uberon
UBERON:0019319
exocrine gland of integumental system
Any substance in the body or expelled from the body that is in a gaseous state.
FMA:84580
gas in anatomical space
portion of gas in anatomical space
uberon
UBERON:0034873
bodily gas
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
FMA:84581
respiratory air
respiratory system air
uberon
UBERON:0034874
air in respiratory system
An multicellular anatomical structure that has subparts of multiple organs as a part.
CARO:0020001
uberon
anatomical cluster
UBERON:0034921
multi organ part structure
A cluster of cells, largely surrounded by a morphological boundary.
CARO:0020002
FMA:62807
uberon
UBERON:0034922
cell cluster
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
uberon
UBERON:0034925
anatomical collection
Any portion of gas located in a part of the respiratory system.
respiratory gas
respiratory system gas
uberon
UBERON:0034947
gas in respiratory system
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
a geopolitical region is a geographic region recognized by social or legal convention.
geopolitical region
A specific surveillance activity that is planned and has (or will have) associated results. A surveillance component or a surveillance system could both be a surveillance activity.
Ideally, every activity would have unique attributes for methods - for instance, only one sampling stage. If samples are collected in a slaughterhouse AND in farms, these would ideally be modeled as two different activities, and the appropriate properties used to declare them as linked. But since activities are not defined the same in every health surveillance sector, nor do all data support such a granularity, the class is able to model methods and results for any surveillance activity declared.
One surveillance activity should have an unique identifier, to which results are linked.
Surveillance Activity
livestock farming system
product oriented farming type
Manufacturing
SAMPNT
E300A
Meat processing
SAMPNT
E310A
abattoir
Slaughterhouse
SAMPNT
E311A
Fish processing
SAMPNT
E320A
Manufacture of prepared animal feeds
SAMPNT
E350A
Veterinary activities
SAMPNT
E011A
vet clinic
Veterinary clinics
SAMPNT
E013A
Zoo
SAMPNT
E012A
Primary production
SAMPNT
E100A
Farm
SAMPNT
E101A
AI station
Artificial insemination station
SAMPNT
E132A
Bee hives
SAMPNT
E112A
Fishery activities
SAMPNT
E150A
Fishing and fish processing
SAMPNT
E151A
Aquaculture
SAMPNT
E152A
Fishing
SAMPNT
E153A
Hatchery
SAMPNT
E160A
Hunting
SAMPNT
E180A
Natural habitat
SAMPNT
E191A
Residential institution (nursing home or prison or boarding school)
SAMPNT
E220A
School or kindergarten
SAMPNT
E240A
Household
SAMPNT
E230A
Distribution: wholesale and retail sale
SAMPNT
E500A
grocery store
Retail
SAMPNT
E520A
restaurant
Catering
SAMPNT
E900A
Official kennel
SAMPNT
E983A
Catering on aircraft or ship or train
SAMPNT
E990A
supra-national geopolitical entity
Nomenclature of Territorial Units for Statistics
https://en.wikipedia.org/wiki/Nomenclature_of_Territorial_Units_for_Statistics
NUTS region
language
matrix type
whole organism
matrix from organism
fluid specimen
organ/tissue specimen
swab specimen
excreta specimen
Surveillance context
PRGTYP
Surveillance sampler type
SAMPLR
sampling strategy
SAMPSTR
sampling unit
SAMPUNTYP
Classification not possible
ANLYMD_PRVAM
F001A
Classification not possible
Analytical method measuring principle is known, but could not be classified.
High Performance Liquid Chromatography (HPLC)/Liquid Chromatography (LC)
ANLYMD_PRVAM
F018A
High Performance Liquid Chromatography (HPLC)/Liquid Chromatography (LC)
High Performance, High Pressure and Liquid Chromatography.
Immunological detection or quantification method
ANLYMD_PRVAM
F077A
Immunological detection or quantification method
Applies to e.g. immunoelectrophoresis
Milk ring-test
ANLYMD_PRVAM
F523A
Milk ring-test
Enzyme-linked immunosorbent assay (ELISA)
ANLYMD_PRVAM
F080A
Enzyme-linked immunosorbent assay (ELISA)
Enzyme-linked Immunosorbent Assay
ELISA, Competitive ELISA (C-ELISA)
ANLYMD_PRVAM
F530A
ELISA, Competitive ELISA (C-ELISA)
PCR
ANLYMD_PRVAM
F086A
PCR
Polymerase Chain Reaction
Real-time PCR (CEN TC275/WG6)
ANLYMD_PRVAM
F123A
Real-time PCR (CEN TC275/WG6)
Real-time polymerase chain reaction (quantitative PCR)
Reverse-transcription PCR (RT-PCR)
ANLYMD_PRVAM
F189A
Reverse-transcription PCR (RT-PCR)
Simplex PCR
ANLYMD_PRVAM
F194A
Simplex PCR
Duplex PCR
ANLYMD_PRVAM
F195A
Duplex PCR
Multiplex PCR
ANLYMD_PRVAM
F196A
Multiplex PCR
Microscopical and histometrical tests
ANLYMD_PRVAM
F095A
Microscopical and histometrical tests
Trichinoscopic examination
ANLYMD_PRVAM
F546A
Trichinoscopic examination
Microbiological tests
ANLYMD_PRVAM
F099A
Microbiological tests
Microbiological standard tests
ANLYMD_PRVAM
F100A
Microbiological standard tests
Applies to e.g. MPN
AFNOR NF U47 100 (2007)
ANLYMD_PRVAM
F133A
AFNOR NF U47 100 (2007)
Isolation and identification of Salmonella or search for particular serovar's in the animal production sector
AFNOR NF U47 101 (2007)
ANLYMD_PRVAM
F134A
AFNOR NF U47 101 (2007)
Isolation and identification of any Salmonella serotypes or of specified salmonella serotypes among birds
ISO 16654:2001
ANLYMD_PRVAM
F135A
ISO 16654:2001
Horizontal method for the detection of Escherichia coli O157
ISO 20776-1:2006
ANLYMD_PRVAM
F136A
ISO 20776-1:2006
Reference method for testing the in vitro activity of antimicrobial agents against rapidly growing aerobic bacteria involved in infectious diseases
ISO 6579:2002
ANLYMD_PRVAM
F137A
ISO 6579:2002
Horizontal method for the detection of Salmonella spp.Â
ISO 6579:2002/Amd 1:2007
ANLYMD_PRVAM
F138A
ISO 6579:2002/Amd 1:2007
Annex D: Detection of Salmonella spp. in animal faeces and in environmental samples from the primary production stageÂ
NMKL 71, 1999, 5th Ed. Salmonella
ANLYMD_PRVAM
F140A
NMKL 71, 1999, 5th Ed. Salmonella
Detection of Salmonella in food
ISO 10272-1:2006Â Campylobacter
ANLYMD_PRVAM
F163A
ISO 10272-1:2006Â Campylobacter
Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 1: Detection method
ISO/TS 10272-2:2006Â Campylobacter
ANLYMD_PRVAM
F164A
ISO/TS 10272-2:2006Â Campylobacter
Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 2: Colony-count technique
ISO/TS 10272-3:2010Â Campylobacter
ANLYMD_PRVAM
F165A
ISO/TS 10272-3:2010Â Campylobacter
Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 3: Semi-quantitative method
ISO/TS 10272-3:2010/Cor 1:2011Â Campylobacter
ANLYMD_PRVAM
F166A
ISO/TS 10272-3:2010/Cor 1:2011Â Campylobacter
ISO 6579:2002 Salmonella
ANLYMD_PRVAM
F167A
ISO 6579:2002 Salmonella
Microbiology of food and animal feeding stuffs -- Horizontal method for the detection of Salmonella spp.
ISO 6579:2002/Amd 1:2007 (Annex D of ISO 6579) Salmonella
ANLYMD_PRVAM
F168A
ISO 6579:2002/Amd 1:2007 (Annex D of ISO 6579) Salmonella
Annex D: Detection of Salmonella spp. in animal faeces and in environmental samples from the primary production stage
ISO 11290-1:1996/Amd 1:2004Â Listeria
ANLYMD_PRVAM
F169A
ISO 11290-1:1996/Amd 1:2004Â Listeria
Modification of the isolation media and the haemolysis test, and inclusion of precision data
ISO 11290-2:1998/Amd 1:2004Â Listeria
ANLYMD_PRVAM
F170A
ISO 11290-2:1998/Amd 1:2004Â Listeria
Modification of the enumeration medium
EN ISO 6888-1:1999/Amdt 1:2003 Coagulase-positives staphylococci
ANLYMD_PRVAM
F171A
EN ISO 6888-1:1999/Amdt 1:2003 Coagulase-positives staphylococci
Inclusion of precision data
EN ISO 6888-2:1999/Amdt 1:2003Â Coagulase-positives staphylococci
ANLYMD_PRVAM
F172A
EN ISO 6888-2:1999/Amdt 1:2003Â Coagulase-positives staphylococci
Inclusion of precision data
ISO/TS 13136:2012 (including the EU-RL adaptation for O104:H4)
ANLYMD_PRVAM
F173A
ISO/TS 13136:2012 (including the EU-RL adaptation for O104:H4)
Microbiology of food and animal feed -- Real-time polymerase chain reaction (PCR)-based method for the detection of food-borne pathogens -- Horizontal method for the detection of Shiga toxin-producing Escherichia coli (STEC) and the determination of O157,
ISO 10273:2003 Yersinia
ANLYMD_PRVAM
F175A
ISO 10273:2003 Yersinia
Microbiology of food and animal feeding stuffs -- Horizontal method for the detection of presumptive pathogenic Yersinia enterocolitica
EN/ISO 7932 Bacillus cereus
ANLYMD_PRVAM
F176A
EN/ISO 7932 Bacillus cereus
Microbiology of food and animal feeding stuffs -- Horizontal method for the enumeration of presumptive Bacillus cereus -- Colony-count technique at 30 degrees C
ISO/TS 22964:2006 (IDF/RM 210: 2006) Cronobacter spp. (Enterobacter sakazakii)
ANLYMD_PRVAM
F177A
ISO/TS 22964:2006 (IDF/RM 210: 2006) Cronobacter spp. (Enterobacter sakazakii)
Milk and milk products -- Detection of Enterobacter sakazakii
Combination disk method
ANLYMD_PRVAM
F555A
Combination disk method
Combination strip test/Epsilometer test
ANLYMD_PRVAM
F556A
Combination strip test/Epsilometer test
NMKL 119, 2007, 3rd Ed. Termotolerante Campylobacter
ANLYMD_PRVAM
F600A
NMKL 119, 2007, 3rd Ed. Termotolerante Campylobacter
NMKL No. 119, 3rd ed. 2007, Thermotolerant Campylobacter. Detection, semi-quantitative and quantitative determination in foods and drinking water
NMKL 187, 2007 Salmonella
ANLYMD_PRVAM
F601A
NMKL 187, 2007 Salmonella
NMKL No. 187, 2007, Salmonella. Detection in foods, animal faeces and environmental materials from primary animal production using MSRV
ISO 6579-1:2017 Salmonella
ANLYMD_PRVAM
F609A
ISO 6579-1:2017 Salmonella
Microbiology of the food chain -- Horizontal method for the detection, enumeration and serotyping of Salmonella -- Part 1: Detection of Salmonella spp.
ISO 11290-1:2017 Listeria
ANLYMD_PRVAM
F610A
ISO 11290-1:2017 Listeria
Microbiology of the food chain -- Horizontal method for the detection and enumeration of Listeria monocytogenes and of Listeria spp. -- Part 1: Detection method
ISO 11290-2:2017 Listeria
ANLYMD_PRVAM
F611A
ISO 11290-2:2017 Listeria
Microbiology of the food chain -- Horizontal method for the detection and enumeration of Listeria monocytogenes and of Listeria spp. -- Part 2: Enumeration method
ISO 19020:2017 Staphylococcal enterotoxins
ANLYMD_PRVAM
F612A
ISO 19020:2017 Staphylococcal enterotoxins
Microbiology of the food chain -- Horizontal method for the immunoenzymatic detection of staphylococcal enterotoxins in foodstuffs
ISO 21528-1:2017 Enterobacteriaceae
ANLYMD_PRVAM
F613A
ISO 21528-1:2017 Enterobacteriaceae
Microbiology of the food chain -- Horizontal method for the detection and enumeration of Enterobacteriaceae -- Part 1: Detection of Enterobacteriaceae
ISO 21528-2:2017 Enterobacteriaceae
ANLYMD_PRVAM
F614A
ISO 21528-2:2017 Enterobacteriaceae
Microbiology of the food chain -- Horizontal method for the detection and enumeration of Enterobacteriaceae -- Part 2: Colony-count technique
ISO 22964:2017 Cronobacter
ANLYMD_PRVAM
F615A
ISO 22964:2017 Cronobacter
Microbiology of the food chain -- Horizontal method for the detection of Cronobacter spp.
ISO 10272-2:2017 Campylobacter
ANLYMD_PRVAM
F616A
ISO 10272-2:2017 Campylobacter
Microbiology of the food chain -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 2: Colony-count technique
ISO 10272-1:2017 Campylobacter
ANLYMD_PRVAM
F617A
ISO 10272-1:2017 Campylobacter
Microbiology of the food chain -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 1: Detection method
ISO 10273:2017 Yersinia enterocolitica
ANLYMD_PRVAM
F618A
ISO 10273:2017 Yersinia enterocolitica
Microbiology of the food chain -- Horizontal method for the detection of pathogenic Yersinia enterocolitica
NMKL 136, 5th ed. 2010, Listeria monocytogenes
ANLYMD_PRVAM
F649A
NMKL 136, 5th ed. 2010, Listeria monocytogenes
NMKL 136, 5th ed. 2010, Listeria monocytogenes. Detection in foods and feeding stuffs and enumeration in foods
Microbiological special tests
ANLYMD_PRVAM
F101A
Microbiological special tests
Applies to e.g. Keimdiff, Salm test, etc.
Molecular detection or quantification method
ANLYMD_PRVAM
F115A
Molecular detection or quantification method
Pulsed field gel electrophoresis (PFGE)
ANLYMD_PRVAM
F504A
Pulsed field gel electrophoresis (PFGE)
Morphological identification
ANLYMD_PRVAM
F120A
Morphological identification
Morphological identification for insect samples
Indirect Immunofluorescent Antibody test (IFAT)
ANLYMD_PRVAM
F121A
Indirect Immunofluorescent Antibody test (IFAT)
A form of fluorescent antibody technique using antigen-antibody complex labelled with flourescein-conjugated anti-immunoglobulin antibody
Enumeration method
ANLYMD_PRVAM
F141A
Enumeration method
ISO 11290-2:1998Â (Horizontal method for the detection and enumeration of Listeria monocytogenes -- Part 2: Enumeration method) and ISO 11290-2:1998/Amd 1:2004 (Modification of the enumeration medium )
Detection method of microorganisms
ANLYMD_PRVAM
F144A
Detection method of microorganisms
ISO 11290-1:1996Â (Horizontal method for the detection and enumeration of Listeria monocytogenes -- Part 1: Detection method) and ISO 11290-1:1996/Amd 1:2004 (Modification of the isolation media and the haemolysis test, and inclusion of precision data )
Complement fixation test (CFT)
ANLYMD_PRVAM
F148A
Complement fixation test (CFT)
A serological test for detecting the presence of a specific antibody or antigen
Modified agglutination test (MAT)
ANLYMD_PRVAM
F149A
Modified agglutination test (MAT)
Latex agglutination test (LAT)
ANLYMD_PRVAM
F150A
Latex agglutination test (LAT)
Immunoblotting (IB)
ANLYMD_PRVAM
F151A
Immunoblotting (IB)
Analytical technique used to detect specific proteins in the given sample of tissue homogenate or extract.
Indirect ELISA (I-ELISA)
ANLYMD_PRVAM
F152A
Indirect ELISA (I-ELISA)
Fluorescent in situ hybridization (FISH)
ANLYMD_PRVAM
F153A
Fluorescent in situ hybridization (FISH)
A cytogenetic technique that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes.
Isolation (Cell, Egg, Mouse)
ANLYMD_PRVAM
F154A
Isolation (Cell, Egg, Mouse)
Immuno Histo Chemistry (IHC)
ANLYMD_PRVAM
F155A
Immuno Histo Chemistry (IHC)
Immunofluorenscence assay tests (IFA)
ANLYMD_PRVAM
F156A
Immunofluorenscence assay tests (IFA)
Staining
ANLYMD_PRVAM
F157A
Staining
Real-Time PCR (qualitative or quantitative)
ANLYMD_PRVAM
F159A
Real-Time PCR (qualitative or quantitative)
Direct agglutination (DA)
ANLYMD_PRVAM
F160A
Direct agglutination (DA)
EU RL method_food_2. Rev. 2 - O104:H4
ANLYMD_PRVAM
F161A
EU RL method_food_2. Rev. 2 - O104:H4
Detection and identification of Verocytotoxin-producing Escherichia coli (VTEC) O104:H4 in food by Real Time PCR
Histology
ANLYMD_PRVAM
F162A
Histology
IgG ELISA
ANLYMD_PRVAM
F190A
IgG ELISA
IgM-capture ELISA (MAC-ELISA)
ANLYMD_PRVAM
F191A
IgM-capture ELISA (MAC-ELISA)
Indirect hemoagglutination test (IHA)
ANLYMD_PRVAM
F192A
Indirect hemoagglutination test (IHA)
Seroneutralisation test
ANLYMD_PRVAM
F193A
Seroneutralisation test
Multiple-locus variable-number tandem repeat analysis (MLVA)
ANLYMD_PRVAM
F197A
Multiple-locus variable-number tandem repeat analysis (MLVA)
Spa-typing
ANLYMD_PRVAM
F198A
Spa-typing
Multi locus sequence typing (MLST)
ANLYMD_PRVAM
F199A
Multi locus sequence typing (MLST)
Unknown
ANLYMD_PRVAM
F500A
Unknown
Analytical method unknown
Whole genome sequencing
ANLYMD_PRVAM
F512A
Whole genome sequencing
Macroscopic identification method
ANLYMD_PRVAM
F533A
Macroscopic identification method
Immunofluorescence method
ANLYMD_PRVAM
F537A
Immunofluorescence method
Automatic digestion method for pooled samples of up to 35 g
ANLYMD_PRVAM
F543A
Automatic digestion method for pooled samples of up to 35 g
Magnetic stirrer method for pooled sample digestion
ANLYMD_PRVAM
F544A
Magnetic stirrer method for pooled sample digestion
Mechanically assisted pooled sample digestion method / on filter isolation technique
ANLYMD_PRVAM
F545A
Mechanically assisted pooled sample digestion method / on filter isolation technique
Mechanically assisted pooled sample digestion method/sedimentation technique
ANLYMD_PRVAM
F547A
Mechanically assisted pooled sample digestion method/sedimentation technique
Skin test
ANLYMD_PRVAM
F567A
Skin test
ISO 16654:2001 or NMKL 164:2005 or DIN 10167
ANLYMD_PRVAM
F593A
ISO 16654:2001 or NMKL 164:2005 or DIN 10167
ISO 16654:2001 or NMKL 164:2005 or DIN 10167 or any alternative method validated against these methods, according to the ISO 16140. In case of testing E. coli O157 in animal faecal samples, also related OIE method is considered an alternative validated me
In house real time PCR methods based on ISO/TS 13136:2012
ANLYMD_PRVAM
F594A
In house real time PCR methods based on ISO/TS 13136:2012
In house real time PCR methods based on ISO/TS 13136:2012 or any alternative method validated against this method, according to the ISO 16140 or PCR methods based on ISO/TS 13136:2012, adapted to animal samples.
Other methods based on PCR detection of vtx genes
ANLYMD_PRVAM
F595A
Other methods based on PCR detection of vtx genes
DIN 10118:2004
ANLYMD_PRVAM
F596A
DIN 10118:2004
DIN 10118:2004 or any alternative method validated against this method, according to the ISO 16140
Other methods based on the immunochemical detection of VT
ANLYMD_PRVAM
F597A
Other methods based on the immunochemical detection of VT
Unspecified
ANLYMD_PRVAM
F598A
Unspecified
OIE method for E.coli O157 in animal faecal samples
ANLYMD_PRVAM
F602A
OIE method for E.coli O157 in animal faecal samples
OIE recommended method for the detection of E.coli O157 in animal faeces and any other cultural methods based on ISO 16654/2001 adapted to animal samples
ISO 19343:2017 Histamine
ANLYMD_PRVAM
F620A
ISO 19343:2017 Histamine
Microbiology of the food chain -- Detection and quantification of histamine in fish and fishery products -- HPLC method
Visual inspection
ANLYMD_PRVAM
F648A
Visual inspection
Post-mortem inspection of carcases carryout according to the Regulation (EC) No 854/2004
Slide agglutination according White Kauffmann Le Minor Scheme
ANLYMD_PRVAM
F650A
Slide agglutination according White Kauffmann Le Minor Scheme
Slide agglutination followed by molecular serotyping (PCR or WGS)
ANLYMD_PRVAM
F651A
Slide agglutination followed by molecular serotyping (PCR or WGS)
Flotation technique for faecal parasites
ANLYMD_PRVAM
F652A
Flotation technique for faecal parasites
Real-time PCR (BAX): detection of STEC and identification of serogroups O26, O111, O121, O145, O103 and O45
ANLYMD_PRVAM
F653A
Real-time PCR (BAX): detection of STEC and identification of serogroups O26, O111, O121, O145, O103 and O45
Detection method presence in x g
ANLYMD_PRVAM
F145A
Detection method presence in x g
ISO 11290-1:1996Â (Horizontal method for the detection and enumeration of Listeria monocytogenes -- Part 1: Detection method) and ISO 11290-1:1996/Amd 1:2004 (Modification of the isolation media and the haemolysis test, and inclusion of precision data )
ISO 15216-1:2017 Hepatitis A virus and norovirus
ANLYMD_PRVAM
F619A
ISO 15216-1:2017 Hepatitis A virus and norovirus
Microbiology of the food chain -- Horizontal method for determination of hepatitis A virus and norovirus using real-time RT-PCR -- Part 1: Method for quantificatation
Rose Bengal plate test (RBT)/Buffered Brucella antigen test (BBAT)
ANLYMD_PRVAM
F520A
Rose Bengal plate test (RBT)/Buffered Brucella antigen test (BBAT)
Serum agglutination test (SAT)
ANLYMD_PRVAM
F521A
Serum agglutination test (SAT)
Sedimentation and Counting Technique
ANLYMD_PRVAM
F188A
Sedimentation and Counting Technique
Eckert J, Deplazes P, Craig PS, Gemmell MA, Gottstein B, Heath D, et al. Echinococcosis in animals: clinical aspects, diagnosis and treatment. In: Eckert J, Gemmell MA, F.-X. Meslin, Pawlowski ZS, editors. WHO/OIE Manual on echinococcosis in humans and an
Fluorescence polarisation assay (FPA)
ANLYMD_PRVAM
F538A
Fluorescence polarisation assay (FPA)
Magnetic stirrer method for pooled sample digestion/on filter isolation and larva detection by a latex agglutination test
ANLYMD_PRVAM
F591A
Magnetic stirrer method for pooled sample digestion/on filter isolation and larva detection by a latex agglutination test
Artificial digestion test for in vivo detection of Trichinella spp. larvae in meat samples, PrioCheck Trichinella AAD Kit
ANLYMD_PRVAM
F592A
Artificial digestion test for in vivo detection of Trichinella spp. larvae in meat samples, PrioCheck Trichinella AAD Kit
NMKL 164, 2005, 2nd Ed. Escherichia coli O157
ANLYMD_PRVAM
F139A
NMKL 164, 2005, 2nd Ed. Escherichia coli O157
Detection of Escherichia coli serogroup O157 in foods and feeding stuffs
ISO 16654:2001Â E. coli
ANLYMD_PRVAM
F174A
ISO 16654:2001Â E. coli
Microbiology of food and animal feeding stuffs -- Horizontal method for the detection of Escherichia coli O157
assay datum
diagnostic test type
specimen from organism type
specimen by origin
animal sample
food sample
environmental sample
Surveillance Protocol
Surveillance System
legislative specification
surveillance objective
surveillance purpose
Sampling design
Reporting protocol
Sample collection protocol
Diagnostic protocol
surveillance methods specification
zObsolete / deprecated / not in use classes
awaiting ontology review/placement
A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories.
INSDC:country:australia
Commonwealth of Australia
Australia
COUNTRY
AU
Australia
Commonwealth of Australia
A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands.
INSDC:country:new zealand
ISO3166-1:NZ
Aotearoa {language: Maori}
New Zealand
COUNTRY
NZ
New Zealand
New Zealand
A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts.
INSDC:country:turkey
ISO3166-1:TR
Republic of Turkey
Turkiye Cumhuriyeti
Turquia {language: Portuguese}
Turkey
COUNTRY
TR
Turkey
Republic of Turkey
A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts.
INSDC:country:sudan
ISO3166-1:729
ISO3166-1:SD
ISO3166-1:SDN
ISO3166-2:SD
Jumhuriyyat as-Sudan
Republic of Sudan
Soudan
as-Sudan {language: Arabic}
Sudan
COUNTRY
SD
Sudan
Republic of the Sudan
A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats).
INSDC:country:tunisia
ISO3166-1:788
ISO3166-1:TN
ISO3166-1:TUN
ISO3166-2:TN
Al-Jumhuriyyah at-Tunisiyyah
Tunisian Republic
Tunisia
COUNTRY
TN
Tunisia
Republic of Tunisia
A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs).
INSDC:country:algeria
ISO3166-1:012
ISO3166-1:DZ
ISO3166-1:DZA
ISO3166-2:DZ
People's Democratic Republic of Algeria
Tagduda tamegdayt ta?erfant tazzayrit {language: Kabyle}
Algeria
COUNTRY
DZ
Algeria
People’s Democratic Republic of Algeria
A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed.
INSDC:country:morocco
ISO3166-1:504
ISO3166-1:MA
ISO3166-1:MAR
ISO3166-2:MA
Al-Mamlaka al-Maghribiyya
Kingdom of Morocco
Morocco
COUNTRY
MA
Morocco
Kingdom of Morocco
A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s.
INSDC:country:libya
ISO3166-1:434
ISO3166-1:LBY
ISO3166-1:LY
ISO3166-2:LY
Al-Jamahiriyyah al-'Arabiyyah al-Libiyyah as-Sa'biyyah al-Istirakiyyah al-'Udhma {1977-2011}
Great Socialist People's Libyan Arab Jamahiriya {1977-2011}
Kingdom of Libya {1951-1969}
Socialist People's Libyan Arab Jamahiriya {1977-2011}
State of Libya
Libya
COUNTRY
LY
Libya
Libya
A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas.
INSDC:country:ethiopia
ISO3166-1:231
ISO3166-1:ET
ISO3166-1:ETH
ISO3166-2:ET
Federal Democratic Republic of Ethiopia
ye-Ityoppya Federalawi Dimokrasiyawi Ripeblik {language: Ge'ez}
Ethiopia
COUNTRY
ET
Ethiopia
Federal Democratic Republic of Ethiopia
A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas").
INSDC:country:eritrea
ISO3166-1:232
ISO3166-1:ER
ISO3166-1:ERI
ISO3166-2:ER
Dawlat Iritriya
Hagere Ertra
State of Eritrea
Eritrea
COUNTRY
ER
Eritrea
State of Eritrea
A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts.
INSDC:country:djibouti
ISO3166-1:262
ISO3166-1:DJ
ISO3166-1:DJI
ISO3166-2:DJ
Jamhuuriyadda Jabuuti
Republic of Djibouti
Republique de Djibouti
Djibouti
COUNTRY
DJ
Djibouti
Republic of Djibouti
A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements).
INSDC:country:mauritania
ISO3166-1:478
ISO3166-1:MR
ISO3166-1:MRT
ISO3166-2:MR
Al-Jumhuriyyah al-Islamiyyah al-Muritaniyyah
Islamic Republic of Mauritania
Republique islamique de Mauritanie {language: French}
Mauritania
COUNTRY
MR
Mauritania
Islamic Republic of Mauritania
A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements.
INSDC:country:mali
ISO3166-1:466
ISO3166-1:ML
ISO3166-1:MLI
ISO3166-2:ML
French Sudan
Republic of Mali
Republique du Mali
Soudan francais
Mali
COUNTRY
ML
Mali
Republic of Mali
A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes.
INSDC:country:niger
ISO3166-1:562
ISO3166-1:NE
ISO3166-1:NER
ISO3166-2:NE
Republic of the Niger
Republique du Niger
Niger
COUNTRY
NE
Niger
Republic of Niger
A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change.
INSDC:country:chad
ISO3166-1:148
ISO3166-1:TCD
ISO3166-1:TD
ISO3166-2:TD
Jumhuriyyat Tshad {language: Arabic}
Republic of Chad
Republique du Tchad {language: French}
Chad
COUNTRY
TD
Chad
Republic of Chad
A country located in southwestern Europe on the Iberian Peninsula, plus the Balearic Islands in the Mediterranean, the Canary Islands in the Atlantic Ocean off the African coast, and two autonomous cities in North Africa that border Morocco. Spain is politically organized into 17 Autonomous Communities (comunidades autonomas) and 2 autonomous cities (ciudades autonomas) - Ceuta and Melilla. Administratively Spain also comprises fifty provinces. Seven autonomous communities are composed of only one province: Asturias, Balearic Islands, Cantabria, La Rioja, Madrid, Murcia, and Navarre. Historically, some provinces are also divided into comarcas (roughly equivalent to a US "county" or an English district). The lowest administrative division of Spain is the municipality (municipio).
INSDC:country:spain
ISO3166-1:724
ISO3166-1:ES
ISO3166-1:ESP
ISO3166-2:ES
Espana {language: Spanish}
Reino de Espana
Spain
Spain
COUNTRY
ES
Spain
Kingdom of Spain
A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland.
INSDC:country:iceland
ISO3166-1:352
ISO3166-1:IS
ISO3166-1:ISL
ISO3166-2:IS
Republic of Iceland
Iceland
COUNTRY
IS
Iceland
Iceland
A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes.
INSDC:country:benin
ISO3166-1:204
ISO3166-1:BJ
ISO3166-2:BJ
Dahomey
Republic of Benin
Republique du Benin
Benin
COUNTRY
BJ
Benin
Republic of Benin
A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes).
INSDC:country:burkina faso
ISO3166-1:854
ISO3166-1:BF
ISO3166-1:BFA
ISO3166-2:BF
Republic of Upper Volta
Republique de Haute-Volta
Burkina Faso
COUNTRY
BF
Burkina Faso
Burkina Faso
A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments.
INSDC:country:cote d'ivoire
ISO3166-1:384
ISO3166-1:CI
ISO3166-1:CIV
ISO3166-2:CI
Ivory Coast {language: English}
Republic of Cote d'Ivoire
Republique de Cote d'Ivoire
Cote d'Ivoire
COUNTRY
CI
Côte d’Ivoire
Republic of Côte d’Ivoire
A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts.
INSDC:country:gambia
ISO3166-1:270
ISO3166-1:GM
ISO3166-1:GMB
ISO3166-2:GM
Republic of The Gambia
The Gambia {alternative name}
Gambia
COUNTRY
GM
The Gambia
Republic of The Gambia
A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts.
INSDC:country:ghana
ISO3166-1:288
ISO3166-1:GH
ISO3166-1:GHA
ISO3166-2:GH
Gold Coast
Republic of Ghana
Ghana
COUNTRY
GH
Ghana
Republic of Ghana
A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip.
INSDC:country:guinea
ISO3166-1:324
ISO3166-1:GIN
ISO3166-1:GN
ISO3166-2:GN
French Guinea
Republic of Guinea
Guinea
COUNTRY
GN
Guinea
Republic of Guinea
A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea.
INSDC:country:guinea-bissau
ISO3166-1:624
ISO3166-1:GNB
ISO3166-1:GW
ISO3166-2:GW
Portuguese Guinea
Republic of Guinea-Bissau
Republica da Guinea-Bissau
Guinea-Bissau
COUNTRY
GW
Guinea-Bissau
Republic of Guinea-Bissau
A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean.
INSDC:country:liberia
ISO3166-1:430
ISO3166-1:LBR
ISO3166-1:LR
ISO3166-2:LR
Republic of Liberia
Liberia
COUNTRY
LR
Liberia
Republic of Liberia
A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs).
INSDC:country:nigeria
ISO3166-1:NG
Federal Republic of Nigeria
Republic nde Naigeria
Republik Federaal bu Niiseriya
Republik Nijeriya
Nigeria
COUNTRY
NG
Nigeria
Federal Republic of Nigeria
A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales.
INSDC:country:senegal
ISO3166-1:686
ISO3166-1:SEN
ISO3166-1:SN
ISO3166-2:SN
Republic of Senegal
Republique du Senegal
Senegal
COUNTRY
SN
Senegal
Republic of Senegal
A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts.
INSDC:country:sierra leone
ISO3166-1:694
ISO3166-1:SL
ISO3166-1:SLE
ISO3166-2:SL
Republic of Sierra Leone
Sierra Leone
COUNTRY
SL
Sierra Leone
Republic of Sierra Leone
A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located.
INSDC:country:togo
ISO3166-1:768
ISO3166-1:TG
ISO3166-1:TGO
ISO3166-2:TG
Republique Togolaise
Togolese Republic
Togo
COUNTRY
TG
Togo
Togolese Republic
A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones.
INSDC:country:belgian congo
INSDC:country:democratic republic of the congo
ISO3166-1:180
ISO3166-1:CD
ISO3166-1:COD
ISO3166-2:CD
Belgian Congo
Congo Free State
Congo Kinshasa {alternative name}
Congo-Kinshasa
Congo-Leopoldville
DR Congo
Republique democratique de Congo
Zaire
Democratic Republic of the Congo
COUNTRY
CG
Congo
Republic of the Congo
A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge).
INSDC:country:rwanda
ISO3166-1:646
ISO3166-1:RW
ISO3166-1:RWA
ISO3166-2:RW
Republic of Rwanda
Republique du Rwanda
Repubulika y'u Rwanda
Rwanda
COUNTRY
RW
Rwanda
Republic of Rwanda
A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts.
INSDC:country:republic of the congo
ISO3166-1:178
ISO3166-1:CG
ISO3166-1:COG
ISO3166-2:CG
Afrique Equatoriale Francaise
Congo Brazzaville {alternative name}
Congo-Brazzaville
French Equatorial Africa
Repubilika ya Kongo
Republiki ya Kongo
Republique du Congo
Republic of Congo
COUNTRY
CD
Democratic Republic of the Congo
Democratic Republic of the Congo
A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines.
INSDC:country:burundi
ISO3166-1:108
ISO3166-1:BDI
ISO3166-1:BI
ISO3166-2:BI
Republic of Burundi
Republika y'u Burundi
Republique du Burundi
Burundi
COUNTRY
BI
Burundi
Republic of Burundi
A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts.
INSDC:country:equatorial guinea
ISO3166-1:226
ISO3166-1:GNQ
ISO3166-1:GQ
ISO3166-2:GQ
Republic of Equatorial Guinea
Republica da Guine Equatorial
Republica de Guinea Ecuatorial
Republique de Guinee Equatoriale
Equatorial Guinea
COUNTRY
GQ
Equatorial Guinea
Republic of Equatorial Guinea
A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments.
French Equatorial Africa {former name}
INSDC:country:gabon
ISO3166-1:266
ISO3166-1:GA
ISO3166-1:GAB
ISO3166-2:GA
Gabonese Republic
Republique Gabonaise
Gabon
COUNTRY
GA
Gabon
Gabonese Republic
A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts.
INSDC:country:cameroon
ISO3166-1:120
ISO3166-1:CM
ISO3166-1:CMR
ISO3166-2:CM
Republic of Cameroon
Republique du Cameroun
Cameroon
COUNTRY
CM
Cameroon
Republic of Cameroon
A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities.
ISO3166-1:710
ISO3166-1:ZA
ISO3166-1:ZAF
ISO3166-2:ZA
IRiphabhulikhi yeNingizimu Afrika
IRiphabliki yaseMzantsi Afrika
IRiphabliki yaseNingizimu Afrika
IRiphabliki yeSewula Afrika
Rephaboliki ya Aforika Borwa
Rephaboliki ya Afrika Borwa
Rephaboliki ya Afrika-Borwa
Republiek van Suid-Afrika
Riphabliki ra Afrika Dzonga
Riphabuliki ya Afurika Tshipembe
Republic of South Africa
COUNTRY
ZA
South Africa
Republic of South Africa
A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo.
INSDC:country:angola
ISO3166-1:024
ISO3166-1:AGO
ISO3166-1:AO
ISO3166-2:AO
Repubilika ya Ngola
Republic of Angola
Republica de Angola
Angola
COUNTRY
AO
Angola
Republic of Angola
A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies.
INSDC:country:namibia
ISO3166-1:516
ISO3166-1:NA
ISO3166-1:NAM
ISO3166-2:NA
Republic of Namibia
South-West Africa
Namibia
COUNTRY
NA
Namibia
Republic of Namibia
A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts.
INSDC:country:botswana
ISO3166-1:072
ISO3166-1:BW
ISO3166-1:BWA
ISO3166-2:BW
Bechuanaland
Lefatshe la Botswana
Republic of Botswana
Botswana
COUNTRY
BW
Botswana
Republic of Botswana
A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils.
INSDC:country:lesotho
ISO3166-1:426
ISO3166-1:LS
ISO3166-1:LSO
ISO3166-2:LS
Basutoland
Kingdom of Lesotho
Muso oa Lesotho
Lesotho
COUNTRY
LS
Lesotho
Kingdom of Lesotho
A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).
INSDC:country:swaziland
ISO3166-1:748
ISO3166-1:SWZ
ISO3166-1:SZ
ISO3166-2:SZ
Kingdom of Swaziland
Umbuso weSwatini
Swaziland
COUNTRY
SZ
Swaziland
Kingdom of Swaziland
A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration.
INSDC:country:mozambique
ISO3166-1:508
ISO3166-1:MOZ
ISO3166-1:MZ
ISO3166-2:MZ
Africa Oriental Portuguesa
Portuguese East Africa
Republic of Mozambique
Republica de Mocambique
Mozambique
COUNTRY
MZ
Mozambique
Republic of Mozambique
A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province.
INSDC:country:kenya
ISO3166-1:404
ISO3166-1:KE
ISO3166-1:KEN
ISO3166-2:KE
Jamhuri ya Kenya
Republic of Kenya {fomal name}
Kenya
COUNTRY
KE
Kenya
Republic of Kenya
A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.
INSDC:country:uganda
ISO3166-1:800
ISO3166-1:UG
ISO3166-1:UGA
ISO3166-2:UG
Jamhuri ya Uganda
Republic of Uganda
Uganda
COUNTRY
UG
Uganda
Republic of Uganda
A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities).
INSDC:country:tanzania
ISO3166-1:834
ISO3166-1:TZ
ISO3166-1:TZA
ISO3166-2:TZ
Jamhuri ya Muungano wa Tanzania
United Republic of Tanzania
Tanzania
COUNTRY
TZ
Tanzania
United Republic of Tanzania
A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir.
INSDC:country:somalia
ISO3166-1:706
ISO3166-1:SO
ISO3166-1:SOM
ISO3166-2:SO
British Somaliland
Jamhuuriyadda Soomaaliya
Somali Republic
Somalia
Italian Somalia {former name}
Somalia Italiana {former name}
Somalia
COUNTRY
SO
Somalia
Federal Republic of Somalia
A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.
INSDC:country:malawi
ISO3166-1:454
ISO3166-1:MW
ISO3166-1:MWI
ISO3166-2:MW
Dziko la Malawi
Nyasaland
Republic of Malawi
Malawi
COUNTRY
MW
Malawi
Republic of Malawi
A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities.
INSDC:country:zimbabwe
ISO3166-1:716
ISO3166-1:ZW
ISO3166-1:ZWE
ISO3166-2:ZW
Republic of Rhodesia
Republic of Zimbabwe
Southern Rhodesia
Zimbabwe Rhodesia
Zimbabwe
COUNTRY
ZW
Zimbabwe
Republic of Zimbabwe
A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts.
INSDC:country:zambia
ISO3166-1:894
ISO3166-1:ZM
ISO3166-1:ZMB
ISO3166-2:ZM
Northern Rhodesia
Republic of Zambia
Zambia
COUNTRY
ZM
Zambia
Republic of Zambia
A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias).
INSDC:country:cape verde
ISO3166-1:CV
Republic of Cape Verde
Republica de Cabo Verde
Cape Verde
COUNTRY
CV
Cape Verde
Republic of Cape Verde
INSDC:country:barbados
ISO3166-1:BB
Barbados
COUNTRY
BB
Barbados
Barbados
A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias.
Al-Mamlakah al-Urdunniyyah al-Hasimiyyah
The Hashemite Kingdom of Jordan
Jordan
COUNTRY
JO
Jordan
Hashemite Kingdom of Jordan
A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia).
INSDC:country:switzerland
ISO3166-1:760
ISO3166-1:SY
ISO3166-1:SYR
ISO3166-2:SY
Al-Jumhuriyyah al-'Arabiyyah as-Suriyyah
Syrian Arab Republic
Syria
COUNTRY
SY
Syria
Syrian Arab Republic
A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions.
INSDC:country:israel
Dawlat Isra'il
Medinat Yisra'el
State of Israel
Israel
COUNTRY
IL
Israel
State of Israel
A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa).
INSDC:country:lebanon
Al-Jumhuriyyah al-Lubnaniyyah {language: Arabic}
Lebanese Republic {alternative name}
Republic of Lebanon
Lebanon
COUNTRY
LB
Lebanon
Lebanese Republic
A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios).
INSDC:country:bolivia
Bulibya Republika {language: Quechua}
Republic of Bolivia
Republica de Bolivia {language: Spanish}
Wuliwya Suyu {language: Aymara}
Bolivia
COUNTRY
BO
Bolivia
Plurinational State of Bolivia
A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils.
INSDC:country:british guiana
INSDC:country:guyana
British Guiana
Co-operative Republic of Guyana
Guyana
COUNTRY
GY
Guyana
Cooperative Republic of Guyana
A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten.
INSDC:country:suriname
Dutch Guiana {alternative name}
Nederlands Guyana {alternative name}
Netherlands Guiana {alternative name}
Republic of Suriname
Republiek Suriname
Sranan {language: Sranan Tongo}
Surinam
Suriname
COUNTRY
SR
Suriname
Republic of Suriname
A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada.
INSDC:country:canada
ISO3166-1:124
ISO3166-1:CA
ISO3166-1:CAN
ISO3166-2:CA
Canada
COUNTRY
CA
Canada
Canada
A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.
INSDC:country:united kingdom
ISO3166-1:826
ISO3166-1:GB
ISO3166-1:GBR
ISO3166-2:GB
Britain
G.B
GB
U.K. {abbrevation}
UK
United Kingdom of Great Britain and Northern Ireland
United Kingdom
COUNTRY
GB
United Kingdom
United Kingdom of Great Britain and Northern Ireland
A country that is part of the United Kingdom. Occupying the northern third of the island of Great Britain, it shares a border with England to the south and is bounded by the North Sea to the east, the Atlantic Ocean to the north and west, and the North Channel and Irish Sea to the southwest. In addition to the mainland, Scotland includes over 790 islands including the Northern Isles and the Hebrides.
ISO3166-2:GB-SCT
Scotland
One of the four constituent countries of the United Kingdom of Great Britain and Northern Ireland. It is located in the south-west of the island of Great Britain and is bordered by England to the east, the Bristol Channel (Mor Hafren) to the south and the Irish Sea (Mor Iwerddon) to the west and north, and also by the estuary of the River Dee (Afon Dyfrdwy) in the north-east. Wales is divided into 22 unitary authorities. There are nine counties, three cities, and ten county boroughs, although all have equal powers. Collectively these are known as the principal areas of Wales. They came into being on 1996-04-01.
ISO3166-2:GB-CYM
ISO3166-2:GB-WLS
Cymru {language: Welsh}
Wales
The largest and most populous constituent country of the United Kingdom of Great Britain and Northern Ireland. The subdivisions of England consists of as many as four levels of subnational division and at some levels there are a variety of types of administrative entity. They have been created for the purposes of local government in England.
ISO3166-1:GB-ENG
England
A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte).
INSDC:country:germany
Bundesrepublik Deutschland
Federal Republic of Germany
begin_date: 1990-10-03.
Germany
COUNTRY
DE
Germany
Federal Republic of Germany
A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni).
INSDC:country:italy
Italian Republic
Repubblica Italiana
Italy
COUNTRY
IT
Italy
Italian Republic
A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom.
ISO3166-1:578
ISO3166-1:NO
ISO3166-1:NOR
ISO3166-2:NO
Kongeriket Noreg {language: Norwegian}
Kongeriket Norge {language: Norwegian}
Norway
Norway
COUNTRY
NO
Norway
Kingdom of Norway
A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district.
INSDC:country:croatia
ISO3166-1:191
ISO3166-1:HR
ISO3166-1:HRV
ISO3166-2:HR
Republic of Croatia
Republika Hrvatska
Croatia
COUNTRY
HR
Croatia
Republic of Croatia
A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts.
INSDC:country:russia
Rossiyskaya Federatsiya
Russian Federation
Russian Soviet Federative Socialist Republic {1917-1991}
begin_date: 1991-12.
Russia
COUNTRY
RU
Russia
Russian Federation
A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units.
INSDC:country:ukraine
Ukrainian Soviet Socialist Republic {1917-1991}
Ukraine
COUNTRY
UA
Ukraine
Ukraine
A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004.
INSDC:country:sweden
Kingdom of Sweden
Konungariket Sverige
Sweden
COUNTRY
SE
Sweden
Kingdom of Sweden
A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government.
INSDC:country:bahamas
Commonwealth of The Bahamas
The Bahamas
COUNTRY
BS
Bahamas
Commonwealth of the Bahamas
An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.
INSDC:country:japan
Nippon-koku
Japan
COUNTRY
JP
Japan
Japan
A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia.
INSDC:country:north korea
Choson Minjujuui Inmin Konghwaguk {language: Korean}
Democratic People's Republic of Korea
North Korea
COUNTRY
KP
North Korea
Democratic People’s Republic of Korea
A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10.
INSDC:country:chile
Republic of Chile
Republica de Chile {language: Spanish}
Chile
COUNTRY
CL
Chile
Republic of Chile
A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South.
INSDC:country:brazil
ISO3166-2:BR
Brasil
Federative Republic of Brazil
Republica Federativa do Brasil {language: Portuguese}
Brazil
COUNTRY
BR
Brazil
Federative Republic of Brazil
A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages.
INSDC:country:india
Bharat Ga?arajya {language: Hindi}
Republic of India
India
A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.
INSDC:country:china
People's Republic of China
Zhonghua Renmin Gongheguo
China
COUNTRY
CN
China
People’s Republic of China
A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City.
INSDC:country:mexico
Estados Unidos Mexicanos {language: Spanish}
United Mexican States
Mexico
COUNTRY
MX
Mexico
United Mexican States
The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports.
INSDC:country:panama
ISO3166-1:591
ISO3166-1:PA
ISO3166-1:PAN
ISO3166-2:PA
Republic of Panama
Republica de Panama {language: Spanish}
Panama
COUNTRY
PA
Panama
Republic of Panama
A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan.
INSDC:country:honduras
ISO3166-1:340
ISO3166-1:HN
ISO3166-1:HND
ISO3166-2:HN
Republic of Honduras
Republica de Honduras
Spanish Honduras
Honduras
COUNTRY
HN
Honduras
Republic of Honduras
A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons.
INSDC:country:costa rica
ISO3166-1:188
ISO3166-1:CR
ISO3166-1:CRI
ISO3166-2:CR
Republic of Costa Rica
Republica de Costa Rica
Costa Rica
COUNTRY
CR
Costa Rica
Republic of Costa Rica
A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias).
INSDC:country:ecuador
Republic of Ecuador
Republica del Ecuador
Ecuador
COUNTRY
EC
Ecuador
Republic of Ecuador
A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos.
INSDC:country:argentina
Argentine Republic
Republica Argentina {language: Spanish}
Argentina
COUNTRY
AR
Argentina
Argentine Republic
A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities.
INSDC:country:colombia
Republic of Colombia
Republica de Colombia {language: Spanish}
Colombia
COUNTRY
CO
Colombia
Republic of Colombia
A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento).
INSDC:country:uruguay
Oriental Republic of Uruguay
Republica Oriental del Uruguay {language: Spanish}
Uruguay
COUNTRY
UY
Uruguay
Eastern Republic of Uruguay
A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias).
INSDC:country:venezuela
Bolivarian Republic of Venezuela
Republica Bolivariana de Venezuela {language: Spanish}
Venezuela
COUNTRY
VE
Venezuela
Bolivarian Republic of Venezuela
A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao.
INSDC:country:peru
Republic of Peru
Republica del Peru {language: Spanish}
Peru
COUNTRY
PE
Peru
Republic of Peru
A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts.
INSDC:country:paraguay
Republic of Paraguay
Republica del Paraguay {language: Spanish}
Teta Paraguaise {language: Guarani}
Paraguay
COUNTRY
PY
Paraguay
Republic of Paraguay
A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies.
INSDC:country:belize
ISO3166-1:084
ISO3166-1:BLZ
ISO3166-1:BZ
ISO3166-2:BZ
British Honduras
Belize
COUNTRY
BZ
Belize
Belize
A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios).
INSDC:country:el salvador
ISO3166-1:222
ISO3166-1:SLV
ISO3166-1:SV
ISO3166-2:SV
Republic of El Salvador
Republica de El Salvador
El Salvador
COUNTRY
SV
El Salvador
Republic of El Salvador
A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios).
INSDC:country:guatemala
ISO3166-1:320
ISO3166-1:GT
ISO3166-1:GTM
ISO3166-2:GT
Republic of Guatemala
Republica de Guatemala
Guatemala
COUNTRY
GT
Guatemala
Republic of Guatemala
A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta).
INSDC:country:finland
ISO3166-1:246
ISO3166-1:FI
ISO3166-1:FIN
ISO3166-2:FI
Republic of Finland
Republiken Finland
Suomen tasavalta
Suomi {language: Finnish}
Finland
COUNTRY
FI
Finland
Republic of Finland
A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977).
INSDC:country:belgium
ISO3166-1:056
ISO3166-1:BE
ISO3166-1:BEL
ISO3166-2:BE
Kingdom of Belgium
Konigreich Belgien {language: German}
Koninkrijk Belgie
Royaume de Belgique
Belgium
COUNTRY
BE
Belgium
Kingdom of Belgium
A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas.
INSDC:country:poland
ISO3166-1:616
ISO3166-1:PL
ISO3166-1:POL
ISO3166-2:PL
Polen {language: German}
Republic of Poland
Rzeczpospolita Polska
Rzeczpospolita Polska {language: German}
Poland
COUNTRY
PL
Poland
Republic of Poland
A country whose metropolitan territory is located in Western Europe and that also comprises various overseas islands and territories located in other continents. France is divided into 26 administrative regions. 22 are in metropolitan France (21 are on the continental part of metropolitan France; one is the territorial collectivity of Corsica), and four are overseas regions. The regions are further subdivided into 100 departments which are numbered (mainly alphabetically). Four of these departments are found in the overseas regions and are simultaneously overseas regions and overseas departments and are an integral part of France (and the European Union) and thus enjoy a status similar to metropolitan departments. The 100 departments are subdivided into 341 arrondissements which are, in turn, subdivided into 4,032 cantons. These cantons are then divided into 36,680 communes, which are municipalities with an elected municipal council. There also exist 2,588 intercommunal entities grouping 33,414 of the 36,680 communes (i.e. 91.1% of all the communes). Three communes, Paris, Lyon and Marseille are also subdivided into 45 municipal arrondissements.
INSDC:country:france
ISO3166-1:250
ISO3166-1:FR
ISO3166-1:FRA
ISO3166-2:FR
France {alternative name}
Republique francaise {language: French}
France
COUNTRY
FR
France
French Republic
A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy.
INSDC:country:switzerland
Confederation suisse
Confederazione Svizzera
Confederaziun svizra
Schweizerische Eidgenossenschaft
Swiss Confederation
Switzerland
COUNTRY
CH
Switzerland
Swiss Confederation
A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities.
INSDC:country:austria
ISO3166-1:040
ISO3166-1:AT
ISO3166-1:AUT
ISO3166-2:AT
Republic of Austria
Republik Osterreich
Austria
COUNTRY
AT
Austria
Republic of Austria
A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties.
ISO3166-1:372
ISO3166-1:IE
ISO3166-1:IRL
ISO3166-2:IE
Eire {1937-12-29-to-1949-04-18}
Irish Free State {1921-12-06-to-1937-12-29}
Poblacht na hEireann
Ireland
COUNTRY
IE
Ireland
Ireland
A country in southwestern Europe on the Iberian Peninsula and including the Atlantic archipelagos of the Azores and Madeira are also part of Portugal. Portugal is divided into 308 municipalities (Portuguese singular/plural: concelho/concelhos), which are subdivided into more than 4,000 parishes (freguesia/freguesias). Municipalities are grouped for administrative purposes into superior units. For continental Portugal the municipalities are gathered in 18 Districts, while the Islands have a Regional Government directly above them.
INSDC:country:portugal
ISO3166-1:620
ISO3166-1:PRT
ISO3166-1:PT
ISO3166-2:PT
Portugal {alternative name}
Republica Portuguesa
Portugal
COUNTRY
PT
Portugal
Portuguese Republic
A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia.
INSDC:country:greece
ISO3166-1:300
ISO3166-1:GR
ISO3166-1:GRC
ISO3166-2:GR
Elliniki Dimokratia
Hellenic Republic
Greece
COUNTRY
GR
Greece
Hellenic Republic
A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest.
INSDC:country:luxembourg
ISO3166-1:442
ISO3166-1:LU
ISO3166-1:LUX
ISO3166-2:LU
Grand Duchy of Luxembourg
Grand-Duche de Luxembourg {language: French}
Grossherzogtum Luxemburg {language: German}
Groussherzogtum Letzebuerg {language: Luxembourgish}
Luxemburg
Luxembourg
COUNTRY
LU
Luxembourg
Grand Duchy of Luxembourg
A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes.
INSDC:country:andorra
ISO3166-1:020
ISO3166-1:AD
ISO3166-1:AND
ISO3166-2:AD
Andorre {language: French}
Principality of Andorra
Principat d'Andorra
Principat d'Andorra {language: Catalan}
Andorra
COUNTRY
AD
Andorra
Principality of Andorra
A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities.
INSDC:country:bulgaria
ISO3166-1:100
ISO3166-1:BG
ISO3166-1:BGR
ISO3166-2:BG
Kingdom of Bulgaria
People's Republic of Bulgaria
Republic of Bulgaria
Republika Balgariya
Bulgaria
COUNTRY
BG
Bulgaria
Republic of Bulgaria
A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities).
INSDC:country:romania
ISO3166-1:642
ISO3166-1:RO
ISO3166-1:ROU
ISO3166-2:RO
Roumania
Rumania
Romania
COUNTRY
RO
Romania
Romania
A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary.
INSDC:country:hungary
Magyar Koztarsasag
Republic of Hungary
Hungary
COUNTRY
HU
Hungary
Hungary
A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna).
INSDC:country:albania
ISO3166-1:008
ISO3166-1:AL
ISO3166-1:ALB
ISO3166-2:AL
Republic of Albania
Republika e Shqiperise
Shqiperia
Albania
COUNTRY
AL
Albania
Republic of Albania
A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices.
INSDC:country:czech republic
INSDC:country:czechoslovakia
ISO3166-1:203
ISO3166-1:CZ
ISO3166-1:CZE
ISO3166-2:CZ
Ceska republika
Czechoslovakia
Czech Republic
COUNTRY
CZ
Czech Republic
Czech Republic
A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status.
INSDC:country:slovenia
ISO3166-1:705
ISO3166-1:SI
ISO3166-1:SVN
ISO3166-2:SI
Republic of Slovenia
Republika Slovenija
Slovenia
COUNTRY
SI
Slovenia
Republic of Slovenia
A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts.
INSDC:country:slovakia
Czechoslovakia
Slovakia
Slovenska republika
Slovakia
COUNTRY
SK
Slovakia
Slovak Republic
A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities).
INSDC:country:serbia
ISO3166-1:688
ISO3166-1:RS
ISO3166-1:SRB
ISO3166-2:RS
Republic of Serbia
Republika Srbija
Serbia
COUNTRY
RS
Serbia
Republic of Serbia
A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions.
INSDC:country:latvia
ISO3166-1:428
ISO3166-1:LV
ISO3166-1:LVA
ISO3166-2:LV
Latvian Soviet Socialist Republic {1940-1991}
Latvijas Republika
Republic of Latvia
ISO3166-2 codes for 2009 revision of admin. units seem not to have been assigned.
Latvia
COUNTRY
LV
Latvia
Republic of Latvia
A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities.
INSDC:country:estonia
ISO3166-1:233
ISO3166-1:EE
ISO3166-1:EST
ISO3166-2:EE
Eesti Vabariik
Estland {language: German}
Estonian Soviet Socialist Republic {1940-1991}
Republic of Estonia
Viro {language: Finnish}
Estonia
COUNTRY
EE
Estonia
Republic of Estonia
A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos).
INSDC:country:lithuania
ISO3166-1:440
ISO3166-1:LT
ISO3166-1:LTU
ISO3166-2:LT
Lietuvos Respublika
Lithuanian Soviet Socialist Republic {1940-1990}
Republic of Lithuania
Lithuania
COUNTRY
LT
Lithuania
Republic of Lithuania
A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya.
INSDC:country:nicaragua
ISO3166-1:558
ISO3166-1:NI
ISO3166-1:NIC
ISO3166-2:NI
Republic of Nicaragua
Republica de Nicaragua {language: Spanish}
Nicaragua
COUNTRY
NI
Nicaragua
Republic of Nicaragua
A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello).
INSDC:country:san marino
ISO3166-1:674
ISO3166-1:SM
ISO3166-1:SMR
ISO3166-2:SM
Most Serene Republic of San Marino
Serenissima Repubblica di San Marino
San Marino
COUNTRY
SM
San Marino
Republic of San Marino
A landlocked sovereign city-state whose territory consists of a walled enclave within the City of Rome. It includes extraterritorial buildings and property in Rome and elsewhere it Italy.
ISO3166-1:336
ISO3166-1:VA
ISO3166-1:VAT
ISO3166-2:VA
State of the Vatican City
Stato della Citta del Vaticano
Status Civitatis Vaticanae
The Holy See {alternative name}
Vatican City
COUNTRY
VA
the Holy See/ Vatican City State
the Holy See/ Vatican City State
An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan).
INSDC:country:indonesia
Republic of Indonesia
Republik Indonesia
Indonesia
COUNTRY
ID
Indonesia
Republic of Indonesia
A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province.
INSDC:country:siam
INSDC:country:thailand
Kingdom of Thailand
Ratcha Anachak Thai
Thailand
COUNTRY
TH
Thailand
Kingdom of Thailand
A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations").
INSDC:country:bangladesh
Gonoprojatontri Bangladesh {language: Bengali}
People's Republic of Bangladesh
Bangladesh
COUNTRY
BD
Bangladesh
People’s Republic of Bangladesh
The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia.
INSDC:country:viet nam
Socialist Republic of Vietnam
Vietnam
Viet Nam
COUNTRY
VN
Vietnam
Socialist Republic of Vietnam
A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba.
INSDC:country:cuba
Republic of Cuba
Republica de Cuba
Cuba
COUNTRY
CU
Cuba
Republic of Cuba
An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands.
INSDC:country:trinidad and tobago
ISO3166-1:780
ISO3166-1:TT
ISO3166-1:TTO
ISO3166-2:TT
Republic of Trinidad and Tobago
Trinidad and Tobago
COUNTRY
TT
Trinidad and Tobago
Republic of Trinidad and Tobago
A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance.
INSDC:country:jamaica
Jamaica
COUNTRY
JM
Jamaica
Jamaica
A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards.
INSDC:country:monaco
ISO3166-1:492
ISO3166-1:MC
ISO3166-1:MCO
ISO3166-2:MC
Principality of Monaco
Principaute de Monaco
Monaco
COUNTRY
MC
Monaco
Principality of Monaco
A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county).
INSDC:country:liechtenstein
ISO3166-1:438
ISO3166-1:LI
ISO3166-1:LIE
ISO3166-2:LI
Furstentum Liechtenstein
Principality of Liechtenstein
Liechtenstein
COUNTRY
LI
Liechtenstein
Principality of Liechtenstein
A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic.
ISO3166-1:498
ISO3166-1:MD
ISO3166-1:MDA
ISO3166-2:MD
Moldavia
Moldavian Soviet Socialist Republic {1940-1991}
Republic of Moldova
Republica Moldova
Moldova
COUNTRY
MD
Moldova
Republic of Moldova
A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages).
INSDC:country:brunei
Negara Brunei Darussalam
State of Brunei, Abode of Peace
Brunei Darussalam
COUNTRY
BN
Brunei
Brunei Darussalam
A country that consists of thirteen states and three federal territories in Southeast Asia. The country is separated into two regions, Peninsular Malaysia and Malaysian Borneo, by the South China Sea. Malaysia borders Thailand, Indonesia, Singapore, Brunei and the Philippines. Malaysia consists of 13 states (Negeri) and 3 federal territories.
INSDC:country:malaysia
Malaysia
COUNTRY
MY
Malaysia
Malaysia
A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog.
INSDC:country:bhutan
Druk Yul {language: Dzongkha}
Kingdom of Bhutan
Bhutan
COUNTRY
BT
Bhutan
Kingdom of Bhutan
INSDC:country:papua new guinea
PNG
The Independent State of Papua New Guinea
Papua New Guinea
COUNTRY
PG
Papua New Guinea
Independent State of Papua New Guinea
An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role.
INSDC:country:singapore
Republic of Singapore
Republik Singapura {language: Malay}
Singapore
COUNTRY
SG
Singapore
Republic of Singapore
An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats.
INSDC:country:sri lanka
Ceylon
Democratic Socialist Republic of Sri Lanka
Sri Lanka
COUNTRY
LK
Sri Lanka
Democratic Socialist Republic of Sri Lanka
An island at the south end of the Malay Archipelago, divided between the independent State of East Timor, and West Timor, part of the Indonesian province of East Nusa Tenggara.
Timor
COUNTRY
TL
Timor-Leste
Democratic Republic of Timor-Leste
A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes).
INSDC:country:egypt
ISO3166-1:818
ISO3166-1:EG
ISO3166-1:EGY
ISO3166-2:EG
Arab Republic of Egypt
Gumhuriyyat Misr al-'Arabiyyah
Kemet {language: Egyptian}
Kimi {language: Coptic}
Masr {language: Egyptian Arabic}
Misr {language: Arabic}
The 2nd level administrative regions of Egypt are very confusuing and different sources conflicting. Those in gaz.obo are from GeoHive (http://www.xist.org/default1.aspx) and are not fully in agreement with those from the WHO (the file EGY_SALB_table.xls downloaded from http://www.who.int/whosis/database/gis/salb/salb_coding.aspx#DATA).
Egypt
COUNTRY
EG
Egypt
Arab Republic of Egypt
A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio).
INSDC:country:dominican republic
Republica Dominicana
Dominican Republic
COUNTRY
DO
Dominican Republic
Dominican Republic
A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions.
INSDC:country:haiti
Repiblik d Ayiti
Republic of Haiti
Republique d'Hauti
Haiti
COUNTRY
HT
Haiti
Republic of Haiti
A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital.
INSDC:country:armenia
ISO3166-1:051
ISO3166-1:AM
ISO3166-1:ARM
ISO3166-2:AM
Armenian Soviet Socialist Republic {1920-1991}
Hayastani Hanrapetut'yun {language: Armenian}
Republic of Armenia
Armenia
COUNTRY
AM
Armenia
Republic of Armenia
A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions.
INSDC:country:nepal
Federal Democratic Republic of Nepal
Kingdom of Nepal {<2007}
Sanghiya Loktantrik Ganatantra Nepal {language: Nepali}
Nepal
COUNTRY
NP
Nepal
Federal Democratic Republic of Nepal
A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan).
INSDC:country:iran
Islamic Republic of Iran
Jomhuri-ye Eslami-ye Iran
Persia
Iran
COUNTRY
IR
Iran
Islamic Republic of Iran
A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts).
INSDC:country:iraq
Jumhuriyat Al-'Iraq {language: Arabic}
Komare Iraq {language: Kurdish}
Republic of Iraq
Iraq
COUNTRY
IQ
Iraq
Republic of Iraq
An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays.
INSDC:country:philippines
Republic of the Philippines
Republika ng Pilipinas
The Philippines
COUNTRY
PH
Philippines
Republic of the Philippines
A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika).
INSDC:country:azerbaijan
ISO3166-1:031
ISO3166-1:AZ
ISO3166-1:AZE
ISO3166-2:AZ
Azarbaycan Respublikasi {language: Azerbaijani}
Azerbaijan Soviet Socialist Republic {1920-1991}
Azerbaydzhan
Republic of Azerbaijan
Azerbaijan
COUNTRY
AZ
Azerbaijan
Republic of Azerbaijan
A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni).
INSDC:country:georgia
ISO3166-1:268
ISO3166-1:GE
ISO3166-1:GEO
ISO3166-2:GE
Georgian Soviet Socialist Republic {1921-1991}
Sakartvelo {language: Georgian}
begin_date: 1936-12-05. end_date: 1990-10-20.
Georgia
COUNTRY
GE
Georgia
Georgia
A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar).
INSDC:country:uzbekistan
O'zbekiston Respublikasi
Republic of Uzbekistan
Uzbek Soviet Socialist Republic {1924-1991}
begin_date: 1991-12-31.
Uzbekistan
COUNTRY
UZ
Uzbekistan
Republic of Uzbekistan
A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions.
INSDC:country:kazakhstan
Kazachstan
Kazakh Soviet Socialist Republic {1936-1991}
Republic of Kazakhstan
Geographically the western regions of Kazakhstan may be in Europe.
Kazakhstan
COUNTRY
KZ
Kazakhstan
Republic of Kazakhstan
A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city.
INSDC:country:turkmenistan
Republic of Turkmenistan
Turcmenistan
Turkmen Soviet Socialist Republic {1921-1991}
Turkmenistan
COUNTRY
TM
Turkmenistan
Turkmenistan
A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan.
INSDC:country:pakistan
Islami Jumhuriyah Pakistan
Islamic Republic of Pakistan
Pakistan
COUNTRY
PK
Pakistan
Islamic Republic of Pakistan
A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates.
INSDC:country:saudi arabia
Kingdom of Saudi Arabia
al-Mamlaka al-'Arabiyya as-Su'udiyya
Saudi Arabia
COUNTRY
SA
Saudi Arabia
Kingdom of Saudi Arabia
A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates.
INSDC:country:bahrain
Kingdom of Bahrain
Mamlakat al-Bahrayn
Bahrain
COUNTRY
BH
Bahrain
Kingdom of Bahrain
A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain.
INSDC:country:united arab emirates
Dowlat Al-Imarat al-'Arabiya al-Muttahida
UAE
United Arab Emirates
COUNTRY
AE
United Arab Emirates
United Arab Emirates
A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat).
INSDC:country:oman
Sultanate of Oman
Oman
COUNTRY
OM
Oman
Sultanate of Oman
A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001).
INSDC:country:yemen
Al-Jumhuriyyah al-Yamaniyyah
Republic of Yemen
Yemen
COUNTRY
YE
Yemen
Republic of Yemen
A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah).
INSDC:country:kuwait
Dawlat al-Kuwayt
State of Kuwait
Kuwait
COUNTRY
KW
Kuwait
State of Kuwait
An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts).
INSDC:country:qatar
Dawlat Al-Qatar
State of Qatar
Qatar
COUNTRY
QA
Qatar
State of Qatar
A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities.
INSDC:country:taiwan
Jhonghua Minguo
Taiwan
Republic of China
COUNTRY
TW
Taiwan
Taiwan
An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique.
INSDC:country:comoros
Union of the Comoros
Comoros
COUNTRY
KM
Comoros
Union of the Comoros
A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships.
INSDC:country:afghanistan
ISO3166-1:004
ISO3166-1:AF
ISO3166-1:AFG
ISO3166-2:AF
De Afganistan Islami Jomhoriyat
Islamic Republic of Afghanistan
Jamhuri-ye Islami-ye Afganistan
Afghanistan
COUNTRY
AF
Afghanistan
Islamic Republic of Afghanistan
An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean.
INSDC:country:antigua and barbuda
ISO3166-1:028
ISO3166-1:AG
ISO3166-1:ATG
ISO3166-2:AG
Antigua and Barbuda
COUNTRY
AG
Antigua and Barbuda
Antigua and Barbuda
A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital.
GAZ:00005045
INSDC:country:belarus
ISO3166-1:112
ISO3166-1:BLR
ISO3166-1:BY
ISO3166-2:BY
Belarusian Soviet Socialist Republic {1919-1991}
Belorussia
Bialorus {language: Polish}
Byelorussia
Republic of Belarus
begin_date: 1990-07-27.
Belarus
COUNTRY
BY
Belarus
Republic of Belarus
A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina.
INSDC:country:bosnia and herzegovina
ISO3166-1:070
ISO3166-1:BA
ISO3166-1:BIH
ISO3166-2:BA
Bosna i Hercegovina
Bosnia and Herzegovina
COUNTRY
BA
Bosnia and Herzegovina
Bosnia and Herzegovina
A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand.
INSDC:country:cambodia
Cambodge {language: French}
Kampuchea
Kingdom of Cambodia
Preah Reacheanachakr Kampuchea {language: Khmer}
Cambodia
COUNTRY
KH
Cambodia
Kingdom of Cambodia
A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang).
INSDC:country:laos
Lao People's Democratic Republic
Sathalanalat Paxathipatai Paxaxon Lao
Laos
COUNTRY
LA
Laos
Lao People’s Democratic Republic
An island nation in the Caribbean Sea. Dominica is divided into ten parishes.
INSDC:country:dominica
Commonwealth of Dominica
Dominica
COUNTRY
DM
Dominica
Commonwealth of Dominica
An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population.
Fidji
Republic of the Fiji Islands
Fiji
COUNTRY
FJ
Fiji
Republic of Fiji
A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions).
INSDC:country:kyrgyzstan
Kirghiz Soviet Socialist Republic {1936-1991}
Kyrgyz Republic
Kyrgyz Respublikasi
Kyrgyzskaya Respublika
Kyrgyzstan
An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea).
INSDC:country:kiribati
ISO3166-1:296
ISO3166-1:KI
ISO3166-1:KIR
ISO3166-2:KI
Republic of Kiribati
Kiribati
COUNTRY
KG
Kyrgyzstan
Kyrgyz Republic
A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts.
INSDC:country:former yugoslav republic of macedonia
ISO3166-1:807
ISO3166-1:MK
ISO3166-1:MKD
ISO3166-2:MK
Republic of Macedonia
Republika Makedonija
The former Yugoslav Republic of Macedonia
Macedonia
COUNTRY
MK
Former Yugoslav Republic of Macedonia, the
Former Yugoslav Republic of Macedonia, the. This code is in accordance with ISO 3166-2, code taken from name in Macedonian: Makedonija.
A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality.
INSDC:country:montenegro
ISO3166-1:499
ISO3166-1:ME
ISO3166-1:MNE
ISO3166-2:ME
Crna Gora {language: Montenegrin}
Republic of Montenegro
Montenegro
COUNTRY
ME
Montenegro
Montenegro
A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages.
INSDC:country:burma
INSDC:country:myanmar
Burma
Pyi-daung-zu Myan-ma Naing-ngan-daw {language: Burmese}
Union of Myanma
Myanmar
COUNTRY
MM
Myanmar/Burma
Myanmar/Burma
An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies.
INSDC:country:nauru
Republic of Nauru
Ripublik Naoero
Nauru
COUNTRY
NR
Nauru
Republic of Nauru
An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state.
ISO3166-1:570
ISO3166-1:NIU
ISO3166-1:NU
ISO3166-2:NU
Niue
Niue Fekai
COUNTRY
NU
Niue
Niue
A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines.
GAZ:00006904
INSDC:country:palau
ISO3166-1:585
ISO3166-1:PLW
ISO3166-1:PW
ISO3166-2:PW
PW
Republic of Palau
The Republic of Palau
Palau
COUNTRY
PW
Palau
Republic of Palau
A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis.
INSDC:country:saint kitts and nevis
ISO3166-1:659
ISO3166-1:KN
ISO3166-1:KNA
ISO3166-2:KN
Federation of Saint Christopher and Nevis
Federation of Saint Kitts-Nevis
Saint Kitts and Nevis
Saint Kitts-Nevis
COUNTRY
KN
Saint Kitts and Nevis
Federation of Saint Kitts and Nevis
An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean.
INSDC:country:saint lucia
ISO3166-1:662
ISO3166-1:LC
ISO3166-1:LCA
ISO3166-2:LC
Saint Lucia
COUNTRY
LC
Saint Lucia
Saint Lucia
A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts).
INSDC:country:samoa
ISO3166-1:882
ISO3166-1:WS
ISO3166-1:WSM
ISO3166-2:WS
Independent State of Samoa
Malo Sa'oloto Tuto'atasi o Samoa
Western Samoa {<1997}
Samoa
COUNTRY
AS
American Samoa
American Samoa: territory of the USA.
A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion).
INSDC:country:tajikistan
Jumhurii Tojikiston
Republic of Tajikistan
Tadzhikistan
Tajik Soviet Socialist Republic {1929-1991}
Tajikistan
COUNTRY
TJ
Tajikistan
Republic of Tajikistan
An island nation in the Pacific Ocean.
Friendly Islands
Kingdom of Tonga
Tonga
COUNTRY
TO
Tonga
Kingdom of Tonga
An island nation located in the South Pacific Ocean.
INSDC:country:vanuatu
ISO3166-1:548
ISO3166-1:VU
ISO3166-1:VUT
ISO3166-2:VU
Anglo-French Condominium of the New Hebrides {<1980}
Condominium des Nouvelles-Hebrides {<1980}
Republic of Vanuatu
Republique de Vanuatu {language: French}
Ripablik blong Vanuatu {language: Bislama}
Vanuatu
COUNTRY
VU
Vanuatu
Republic of Vanuatu
An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29).
INSDC:country:sao tome and principe
Democratic Republic of Sao Tome and Principe
Republica Democratica de Sao Tome e Principe
Sao Tome and Principe
COUNTRY
ST
São Tomé and PrÃncipe
Democratic Republic of São Tomé and PrÃncipe
A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status.
INSDC:country:mongolia
Mongol uls
Mongolia
COUNTRY
MN
Mongolia
Mongolia
A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia.
GAZ:00009563
INSDC:country:tuvalu
ISO3166-1:798
ISO3166-1:TUV
ISO3166-1:TV
ISO3166-2:TV
District (Tuvalu)
Tuvalu
COUNTRY
TV
Tuvalu
Tuvalu
A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija.
INSDC:country:kosovo
Autonomna Pokrajina Kosovo i Metohija
Autonomous Province of Kosovo
Autonomous Province of Kosovo and Metohija
Kosova {language: Albanian}
Republic of Kosovo
Republika e Kosoves
Kosovo
A former state. The six countries that were once part of Yugoslavia are Bosnia-Herzegovina, Croatia, Macedonia, Montenegro, Serbia, and Slovenia.
INSDC:country:yugoslavia
Democratic Federation of Yugoslavia
Federal People's Republic of Yugoslavia
Jugoslavia
Socialist Federal Republic of Yugoslavia
begin_date: 1943-11-29. end_date: 1991-06-25. Previous to 1943: Kingdom of Yugoslavia, begins_in: 1918-12-01; end_date: 1941-04_17.
[Former] Yugoslavia
A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel.
INSDC:country:south sudan
ISO3166-1:728
ISO3166-1:SS
ISO3166-1:SSD
ISO3166-2:SS
Autonomous Government of Southern Sudan
Republic of South Sudan
Southern Sudan
South Sudan
COUNTRY
SS
South Sudan
Republic of South Sudan
A populated place. A village.
INSDC:country:tokelau
Tokelau
COUNTRY
TK
Tokelau
Tokelau: territory of New Zealand.
An island nation in the Lesser Antilles chain of the Caribbean Sea.
INSDC:country:saint vincent and the grenadines
ISO3166-1:670
ISO3166-1:VC
ISO3166-1:VCT
ISO3166-2:VC
Saint Vincent and the Grenadines
COUNTRY
VC
Saint Vincent and the Grenadines
Saint Vincent and the Grenadines
INSDC:country:grenada
Grenada
COUNTRY
GD
Grenada
Grenada
example to be eventually removed
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.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
PERSON:Alan Ruttenberg
organizational term
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."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
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.
pending final vetting
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
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.
Alan Ruttenberg
group:OBI
requires discussion
NCBITaxon:1031542
Campylobacter volucris
NCBITaxon:1031919
Campylobacter sputorum biovar faecalis
NCBITaxon:1045010
Escherichia coli O157
PARAM
RF-00000202-MCG
VTEC O157
NCBITaxon:1055535
Escherichia coli O111
PARAM
RF-00000182-MCG
VTEC O111
NCBITaxon:1055536
Escherichia coli O103
PARAM
RF-00000175-MCG
VTEC O103
NCBITaxon:1078021
Escherichia coli O113:H21
PARAM
RF-00000181-MCG
VTEC O113
NCBITaxon:1078032
Escherichia coli O45:H2
PARAM
RF-00003254-PAR
VTEC O45
NCBITaxon:108619
Salmonella enterica subsp. enterica serovar Newport
PARAM
RF-00000960-MCG
NCBITaxon:1095706
Escherichia coli O18
PARAM
RF-00003235-PAR
VTEC O18
NCBITaxon:119231
Campylobacter faecalis
NCBITaxon:1232152
Escherichia coli O103:H11
PARAM
RF-00000175-MCG
VTEC O103
NCBITaxon:1244531
Campylobacter iguaniorum
NCBITaxon:1365258
Escherichia coli 151_06
PARAM
RF-00003301-PAR
VTEC O151
NCBITaxon:1448857
Campylobacter corcagiensis
NCBITaxon:149385
Salmonella enterica subsp. enterica serovar Hadar
PARAM
RF-00001843-MCG
NCBITaxon:149539
Salmonella enterica subsp. enterica serovar Enteritidis
PARAM
RF-00002135-MCG
NCBITaxon:1507806
Campylobacter fetus subsp. testudinum
NCBITaxon:1780362
Campylobacter geochelonis
NCBITaxon:1813019
Campylobacter hepaticus
NCBITaxon:1848766
Campylobacter ornithocola
NCBITaxon:192953
Salmonella enterica subsp. enterica serovar Stanley
PARAM
RF-00001316-MCG
NCBITaxon:195
Campylobacter hyoilei
Vibrio coli
Campylobacter coli
PARAM
RF-00000054-MCG
NCBITaxon:196
Spirillum fetus
Vibrio fetus
Campylobacter fetus
PARAM
RF-00000055-MCG
NCBITaxon:1965231
Campylobacter pinnipediorum
NCBITaxon:197
Ampylobacter jejuni
Vibrio hepaticus
Vibrio jejuni
Campylobacter jejuni
PARAM
RF-00000061-MCG
NCBITaxon:198
Campylobacter hyointestinalis
PARAM
RF-00000058-MCG
NCBITaxon:199
Campylobacter concisus
NCBITaxon:200
Campylobacter curvus
PARAM
RF-00000049-MCG
NCBITaxon:201
Campylobacter lari
PARAM
RF-00000048-MCG
NCBITaxon:202
Campylobacter mucosalis
PARAM
RF-00000047-MCG
NCBITaxon:203
Wolinella recta
Campylobacter rectus
PARAM
RF-00000045-MCG
NCBITaxon:204
Campylobacter showae
NCBITaxon:205
Campylobacter spp
PARAM
RF-00000042-MCG
NCBITaxon:206
Campylobacter sputorum
PARAM
RF-00000064-MCG
NCBITaxon:207
Campylobacter jejuni-like bacterium
NCBITaxon:244317
Escherichia coli O128:H2
PARAM
RF-00000184-MCG
VTEC O128
NCBITaxon:244319
Escherichia coli O26:H11
PARAM
RF-00000139-MCG
VTEC O26
NCBITaxon:260714
Campylobacter insulaenigrae
NCBITaxon:28079
Campylobacter mucosalis-like bacterium
NCBITaxon:28080
Campylobacter upsaliensis
PARAM
RF-00000043-MCG
NCBITaxon:28898
Campylobacter helveticus
NCBITaxon:28901
Salmonella enterica
PARAM
RF-00003200-PAR
NCBITaxon:303118
Campylobacter lawrenci
Campylobacter lawrenceae
NCBITaxon:32019
Campylobacter fetus fetus
Vibrio fetus subsp. Intestinalis
Campylobacter fetus subsp. fetus
PARAM
RF-00000056-MCG
NCBITaxon:32020
Campylobacter fetus venerealis
Vibrio foetus venerealis
Campylobacter fetus subsp. venerealis
PARAM
RF-00000057-MCG
NCBITaxon:32023
Campylobacter sputorum subsp. bubulus
PARAM
RF-00000065-MCG
NCBITaxon:32024
Campylobacter sputorum biovar sputorum
PARAM
RF-00000067-MCG
NCBITaxon:363569
Salmonella enterica subsp. enterica serovar Javiana
PARAM
RF-00000895-MCG
NCBITaxon:374106
Campylobacter cuniculorum
NCBITaxon:376725
Escherichia coli O103:H2
PARAM
RF-00000175-MCG
VTEC O103
NCBITaxon:397454
Escherichia coli O142:H6
PARAM
RF-00002684-PAR
VTEC O142
NCBITaxon:404394
Escherichia coli O26:NM
PARAM
RF-00000139-MCG
VTEC O26
NCBITaxon:404399
Escherichia coli O26
PARAM
RF-00000139-MCG
VTEC O26
NCBITaxon:449520
Campylobacter canadensis
NCBITaxon:48409
Salmonella enterica subsp. enterica serovar Virchow
PARAM
RF-00001152-MCG
NCBITaxon:488546
Campylobacter peloridis
NCBITaxon:497724
Campylobacter subantarcticus
NCBITaxon:522485
Campylobacter avium
NCBITaxon:54736
Salmonella bongori
PARAM
RF-00001328-PAR
NCBITaxon:59201
Salmonella enterica subsp. enterica
PARAM
RF-00003052-MCG
NCBITaxon:593874
Campylobacter sputorum biovar paraureolyticus
NCBITaxon:595
Salmonella enterica subsp. enterica serovar Infantis
PARAM
RF-00001894-MCG
NCBITaxon:590
Salmonella spp
PARAM
RF-00000304-MCG
NCBITaxon:611
Salmonella enterica subsp. enterica serovar Heidelberg
PARAM
RF-00001957-MCG
NCBITaxon:654366
Campylobacter troglodytis
NCBITaxon:75658
Campylobacter lanienae
NCBITaxon:76517
Candidatus Campylobacter hominis
Campylobacter hominis
PARAM
RF-00000051-MCG
NCBITaxon:824
Bacteroides gracilis
Campylobacter gracilis
PARAM
RF-00000053-MCG
NCBITaxon:827
Campylobacter ureolyticus
NCBITaxon:90371
Salmonella enterica subsp. enterica serovar Typhimurium
PARAM
RF-00002265-MCG
NCBITaxon:91352
Campylobacter hyointestinalis subsp. hyointestinalis
PARAM
RF-00000060-MCG
NCBITaxon:91353
Campylobacter hyointestinalis subsp. lawsonii
PARAM
RF-00000059-MCG
NCBITaxon:991913
Escherichia coli O103:H25
PARAM
RF-00000175-MCG
VTEC O103
NCBITaxon:991915
Escherichia coli O121:H19
PARAM
RF-00000177-MCG
VTEC O121
NCBITaxon:991919
Escherichia coli O145:NM
PARAM
RF-00000155-MCG
VTEC O145
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
kilogram
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
kg
kilogram
UNIT
G167A
gram
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
g
gram
UNIT
G148A
milligram
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
mg
milligram
microgram
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
ug
microgram
nanogram
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
ng
nanogram
picogram
A mass unit which is equal to 10^[-12] g.
pg
picogram
en
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Alan Ruttenberg
Allyson Lister
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James A. Overton
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philip Lord
Philippe Rocca-Serra
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
2009-07-31
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
OWL-DL
An ontology for the annotation of biomedical and functional genomics experiments.
http://creativecommons.org/licenses/by/4.0/
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
2018-08-27
2019-06-05
Detection
ANLYTYP
AT01A
Detection
Serotyping
ANLYTYP
AT02A
Serotyping
Phagetyping
ANLYTYP
AT03A
Phagetyping
Susceptibility test
ANLYTYP
AT04A
Susceptibility test
Speciation
ANLYTYP
AT05A
Speciation
Screening
ANLYTYP
AT06A
Screening
Quantification
ANLYTYP
AT07A
Quantification
Confirmation
ANLYTYP
AT08A
Confirmation
Determination
ANLYTYP
AT09A
Determination
Enumeration
ANLYTYP
AT10A
Enumeration
Isolate characterisation
ANLYTYP
AT11A
Isolate characterisation
Discriminatory test
ANLYTYP
AT12A
Discriminatory test
Molecular characterisation/genotyping
ANLYTYP
AT13A
Molecular characterisation/genotyping
Cyprus
COUNTRY
CY
Cyprus
Republic of Cyprus
Denmark
COUNTRY
DK
Denmark
Kingdom of Denmark
European Union
COUNTRY
EU
European Union
European Union
South Korea
COUNTRY
KR
South Korea
Republic of Korea
Malta
COUNTRY
Malta
MT
Republic of Malta
Netherlands
COUNTRy
NL
Netherlands
Netherlands: use ‘the Netherlands’ not Holland, which is only part of the Netherlands (the provinces of North and South Holland); a capital T is not necessary on ‘the’. In tables ‘Netherlands’ will suffice.
United States of America
COUNTRY
US
United States
United States of America
Non European Union
COUNTRY
XE
broilers
broiler chickens
MTX
A0C78
Gallus gallus broiler
Gallus gallus animals raised for meat production purposes. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Broiler
'broiler chicken','broiler chickens','broiler','broilers','meat chicken','meat chickens','meat poultry','broiler poultry','slaughter chicken','slaughter chickens','slaughter poultry'
'dairy cow','dairy cows','daity cattle','milk cow','milk cows','milk cattle'
dairy cows
dairy cattle
MTX
A0C9L
Dairy cows
Cattle having reached the physical maturity, for milk production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Dairy_cattle
beef cows
beef cattle
MTX
A0C9Q
Meat production cattle
Cattle having reached the physical maturity, for meat production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Beef_cattle
'beef cattle','beef cows','meat cattle','meat cows'
whole organism sample
fluid sample
organ/tissue sample
excreta sample
swab sample
https://github.com/SVA-SE/AHSURED/wiki
case detection
https://github.com/SVA-SE/AHSURED/wiki
demonstration of disease freedom
https://github.com/SVA-SE/AHSURED/wiki
early detection
https://github.com/SVA-SE/AHSURED/wiki
prevalence estimation
https://github.com/SVA-SE/AHSURED/wiki
verify success
https://github.com/SVA-SE/AHSURED/wiki
maintain freedom
https://github.com/SVA-SE/AHSURED/wiki
detect introduction
https://github.com/SVA-SE/AHSURED/wiki
control outbreak
https://github.com/SVA-SE/AHSURED/wiki
inform intervention
https://github.com/SVA-SE/AHSURED/wiki
detect changes
https://github.com/SVA-SE/AHSURED/wiki
control
https://github.com/SVA-SE/AHSURED/wiki
eradicate
https://github.com/SVA-SE/AHSURED/wiki/
Continuous data collection
https://github.com/SVA-SE/AHSURED/wiki/
Sentinel surveillance
https://github.com/SVA-SE/AHSURED/wiki/
Participatory surveillance
https://github.com/SVA-SE/AHSURED/wiki/
Indicator−based surveillance
https://github.com/SVA-SE/AHSURED/wiki/
Syndromic surveillance
Bulgarian
LANG
BG
Bulgarian
Czech
LANG
CS
Czech
Danish
LANG
DA
Danish
German
LANG
DE
German
Greek
LANG
EL
Greek
English
LANG
EN
English
Spanish
LANG
ES
Spanish
Estonian
LANG
ET
Estonian
Finnish
LANG
FI
Finnish
French
LANG
FR
French
Irish
LANG
GA
Irish
Croatian
LANG
HR
Croatian
Hungarian
LANG
HU
Hungarian
Icelandic
LANG
IS
Icelandic
Italian
LANG
IT
Italian
Lithuanian
LANG
LT
Lithuanian
Latvian
LANG
LV
Latvian
Montenegrin
LANG
ME
Montenegrin
Macedonian
LANG
MK
Macedonian
Maltese
LANG
MT
Maltese
Dutch
LANG
NL
Dutch
Norwegian
LANG
NO
Norwegian
Polish
LANG
PL
Polish
Portuguese
LANG
PT
Portuguese
Romanian
LANG
RO
Romanian
Serbian
LANG
RS
Serbian
Russian
LANG
RU
Russian
Slovakian
LANG
SK
Slovakian
Slovene
LANG
SL
Slovene
Swedish
LANG
SV
Swedish
Turkish
LANG
TR
Turkish
Chinese
LANG
ZH
Chinese
animal sample
MTXTYP
S000A
food sample
MTXTYP
S023A
food simulant
MTXTYP
S023A
feed sample
MTXTYP
S026A
environmental sample
MTXTYP
S027A
unknown
MTXTYP
S030A
contact material
MTXTYP
S031A
Campylobacter, unspecified sp.
PARAM
RF-00000044-MCG
Campylobacter cryaerophilus
PARAM
RF-00000050-MCG
thermotolerant Campylobacter, unspecified
PARAM
RF-00000052-MCG
Campylobacter jejuni jejuni
Campylobacter jejuni subsp. jejuni
PARAM
RF-00000062-MCG
Campylobacter sputorum subsp. mucosalis
PARAM
RF-00000066-MCG
Escherichia coli, non-pathogenic
PARAM
RF-00000125-MCG
Escherichia coli, non-pathogenic
VTEC non-O157
PARAM
RF-00000193-MCG
VTEC non-O157
Escherichia coli, non-pathogenic, unspecified
PARAM
RF-00003897-MCG
Escherichia coli, non-pathogenic, unspecified
Official (National) programme
PRGTYP
K005A
Official (National) programme
Official (EU) programme
PRGTYP
K009A
Official (EU) programme
Diet study
PRGTYP
K010A
Diet study
Industry/ private programme
PRGTYP
K012A
Industry/ private programme
Survey
PRGTYP
K013A
Survey
Other/ Combination of several programmes
PRGTYP
K014A
Other/ Combination of several programmes
Official (National and EU) programme
PRGTYP
K018A
Official (National and EU) programme
EU increased control programme on imported food
PRGTYP
K019A
EU increased control programme on imported food
Clinical investigations
PRGTYP
K020A
Clinical investigations
Control and eradication programmes
PRGTYP
K021A
Control and eradication programmes
Monitoring
PRGTYP
K022A
Monitoring
Monitoring - active
PRGTYP
K023A
Monitoring - active
Monitoring - passive
PRGTYP
K024A
Monitoring - passive
Monitoring - EFSA specifications
PRGTYP
K025A
Monitoring - EFSA specifications
Surveillance
PRGTYP
K026A
Surveillance
Survey - EU baseline survey
PRGTYP
K027A
Survey - EU baseline survey
Survey - national survey
PRGTYP
K028A
Survey - national survey
Unspecified
PRGTYP
K029A
Unspecified
Surveillance active
PRGTYP
K030A
Surveillance active
Surveillance passive
PRGTYP
K031A
Surveillance passive
Outbreak investigation
PRGTYP
K032A
Outbreak investigation
RASSF alert notification
PRGTYP
K033A
RASSF alert notification
Industry sampling
SAMPLR
CX01A
Industry sampling
Sampling performed by the industry.
Official sampling
SAMPLR
CX02A
Official sampling
Sampling performed under the control of the competent authority.
Official and industry sampling
SAMPLR
CX03A
Official and industry sampling
Sampling performed under the control of the competent authority and by industry.
HACCP and own check
SAMPLR
CX04A
HACCP and own check
Programme designed to effectively control processes by identifying critical control points (CCPs), establishing critical limits for each CCP, monitoring CCPs, gathering data, keeping records, and implementing corrective actions and verification procedures. HACCP is applied by the food or feed business operators (Codex Alimentarius).
Private sampling
SAMPLR
CX05A
Private sampling
Sampling performed by private people/entities like pet owner, farmer, pet shop employee, private veterinarian (on request of a farmer or a pet owner or another private entity). Private sampler should be used in the following cases: the owner of a pet who takes a sample from its clinical suspected pet animal; the owner or vet of a zoo/circus who collects samples from animals of the zoo/circus to be diagnosed for a specific disease. Private sampler should not be used when veterinarians/owner/hunters are commissioned by the Competent Authorities or perform sampling within a specific legislation and for which a pre-determined sampling programme for monitoring/surveillance exists (in this case the sampler should be ‘Official sampling’).
Official, based on Regulation 854/2004
SAMPLR
CX06A
Official, based on Regulation 854/2004
Official, based on Regulation 854/2004
Not applicable
SAMPLR
CX99A
Not applicable
zoo
veterinary clinic
farm
bee hives
artifical insemination station
fishing and processing
aquaculture
fishing
hatchery
hunting
natural habitat
hospital
residential institution
household
school
meat processing plant
slaughterhouse
fish processing
feed processing
retail
catering
canteen
official kennel
Catering on aircraft or ship or train
Objective sampling
SAMPSTR
ST10A
Objective sampling
Objective sampling—planned strategy based on the selection of a random sample, which is statistically representative of the population to be analysed. Each unit, within the framework population, has a specified probability of being selected. This strategy provides data from which statistical inference can be implemented. That means that the results inferred are comparable. Objective sampling is often the case in monitoring and surveillance schemes as well as in surveys.
Selective sampling
SAMPSTR
ST20A
Selective sampling
Selective sampling—planned strategy whereby the selection of the sample is from previously defined ‘high-risk’ population groups. Samples are normally selected to either illustrate or document unsatisfactory conditions or suspected adulteration of a product. The sampling is deliberately biased and is directed at the particular products or manufacturers. The sampling procedure can be random or not. The specification of the ‘high-risk’ population comes from either scientific studies or previous analysis and information of other regions or countries. The comparability of the results lies on both the definition of the population to be analysed and the way the samples have been drawn
Suspect sampling
SAMPSTR
ST30A
Suspect sampling
Suspect sampling—unplanned selection of a sample whereby the individual units are selected based on the recent judgement and experience regarding the population, lot or sampling frame, e.g. earlier positive samples. The samples obtained from this procedure are not randomly extracted.
Convenient sampling
SAMPSTR
ST40A
Convenient sampling
Convenient sampling—is used in exploratory research when the researcher is interested in getting an inexpensive approximation of the truth. The samples are selected because they are convenient and easy to obtain. This non-probability method is often used during preliminary research efforts to get a gross estimate of the results, without incurring the cost or time required to select a random sample. This methodology is potentially subject to serious bias
Census
SAMPSTR
ST50A
Census
Census—strategy whereby all units of the population are sampled
Import sampling
SAMPSTR
ST60A
Import sampling
Other
SAMPSTR
ST90A
Other
Not specified
SAMPSTR
STXXA
Not specified
holding
SAMPUNTYP
G198A
holding
'farm','farms','PPN','property','properties','holding','holdings'
animal
SAMPUNTYP
G199A
animal
'animal','animals','individual','individuals','human','person','humans','cases','case','single'
slaughter batch
SAMPUNTYP
G200A
slaughter batch
'slaughter batch','slaughter batches','slaughter group','slaughter groups'
slaughter animal (heads)
SAMPUNTYP
G201A
slaughter animal (heads)
herd/flock
SAMPUNTYP
G202A
herd/flock
'herd','herds','flock','flocks'
single
SAMPUNTYP
G203A
single
batch
SAMPUNTYP
G204A
batch
pen
SAMPUNTYP
G243A
pen
animal sample - no specified matrix
ZOO_CAT_SMPTYP
S000A
animal sample
animal sample - blood
ZOO_CAT_SMPTYP
S001A
animal sample - blood
animal sample - caecum
ZOO_CAT_SMPTYP
S002A
animal sample - caecum
'caecum','caeca','ceca','cecum'
animal sample - ear
ZOO_CAT_SMPTYP
S003A
animal sample - ear
animal sample - eggs
ZOO_CAT_SMPTYP
S004A
animal sample - eggs
animal sample - faeces
ZOO_CAT_SMPTYP
S005A
animal sample - faeces
'feces','faeces','fecal','faecal'
animal sample - fleece
ZOO_CAT_SMPTYP
S006A
animal sample - fleece
animal sample - foetus/stillbirth
ZOO_CAT_SMPTYP
S007A
animal sample - foetus/stillbirth
animal sample - lymph nodes
ZOO_CAT_SMPTYP
S008A
animal sample - lymph nodes
animal sample - meat juice
ZOO_CAT_SMPTYP
S009A
animal sample - meat juice
animal sample - milk
ZOO_CAT_SMPTYP
S010A
animal sample - milk
animal sample - rectum-anal swab
ZOO_CAT_SMPTYP
S012A
animal sample - rectum-anal swab
animal sample - vaginal swab
ZOO_CAT_SMPTYP
S013A
animal sample - vaginal swab
animal sample - placental swab
ZOO_CAT_SMPTYP
S014A
animal sample - placental swab
animal sample - nasal swab
ZOO_CAT_SMPTYP
S015A
animal sample - nasal swab
animal sample - organ/tissue
ZOO_CAT_SMPTYP
S017A
animal sample - organ/tissue
animal sample - tonsil
ZOO_CAT_SMPTYP
S018A
animal sample - tonsil
food sample - no specified matrix
ZOO_CAT_SMPTYP
S019A
food sample
food sample - blood
ZOO_CAT_SMPTYP
S020A
food sample - blood
food sample - carcase swabs
ZOO_CAT_SMPTYP
S021A
food sample - carcase swabs
food sample - meat
ZOO_CAT_SMPTYP
S022A
food sample - meat
food sample - milk
ZOO_CAT_SMPTYP
S023A
food sample - milk
food sample - neck skin
specimen by origin
ZOO_CAT_SMPTYP
S024A
food sample - neck skin
food sample - tonsil
ZOO_CAT_SMPTYP
S025A
food sample - tonsil
feed sample - no specified matrix
ZOO_CAT_SMPTYP
S026A
feed sample
environmental sample - no specified matrix
ZOO_CAT_SMPTYP
S027A
environmental sample
environmental sample - boot swabs
ZOO_CAT_SMPTYP
S028A
environmental sample - boot swabs
environmental sample - dust
ZOO_CAT_SMPTYP
S029A
environmental sample - dust
animal sample - cloacal swab
ZOO_CAT_SMPTYP
S031A
animal sample - cloacal swab
animal sample - eggshells
ZOO_CAT_SMPTYP
S032A
animal sample - eggshells
environmental sample - air
ZOO_CAT_SMPTYP
S033A
environmental sample - air
environmental sample - fabric swab
ZOO_CAT_SMPTYP
S034A
environmental sample - fabric swab
environmental sample - hatcher basket liner
ZOO_CAT_SMPTYP
S035A
environmental sample - hatcher basket liner
animal sample - brain
ZOO_CAT_SMPTYP
S036A
animal sample - brain
environmental sample - delivery box liner
ZOO_CAT_SMPTYP
S037A
environmental sample - delivery box liner
animal sample - hide
ZOO_CAT_SMPTYP
S038A
animal sample - hide
environmental sample - boot swabs and dust
ZOO_CAT_SMPTYP
S039A
environmental sample - boot swabs and dust
Person:Alan Ruttenberg
RF-00003072-PAR
NCBITaxon:562
E. coli
PARAM
Escherichia/Shigella coli
PARAM
RF-00003072-PAR
Escherichia coli
Escherichia coli
bantam
Gallus gallus
GC_ID:1
MTX
chicken
Gallus gallus domesticus
chickens
Gallus gallus
Live animal of the taxonomic species Gallus gallus domesticus L. The animals are commonly known as Gallus gallus (chicken) or Fowl or Chicken. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Chicken
ncbi_taxonomy
A057Z
Gallus domesticus
GC_ID:1
ncbi_taxonomy
Home sapiens
MTX
Homo sapians
Homo sapien
Homo sapients
human
Homo sapiense
Homo sapines
A056J
Homo sapeins
Humo sapiens
Homo sapiens
Humans as living organisms of the taxonomic group Homo sapiens (family Hominidae). The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Human
Homo spiens
Homo sapian
man
Homo sapience
Homo sampiens
Homo spaiens
Homo sapiens
MTX
Sus scrofus
GC_ID:1
ncbi_taxonomy
Live animals of the taxonomic species Sus domestica L., Sus scrofa domesticus L. The animals are commonly known as Pig or swine. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Domestic_pig
wild boar
pig
A057F
pigs
Sus scrofa
Sus scrofa
swine
dairy cow
Live animal of the taxonomic species Bos taurus Bojanus. The animals are commonly known as Cattle. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Cattle
A057E
NCBITaxon:272461
domestic cattle
ncbi_taxonomy
Cattle (as animal)
bovine
Bos taurus
cattle
Bos primigenius taurus
Bos taurus
Bos Tauurus
cow
GC_ID:1
MTX
domestic cow
Bos bovis
CALOHA:TS-1241
EMAPA:35328
UMLS:C0553695
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
VHOG:0000048
XAO:0000137
pars exocrina pancreatis
exocrine component of pancreas
The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
MA:0002415
exocrine pancreas
EV:0100093
TAO:0001249
uberon
UBERON:0000017
The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]
BTO:0000434
The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]
exocrine part of pancreas
FMA:16017
AAO:0010407
ZFA:0001249
NCIT:C32546
exocrine pancreas
ZFA_RETIRED:0005318
UBERON:0000029
uberon
GAID:947
nodus lymphaticus
MA:0000139
UMLS:C0024204
NCIT:C33027
lymph gland
EFO:0000872
EV:0100050
Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]
OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA
galen:Lymphnode
MAT:0000442
BTO:0000784
CALOHA:TS-0579
Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
MESH:D008198
NCIT:C12745
lymph node
TAO_RETIRED:0005318
EMAPA:35523
VHOG:0001273
FMA:5034
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
AAO:0010396
VHOG:0000054
BTO:0000706
XAO:0000131
FMA:7201
OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA
MIAA:0000046
GAID:306
NCIT:C12379
UMLS:C0021851
galen:LargeIntestine
EV:0100077
uberon
MESH:A03.492.411.495
EMAPA:19252
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
CALOHA:TS-1306
MA:0000333
UBERON:0000059
EFO:0000840
large intestine
intestinum crassum
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
ISBN10:0073040584
UMLS:C0021851
ncithesaurus:Large_Intestine
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
2012-09-17
VHOG:0000054
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
intestinum crassum
BTO:0000706
MESH:A03.492.411
XAO:0000129
VHOG:0000056
EMAPA:32874
galen:Intestine
GAID:295
CALOHA:TS-0490
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
MA:0001524
This class is probably too inclusive
MA:0000328
intestinal
FMA:7199
EV:0100071
BSA:0000093
TAO:0001338
UBERON:0000160
BTO:0000648
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
ANISEED:1235303
intestinal tract
UMLS:C0021853
AAO:0000246
WBbt:0005772
NCIT:C12736
bowel
EFO:0000834
intestine
uberon
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
ZFA:0001338
MIAA:0000043
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
GOC:GO
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000056
VHOG
UMLS:C0021853
ncithesaurus:Intestine
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
2012-06-20
AAO:0000246
AAO
AAO:EJS
ZFA:0000007
CALOHA:TS-0079
UBERON:0000178
FMA:9670
portion of blood
GAID:965
AAO:0000046
uberon
A fluid that is composed of blood plasma and erythrocytes.
UMLS:C0005767
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
EHDAA:418
ENVO:02000027
EFO:0000296
VHOG:0000224
whole blood
MIAA:0000315
vertebrate blood
EMAPA:16332
galen:Blood
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
BTO:0000089
EV:0100047
EHDAA2:0000176
MA:0000059
NCIT:C12434
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
XAO:0000124
TAO:0000007
MESH:D001769
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
blood
MESH:D005333
UBERON:0000323
An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus.
UMLS:C0015965
uberon
late embryo
GAID:552
embryo late growth stage
NCIT:C13235
FBbt:00005333
CALOHA:TS-0360
OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA
FMA:63919
EFO:0001323
Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919].
fetus
BTO:0000449
embryo late stage
MESH:D009093
CALOHA:TS-2144
mucous
mucus
NCIT:C13259
mucoid
UMLS:C0026727
uberon
ENVO:02000040
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
galen:Mucus
UBERON:0000912
FMA:66938
GAID:1164
OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA
MAT:0000226
XAO:0000113
EMAPA:16039
developmental tissue
AEO:0000169
NCIT:C28147
AAO:0011035
EFO:0001367
EHDAA2:0000002
developing organism
uberon
FMA:69068
GAID:963
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
EHDAA2_RETIRED:0003236
BTO:0000379
CALOHA:TS-0229
MIAA:0000019
MESH:D004622
UBERON:0000922
OGEM:000001
EHDAA:38
embryonic
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
VHOG:0001766
FBbt:00000052
BSA:0000039
ZFA:0000103
embryonic organism
embryo
UMLS:C0013935
BILA:0000056
anterior intestine
EMAPA:17021
TAO:0002121
gaster
mesenteron
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
FMA:7148
EV:0100070
MESH:A03.492.766
galen:Stomach
stomach chamber
AAO:0000579
VHOG:0000408
uberon
MA:0000353
MIAA:0000051
CALOHA:TS-0980
MAT:0000051
EHDAA2:0001915
BTO:0001307
EHDAA:2993
ANISEED:1235297
NCIT:C12391
ventriculus
UMLS:C0038351
OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
XAO:0000128
GAID:293
UBERON:0000945
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
stomach
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
EFO:0000837
gaster
BTO:0001307
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
2012-09-17
VHOG:0000408
VHOG
DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
ISBN10:0073040584
ventriculus
UMLS:C0038351
ncithesaurus:Stomach
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
2012-06-20
AAO:0000579
AAO
AAO:EJS
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
WP:Stomach#In_other_animals
TAO:0000008
VHOG:0000157
BAMS:Br
suprasegmental levels of nervous system
MBA:997
MBA:8
MESH:D001921
FMA:50801
BAMS:Brain
UMLS:C0006104
EFO:0000302
MA:0000168
uberon
BILA:0000135
EHDAA:6485
galen:Brain
DHBA:10155
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
EHDAA2:0000183
FBbt:00005095
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
GAID:571
CALOHA:TS-0095
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
UBERON:0000955
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
NCIT:C12439
HBA:4005
synganglion
brain
ABA:Brain
EMAPA:16894
EV:0100164
requires review for applicability to invertebrate structures, e.g. synganglion
OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
the brain
AAO:0010478
UMLS:C1269537
encephalon
PBA:3999
MIAA:0000098
ZFA:0000008
suprasegmental structures
BTO:0000142
MAT:0000098
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
XAO:0000010
EHDAA:2641
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
UBERON:0001043
MESH:A03.365
uberon
FMA:7131
UMLS:C0014876
OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA
CALOHA:TS-0700
XAO:0000127
EMAPA:16833
gullet
TAO:0000204
VHOG:0000450
esophageal
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
AAO:0000145
ANISEED:1235301
oesophagus
esophagus
ZFA:0000204
EFO:0000835
MAT:0000048
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
MIAA:0000048
BTO:0000959
galen:Esophagus
NCIT:C12389
MA:0000352
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
EV:0100069
EHDAA:2937
EHDAA2:0001285
GAID:291
UMLS:C0014876
ncithesaurus:Esophagus
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
2012-09-17
VHOG:0000450
VHOG
DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
2012-06-20
AAO:0000145
AAO
AAO:EJS
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
MA
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
NCIT:C12390
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
rectal
CALOHA:TS-1180
rectal sac
VHOG:0001751
XAO:0000238
MA:0000336
MAT:0000050
UMLS:C0034896
MIAA:0000050
BTO:0001158
OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA
EHDAA:5836
EMAPA:17896
intestinum rectum
EV:0100081
terminal portion of intestine
uberon
galen:Rectum
MESH:A03.492.411.495.767
the terminal portion of the intestinal tube, terminating with the anus
EHDAA2:0001592
GAID:311
UBERON:0001052
EFO:0000848
rectum
terminal portion of large intestine
AAO:0010401
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
FMA:14544
UMLS:C0034896
ncithesaurus:Rectum
intestinum rectum
BTO:0001158
the terminal portion of the intestinal tube, terminating with the anus
ISBN:0-683-40008-8
MP:0000492
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0001751
VHOG
MA:0002544
GAID:265
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
UBERON:0001090
galen:SynovialFluid
UMLS:C0039097
ENVO:02000039
joint fluid
synovial fluid
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
ZFA:0005154
It provides nutrients and lubrication for articular cartilage
BTO:0001339
NCIT:C33718
TAO:0005154
CALOHA:TS-0996
MESH:D013582
uberon
FMA:12277
blind intestine
BTO:0000166
MIAA:0000288
UBERON:0001153
FMA:14541
intestinum crassum cecum
galen:Cecum
intestinum caecum
caecum
ceca
EHDAA:3913
caeca
NCIT:C12381
caecum
MA:0000334
Kardong: in some herbivorous lizards, a cecum is present between small and large intestines
blindgut
GAID:307
caecal
intestinum crassum caecum
CALOHA:TS-0122
EHDAA2:0000206
UMLS:C0007531
uberon
EMAPA:35197
A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA
cecum
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
MESH:A03.492.411.495.209
EV:0100397
EFO:0000850
VHOG:0001559
blind intestine
BTO:0000166
intestinum crassum cecum
BTO:0000166
intestinum caecum
BTO:0000166
ceca
NCBITaxon:8782
caeca
NCBITaxon:8782
caecum
VHOG:0001559
blindgut
BTO:0000166
UMLS:C0007531
ncithesaurus:Cecum
A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates.
WP
cecum
FMA:14541
A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
BTO:0000269
hindgut
FMA:14543
posterior intestine
OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA
TODO - abstract this such that it legitimately covers all vertebrates
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
EV:0100079
EMAPA:18939
UMLS:C0009368
AAO:0010400
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
Last portion of the large intestine before it becomes the rectum.
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
colon
UBERON:0001155
colonic
TAO:0000706
ZFA:0000706
uberon
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
XAO:0000243
MAT:0000526
CALOHA:TS-0158
MAP:0000001
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
GAID:309
VHOG:0000648
MA:0000335
galen:Colon
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
EFO:0000361
NCIT:C12382
MESH:A03.492.411.495.356
large bowel
UMLS:C0009368
ncithesaurus:Colon
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
2012-08-14
TAO:0000706
TAO
ZFIN:curator
Last portion of the large intestine before it becomes the rectum.
ZFIN:curator
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
2012-09-17
VHOG:0000648
VHOG
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
2012-06-20
AAO:0010400
AAO
UBERON:0001155
UBERON:0001173
Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]
FMA:14665
A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
biliary tree
biliary tract
EMAPA:35172
XAO:0000455
uberon
The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]
UMLS:C0005423
AAO:0011020
pancreatic
FMA:7198
EHDAA:6893
UBERON:0001264
EV:0100092
BTO:0000988
MESH:D010179
VHOG:0000050
MA:0000120
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
NCIT:C12393
EMAPA:17503
GAID:334
EFO:0000855
UMLS:C0030274
CALOHA:TS-0736
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
TAO:0000140
uberon
MAT:0000075
XAO:0000136
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
ZFA:0000140
AAO:0010112
OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
MIAA:0000075
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
pancreas
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
EHDAA2:0001367
galen:Pancreas
capsulae articulares
FMA:34836
check ncita
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
galen:JointCapsule
UBERON:0001484
EMAPA:37621
NCIT:C84388
joint fibrous capsule
GAID:263
UMLS:C0206207
articular capsule
joint capsule
capsula articularis
fibrous capsule of joint
MESH:D017746
NCIT:C32259
MA:0001519
uberon
CALOHA:TS-0595
OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA
Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]
dug
glandula mammaria
uberon
UMLS:C0929301
The BTO class represents the combination of nipple plus lobe
The FMA class represents an individule lobe. The nipple is not a part
mamma
Originally this was classified as a female reproductive structure, as it was in the MP in 2011
BTO:0000817
EV:0100125
mammary gland
EFO:0000854
MA:0000145
MIAA:0000073
The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts
MESH:D008321
MAT:0000073
A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males.
Brustdruese
mammary
mammae
lobe of mammary gland
FMA:286452
VHOG:0000398
milk patch
The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
lobe of breast
EMAPA:17759
The male Dayak fruit bat has lactating mammary glands
A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts
glandula mammaria
The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges.
lactiferous gland
NCIT:C12367
UBERON:0001911
MIAA:0000056
ncit:Milk refers specifically to cow milk
CALOHA:TS-0636
MAT:0000056
ENVO:02000031
FMA:62100
EMAPA:36540
GAID:1230
uberon
NCIT:C13401
OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA
milk
An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular.
galen:Milk
UBERON:0001913
BTO:0000868
VHOG:0001263
MESH:A13.622
The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]
mammary gland milk
UMLS:C1511310
EV:0100126
MA:0002552
blood plasm
FMA:62970
CALOHA:TS-0800
blood plasma
NCIT:C13356
MESH:D010949
EFO:0001905
MA:0002501
uberon
BTO:0000131
OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
portion of blood plasma
The liquid component of blood, in which erythrocytes are suspended.
EMAPA:35690
portion of plasma
GAID:1178
UMLS:C0032105
MIAA:0000052
UBERON:0001969
plasma
MAT:0000052
fel
uberon
galen:Bile
MESH:D001646
ZFA:0005857
BTO:0000121
FMA:62971
CALOHA:TS-1172
aids the process of digestion of lipids in the small intestine
vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
MA:0002513
protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
elimination of cholesterol
UBERON:0001970
GAID:1157
many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
ENVO:02000023
NCIT:C13192
bile salts function to emulsify dietary fats and facilitate their intestinal absorption
major excretory route for potentially harmful exogenous lipophilic substances
gall
bile
UMLS:C0005388
GAID:379
EV:0100119
Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities.
Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011
UMLS:C0032043
MESH:A16.759
EMAPA:35689
OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA
placental
VHOG:0001266
FMA:63934
UBERON:0001987
CALOHA:TS-0799
eutherian placenta
allantoic placenta
EFO:0001407
MA:0000386
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
NCIT:C13272
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
MAT:0000279
placenta
MIAA:0000279
uberon
BTO:0001078
excrement
merde@fr
galen:Feces
teil der fäkalien@de
ordure
ENVO:00002003
partie de la merde@fr
stool
faeces
GAID:1199
UBERON:0001988
FMA:64183
MIAA:0000053
uberon
portion of faeces
portion of excrement
BTO:0000440
MAT:0000053
fecal matter
MA:0002509
portion of scat
frass
excreta
droppings
portion of feces
portion of fecal matter
spoor
Excretion in semisolid state processed by the intestine.[FMA]
scat
UMLS:C0015733
fecal material
cow dung
CALOHA:TS-2345
portion of dung
MESH:D005243
portion of fecal material
guano
portionem cacas
fecal
dung
feces
spraint
fewmet
portion of guano
OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
piece of shit
matières fécales@fr
cow pat
Portion of semisolid bodily waste discharged through the anus[MW,modified]
NCIT:C13234
porción de mierda@es
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
VHOG:0000310
uberon
galen:Lung
FMA:7195
BTO:0000763
CALOHA:TS-0568
GAID:345
pulmo
UMLS:C0024109
pulmonary
EV:0100042
EHDAA2:0001042
XAO:0000119
EMAPA:16728
EHDAA:2205
OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA
EHDAA:1554
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
MIAA:0000135
MAT:0000135
EFO:0000934
AAO:0010567
NCIT:C12468
MA:0000415
MESH:D008168
lung
Respiration organ that develops as an oupocketing of the esophagus.
UBERON:0002048
AAO:0000275
galen:Skin
skin of body
UMLS:C1123023
integumental organ
UBERON:0002097
entire skin
skin organ
MFMO:0000099
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
consider 'integumentary system' for invertebrates
BTO:0001253
entire integument
MESH:D012867
uberon
XAO:0000023
EFO:0000962
integument
EMAPA:17525
NCIT:C12470
EHDAA2:0001844
skin
pelt
FMA:7163
MA uses the term skin to refer to what is called here: zone of skin
CALOHA:TS-0934
The organ covering the body that consists of the dermis and epidermis.
BTO:0000759
liver
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
FMA:7197
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
EHDAA:2197
MAT:0000097
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
MIAA:0000097
uberon
CALOHA:TS-0564
EHDAA2:0000997
GAID:288
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
UMLS:C0023884
OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
jecur
galen:Liver
NCIT:C12392
XAO:0000133
TAO:0000123
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
UBERON:0002107
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
MA:0000358
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
MESH:D008099
ZFA:0000123
hepatic
EFO:0000887
EV:0100089
AAO:0010111
iecur
VHOG:0000257
EMAPA:16846
mid intestine
TAO:0001323
BTO:0000651
small intestine
ZFA:0001323
small intestine
EMAPA:32834
EFO:0000841
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
AAO:0010397
OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA
intestinum tenue
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
galen:SmallIntestine
VHOG:0000055
FMA:7200
UBERON:0002108
XAO:0000130
MAT:0000047
small bowel
CALOHA:TS-0942
MIAA:0000047
uberon
MA:0000337
GAID:313
anterior intestine
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
NCIT:C12386
UMLS:C0021852
MESH:A03.492.411.620
EV:0100072
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
2012-09-17
VHOG:0000055
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
intestinum tenue
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
2012-08-14
TAO:0001323
TAO
ZFIN:curator
intestinum tenue
BTO:0000651
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
ISBN10:0073040584
UMLS:C0021852
ncithesaurus:Small_Intestine
NCIT:C12263
GAID:284
MESH:A03.492.411.620.270
VHOG:0000052
duodenal
XAO:0000236
UMLS:C0013303
MAT:0000044
duodenum
proximal intestine
CALOHA:TS-0214
The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
MIAA:0000044
MA:0000338
EFO:0000851
galen:Duodenum
AAO:0010402
OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA
EMAPA:18852
In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
FMA:7206
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
EV:0100073
upper intestine
BTO:0000365
UBERON:0002114
uberon
In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
UMLS:C0013303
ncithesaurus:Duodenum
proximal intestine
BTO:0000365
The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000052
VHOG
In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.
NCBITaxon:9606
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
ISBN:0815318960
upper intestine
BTO:0000365
In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.
NCBITaxon:32443
MA:0000340
MESH:A03.492.411.620.625
EMAPA:18666
VHOG:0000053
intestinum jejunum
mid-intestine
MAT:0000045
TODO consider ZFA:0001323 mid intestine, see also small intestine
OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA
The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum]
UMLS:C0022378
uberon
the portion of the small intestine that extends from the duodenum to the ileum
middle intestine
MIAA:0000045
NCIT:C12388
jejunal
EFO:0001333
The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
galen:Jejunum
jejunum
EV:0100074
FMA:7207
UBERON:0002115
BTO:0000657
CALOHA:TS-0496
GAID:318
intestinum jejunum
BTO:0000657
mid-intestine
UMLS:C0022378
ncithesaurus:Jejunum
the portion of the small intestine that extends from the duodenum to the ileum
MGI:monikat
MP:0004002
middle intestine
BTO:0000657
The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000053
VHOG
TODO consider ZFA:0000706 posterior intestine, see also colon
AAO:0010403
EMAPA:32764
intestinum ileum
MESH:A03.492.411.620.484
ileum
galen:Ileum
ileal
The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum]
MAT:0000282
MIAA:0000282
distal intestine
OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA
CALOHA:TS-0472
EFO:0001334
NCIT:C12387
the portion of the small intestine that extends from the jejunum to the colon
VHOG:0000647
XAO:0000237
FMA:7208
EV:0100075
lower intestine
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
BTO:0000620
UBERON:0002116
UMLS:C0020885
GAID:315
MA:0000339
uberon
posterior intestine
intestinum ileum
BTO:0000620
distal intestine
BTO:0000620
the portion of the small intestine that extends from the jejunum to the colon
ISBN:0-683-40008-8
MGI:csmith
MP:0002581
lower intestine
BTO:0000620
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
2012-09-17
VHOG:0000647
VHOG
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
UMLS:C0020885
ncithesaurus:Ileum
posterior intestine
FMA:9671
ENVO:02000041
galen:Lymph
BTO:0000855
lympha
OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA
EFO:0000871
MA:0002520
EV:0100049
ZFA:0005658
MAT:0000055
VHOG:0001590
GAID:1186
MESH:A12.207.630
NCIT:C13252
CALOHA:TS-0580
UMLS:C0024202
lymph
UBERON:0002391
Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
uberon
MIAA:0000055
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
uberon
external genitalia
external genitalia
external sex organ
external reproductive organ
FMA:45643
UBERON:0004176
The external genitalia are the outer sex organs, such as the penis or vulva in mammals
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
pharyngeal tube
MIAA:0000049
UBERON:0006562
pharynx
branchial
MAT:0000049
FBbt:00005380
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
pharyngeal
uberon
anterior part of foregut
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
GO:0060465
The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
UBERON:0007364
uberon
retriculo-rumen
reticulorumen
The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum.
The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food.
UBERON:0007379
BSA:0000081
uberon
BTO:0000369
shelled egg
egg
EMAPA:27211
uberon
The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP].
pyloric mucuous gland
UMLS:C0227239
NCIT:C33431
pyloric gastric gland
glandula pylorica
pyloric gland
UBERON:0008861
pyloric antrum gland
check relationship to pylorus vs antrum
FMA:14922
dorsal pancreas
UBERON:0009708
uberon
EHDAA2:0001371
pancreatis dorsalis
pancreatis ventralis
ventral pancreas
uberon
EHDAA2:0001393
UBERON:0009709
2018-06-15
Genomic Epidemiology Ontology
GENEPIO
The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types.
EHDAA2 part_of NCBITaxon:9606
http://uberon.org
FBdv part_of NCBITaxon:7227
ISBN10:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber
Terry Hayamizu
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/reflexivity_axioms.owl>) VersionIRI(<null>))) [Axioms: 2 Logical Axioms: 2]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/TEMP>) VersionIRI(<null>))) [Axioms: 437 Logical Axioms: 0]
PBA part_of NCBITaxon:9443
HAO part_of NCBITaxon:7399
ISBN:0683400088 Stedman's Medical Dictionary
Yvonne Bradford
MFO part_of NCBITaxon:8089
AAO part_of NCBITaxon:8292
http://uberon.org
Suzanna Lewis
Anna Anagnostopoulos
ISBN-10:0443065837 Human embryology, Larsen
HBA part_of NCBITaxon:9606
uberon
James Malone
XAO part_of NCBITaxon:8353
https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0
NIF Project - http://neuinfo.org/
EFO
George Gkoutos
FMA part_of NCBITaxon:9606
BSPO
MmusDv part_of NCBITaxon:10090
PATO Project
Bill Bug
DMBA part_of NCBITaxon:10090
Rebecca Foulger
http://genomebiology.com/2012/13/1/R5
Marc Robinson-Rechavi
https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit#
Phenoscape Project
James Balhoff
Shahim Essaid
FBbt part_of NCBITaxon:7227
Robert Druzinsky
Nizar Ibrahim
Melissa Haendel
ISBN10:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher
Chris Mungall - http://orcid.org/0000-0002-6601-2165
ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody
ZFA part_of NCBITaxon:7954
Brian K Hall
ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte
Paula Mabee
https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit
VHOG
David Osumi-Sutherland
ISBN:9780120749034 The laboratory rat
Paul Sereno
Sarah Whitcher Kansa - https://orcid.org/0000-0001-7920-5321
ZFS part_of NCBITaxon:7954
David Blackburn
OlatDv part_of NCBITaxon:8089
Alan Ruttenberg
AEO
VSAO
ISBN10:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack
http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop
Ann Maglia
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/insect-anatomy.owl>) VersionIRI(<null>))) [Axioms: 2098 Logical Axioms: 650]
MBA part_of NCBITaxon:10090
https://lists.sourceforge.net/lists/listinfo/obo-anatomy
SCTID
PMID:11433360 Placental development: lessons from mouse mutants
neXtProt project
SPD part_of NCBITaxon:6893
Paul Schofield
Alexander Diehl
https://obo.svn.sourceforge.net/svnroot/obo/uberon/
TADS part_of NCBITaxon:6939
WBls part_of NCBITaxon:6237
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon-bridge-to-bfo.owl>) VersionIRI(<null>))) [Axioms: 20 Logical Axioms: 9]
Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
Frederic Bastian
Erik Segerdell
ISBN:0030229073 Invertebrate Zoology, Barnes
Aurelie Comte
Gene Ontology Consortium
https://github.com/cmungall/uberon/
TAO part_of NCBITaxon:32443
Terry Meehan
Mark Engelstad - https://orcid.org/0000-0001-5889-4463
Carlo Torniai
ISBN10:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos
Maryann Martone
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/ext.owl>) VersionIRI(<null>))) [Axioms: 26298 Logical Axioms: 4860]
MESH
EV
MA part_of NCBITaxon:10090
PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen
ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader
ISBN10:0073040584 Vertebrates, Kardong
EMAPA part_of NCBITaxon:10090
BILA
https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit
Duncan Davidson
Bgee Project - http://bgee.unil.ch
https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit
GO
ISBN10:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis
David Hill
Hilmar Lapp
Cynthia Smith
https://github.com/obophenotype/uberon/issues/
WBbt part_of NCBITaxon:6237
OG
DHBA part_of NCBITaxon:9606
NCIT
Anne Niknejad
Jonathan Bard
HsapDv part_of NCBITaxon:9606
Wasila Dahdul
Catherine Leroy
Onard Mejino
Uber-anatomy ontology
Trish Whetzel
TGMA part_of NCBITaxon:44484
http://wiki.phenotypercn.org/wiki/August_2012_Notes
ISBN-10:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall
http://www.ncbi.nlm.nih.gov/pubmed/22293552
CARO
Paula Duek Roggli
Alex Dececchi
Lydie Lane
EHDAA
ISBN:9780878932504 Developmental Biology
OGES
Ceri Van Slyke
A0C7P
MTX
egg production
Animals farmed for egg production purposes
A0C7G
MTX
meat production
Animals farmed for meat production purposes
A0C7N
MTX
milk production
Animals farmed for milk production purposes
MTX
Animals farmed for breeding purposes
A0C7G
reproducer