Philip E. Empey
Dan Malone
Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
Anuj Shah
Mathias Brochhausen
development version 2016-07-06
http://creativecommons.org/licenses/by/4.0/
Jodi Schneider
Richard D. Boyce
William R. Hogan
The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0
(https://creativecommons.org/licenses/by/4.0/).
DIDEO
The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and
indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
BFO OWL specification label
BFO CLIF specification label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example of usage
has curation status
definition
definition
definition
textual definition
editor note
editor note
definition editor
definition editor
term editor
alternative term
alternative term
definition source
definition source
curator note
curator note
imported from
expand expression to
OBO foundry unique label
elucidation
has associated axiom(fol)
ISA alternative term
IEDB alternative term
temporal interpretation
is direct form of
is indirect form of
external_definition
has_relational_adjective
alternative_term
definition
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_namespace
has_related_synonym
in_subset
label
see also
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
http://purl.obolibrary.org/obo/ro.owl
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
http://purl.obolibrary.org/obo/obi.owl
has part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://purl.obolibrary.org/obo/ro.owl
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
http://purl.obolibrary.org/obo/ro.owl
precedes
continuant(c) and process(p) and first_time_point(p,t1) and last_time_point(p,t2) and not(exists_at(c,t1)) and exists_at(c,t2)
Alan Ruttenberg
https://code.google.com/p/bfo/issues/detail?id=50&colspec=ID%20Type%20Status%20Owner%20Summary%20Reporter%20Modified
begins_to_exist_during
o-has-part
hasOccurrentPart
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
http://purl.obolibrary.org/obo/bfo.owl
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
there is some extended organism e
& there is some temporal region tr
& p occupies temporal region tr
& p occurs_in e
& c begins to exist during p
& there is some t
( t part-of tr & c located-in e at t )
Alan Ruttenberg
Mathias Brochhausen
William R. Hogan
organismally_begins_to_exist_during
there is some extended organism e
& p1 occurs_in e
& p2 occurs_in e
& p1 immediately precedes p2
Mathias Brochhausen
for immediatly precedes please see: http://krr.meraka.org.za/~aow2010/Trentelman-etal.pdf
organismally immediately precedes
is organismally immediately preceded by
A pharmaeutic ingredient or a metabolite X is the substrate of an enzyme E, iff E catalyzes X to M.
Mathias Brochhausen
is substrate of
realizes substrate role
true
involves substrate
true
inhibits-catalyzes metabolism of
catalyzes a Phase I or Phase II enzymatic reaction involving
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
http://purl.obolibrary.org/obo/obi.owl
is_specified_input_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
http://purl.obolibrary.org/obo/obi.owl
is_specified_output_of
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
http://purl.obolibrary.org/obo/obi.owl
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
http://purl.obolibrary.org/obo/obi.owl
inheres in
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
http://purl.obolibrary.org/obo/ro.owl
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://purl.obolibrary.org/obo/dron.owl
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
David Osumi-Sutherland
http://purl.obolibrary.org/obo/ro.owl
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
ends_at_start_of
meets
http://purl.obolibrary.org/obo/ro.owl
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process.
http://purl.obolibrary.org/obo/ro.owl
regulates (processual)
false
regulates
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
negatively regulates (process to process)
negatively regulates
'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
has prototype
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
http://purl.obolibrary.org/obo/ro.owl
RO_0000053 some (RO_0000054 only ?Y)
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
http://purl.obolibrary.org/obo/ro.owl
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
capable of part of
x actively participates in y if and only if x participates in y and x realizes some active role
Chris Mungall
agent in
http://purl.obolibrary.org/obo/ro.owl
actively participates in
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
http://purl.obolibrary.org/obo/ro.owl
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
started by
http://purl.obolibrary.org/obo/ro.owl
starts with
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Chris Mungall
finished by
http://purl.obolibrary.org/obo/ro.owl
ends with
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
http://purl.obolibrary.org/obo/ro.owl
enables
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
http://purl.obolibrary.org/obo/ro.owl
functionally related to
inverse of enables
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
enabled by
inverse of regulates
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
regulated by (processual)
regulated by
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
negatively regulated by
inverse of upstream of
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
causally downstream of
Chris Mungall
directly negatively regulates
http://purl.obolibrary.org/obo/ro.owl
directly inhibits (process to process)
directly inhibits
Chris Mungall
indirectly negatively regulates
http://purl.obolibrary.org/obo/ro.owl
indirectly inhibits
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
http://purl.obolibrary.org/obo/ro.owl
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
http://purl.obolibrary.org/obo/ro.owl
causally upstream of or within
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
causally downstream of or within
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
http://purl.obolibrary.org/obo/ro.owl
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://code.google.com/p/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected.
Chris Mungall
binds
molecularly binds with
http://purl.obolibrary.org/obo/ro.owl
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
molecularly controls
Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
Chris Mungall
inhibits
http://purl.obolibrary.org/obo/ro.owl
molecularly decreases activity of
A relationship between a material entity and a process where the material entity has some causal role that influences the process
http://purl.obolibrary.org/obo/ro.owl
causal agent in
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
https://docs.google.com/document/d/1WxocTXZaGVhEV1n7NB86pCF3SUcBJh8bq4vQrVCkjSU/edit#
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
http://purl.obolibrary.org/obo/ro.owl
causal relation between processes
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
http://purl.obolibrary.org/obo/ro.owl
causal relation between material entities
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
causally influences (material entity to material entity)
causally influences
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
http://purl.obolibrary.org/obo/ro.owl
causal relation between material entity and a process
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
http://purl.obolibrary.org/obo/ro.owl
related via dependence to
DIDEO uses this object property from the old (depracted) RO, since we need to infer parts of drug products as represented by DRON (and DRON [along with many other OBO Foundry candidate ontologies] uses this object property).
http://purl.obolibrary.org/obo/ido.owl
OBO_REL:0000007
relationship
has_proper_part
DIDEO uses this object property from the old (depracted) RO, since we need to infer parts of drug products as represented by DRON (and DRON [along with many other OBO Foundry candidate ontologies] uses this object property).
http://purl.obolibrary.org/obo/ido.owl
OBO_REL:0000006
relationship
proper_part_of
has specified value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
PERSON: James A. Overton
OBI
has specified value
A 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate in which both stereocentres have S configuration. A calcium-channel blocker and vasodilator, it is used as the hydrochloride in the management of angina pectoris and hypertension.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:4602
Beilstein:3573079
ChemIDplus:42399-41-7
CiteXplore:11937779
CiteXplore:16651034
CiteXplore:19167257
CiteXplore:23687551
CiteXplore:24261918
CiteXplore:25122162
CiteXplore:8369596
DrugBank:DB00343
HMDB:HMDB14487
KEGG COMPOUND:42399-41-7
KEGG COMPOUND:C06958
KEGG DRUG:D07845
NIST Chemistry WebBook:42399-41-7
Patent:DE1805714
Patent:DE3415035
Patent:US3562257
Patent:US4552695
Reaxys:3573079
Wikipedia:Diltiazem
(2S,3S)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate
DILTIAZEM
Diltiazem
chebi_ontology
(+)-cis-5-[2-(dimethylamino)ethyl]-2,3-dihydro-3-hydroxy-2-(p-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one acetate ester
(2S,3S)-5-(2-(dimethylamino)ethyl)-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]thiazepin-3-yl acetate
(2S-cis)-3-(acetyloxy)-5-[2-(dimethylamino)ethyl]-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one
Acetic acid (2S,3S)-5-(2-dimethylamino-ethyl)-2-(4-methoxy-phenyl)-4-oxo-2,3,4,5-tetrahydro-benzo[b][1,4]thiazepin-3-yl ester
C22H26N2O4S
COc1ccc(cc1)[C@@H]1Sc2ccccc2N(CCN(C)C)C(=O)[C@@H]1OC(C)=O
D-cis-diltiazem
InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3/t20-,21+/m1/s1
InChIKey=HSUGRBWQSSZJOP-RTWAWAEBSA-N
d-cis-diltiazem
diltiazem
diltiazemum
CHEBI:101278
diltiazem
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:13672
CHEBI:14859
CHEBI:8312
KEGG COMPOUND:C00419
Polynucleotide
chebi_ontology
C10H17O10PR2(C5H8O6PR)n
polynucleotides
CHEBI:15986
polynucleotide
A lactone having a six-membered lactone ring.
http://purl.obolibrary.org/obo/chebi.owl
delta-lactone
chebi_ontology
.
1,5-lactone
1,5-lactones
delta-lactona
delta-lactonas
delta-lactones
CHEBI:18946
delta-lactone
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
http://purl.obolibrary.org/obo/chebi.owl
molecular entity
chebi_ontology
.
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
diazoles
CHEBI:23677
diazole
chemical entity
A role played by the molecular entity or part thereof within a biological context.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
biological function
grouped_by_functions
CHEBI:24432
biological role
A cyclic compound having as ring members atoms of carbon and at least of one other element.
http://purl.obolibrary.org/obo/chebi.owl
ChEBI:C03123
chebi_ontology
.
organic heterocycle
organic heterocyclic compounds
CHEBI:24532
organic heterocyclic compound
Any carboxylic acid with at least one hydroxy group.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
hydroxy carboxylic acids
hydroxyacids
CHEBI:24669
hydroxy carboxylic acid
A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.
http://purl.obolibrary.org/obo/chebi.owl
imidazoles
chebi_ontology
CHEBI:24780
imidazoles
Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
http://purl.obolibrary.org/obo/chebi.owl
lactone
lactones
chebi_ontology
.
Lacton
Lakton
Laktone
lactona
lactonas
CHEBI:25000
lactone
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:26619
CHEBI:35220
metabolite
chebi_ontology
metabolites
primary metabolites
secondary metabolites
CHEBI:25212
metabolite
An organoiodine compound that has formula C25H29I2NO3.
http://purl.obolibrary.org/obo/chebi.owl
Beilstein:1271711
ChemIDplus:1951-25-3
DrugBank:DB01118
KEGG COMPOUND:1951-25-3
KEGG COMPOUND:C06823
KEGG DRUG:D02910
Wikipedia:Amiodarone
(2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone
Amiodarone
chebi_ontology
2-Butyl-3-(3,5-diiodo-4-(2-diethylaminoethoxy)benzoyl)benzofuran
2-Butyl-3-benzofuranyl 4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl ketone
2-n-Butyl-3',5'-diiodo-4'-N-diethylaminoethoxy-3-benzoylbenzofuran
C25H29I2NO3
CCCCc1oc2ccccc2c1C(=O)c1cc(I)c(OCCN(CC)CC)c(I)c1
InChI=1S/C25H29I2NO3/c1-4-7-11-22-23(18-10-8-9-12-21(18)31-22)24(29)17-15-19(26)25(20(27)16-17)30-14-13-28(5-2)6-3/h8-10,12,15-16H,4-7,11,13-14H2,1-3H3
InChIKey=IYIKLHRQXLHMJQ-UHFFFAOYSA-N
CHEBI:2663
amiodarone
An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
heterotricyclic compounds
organic heterotricyclic compounds
CHEBI:26979
organic heterotricyclic compound
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
heterobicyclic compounds
organic heterobicyclic compounds
two-ring heterocyclic compounds
CHEBI:27171
organic heterobicyclic compound
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
heteroorganic entities
organoelement compounds
CHEBI:33285
heteroorganic entity
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:13204
CHEBI:23028
CHEBI:3408
KEGG COMPOUND:C02391
Wikipedia:Ester
Carboxylic ester
carboxylic esters
chebi_ontology
CO2R2
[*]C(=O)O[*]
a carboxylic ester
carboxylic acid esters
CHEBI:33308
carboxylic ester
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:13428
CHEBI:13627
CHEBI:23027
CiteXplore:17147560
CiteXplore:18433345
carboxylic acid
carboxylic acids
chebi_ontology
CHO2R
Carbonsaeure
Carbonsaeuren
Karbonsaeure
OC([*])=O
RC(=O)OH
acide carboxylique
acides carboxyliques
acido carboxilico
acidos carboxilicos
CHEBI:33575
carboxylic acid
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
main group compounds
main group molecular entities
CHEBI:33579
main group molecular entity
http://purl.obolibrary.org/obo/chebi.owl
carbon group molecular entity
chebi_ontology
.
carbon group molecular entities
CHEBI:33582
carbon group molecular entity
A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
p-block compounds
p-block molecular entities
p-block molecular entitiy
CHEBI:33675
p-block molecular entity
A macromolecule formed by a living organism.
http://purl.obolibrary.org/obo/chebi.owl
biopolymer
chebi_ontology
Biopolymere
biomacromolecules
biopolymers
CHEBI:33694
biomacromolecule
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
genetically encoded biomacromolecules
genetically encoded biopolymers
information biomacromolecules
information biopolymers
information macromolecule
information macromolecules
CHEBI:33695
information biomacromolecule
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
http://purl.obolibrary.org/obo/chebi.owl
nucleic acids
chebi_ontology
NA
Nukleinsaeure
Nukleinsaeuren
acide nucleique
acides nucleiques
acido nucleico
acidos nucleicos
CHEBI:33696
nucleic acid
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
http://purl.obolibrary.org/obo/chebi.owl
ChemIDplus:63231-63-0
ribonucleic acid
ribonucleic acids
chebi_ontology
RNA
RNS
Ribonukleinsaeure
pentosenucleic acids
ribonucleic acids
ribose nucleic acid
yeast nucleic acid
CHEBI:33697
ribonucleic acid
Any organic molecule that consists of atoms connected in the form of a ring.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
organic cyclic compounds
CHEBI:33832
organic cyclic compound
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
http://purl.obolibrary.org/obo/chebi.owl
heteroarenes
chebi_ontology
.
hetarenes
CHEBI:33833
heteroarene
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
http://purl.obolibrary.org/obo/chebi.owl
Wikipedia:Macromolecule
macromolecule
chebi_ontology
macromolecules
polymer
polymer molecule
polymers
CHEBI:33839
macromolecule
http://purl.obolibrary.org/obo/chebi.owl
COMe:PRX000002
metalloprotein
chebi_ontology
metalloproteine
metalloproteins
CHEBI:35134
metalloprotein
http://purl.obolibrary.org/obo/chebi.owl
COMe:PRX000004
iron protein
chebi_ontology
iron proteins
iron-containing proteins
CHEBI:35136
iron protein
Conjugated proteins containing heme as the prosthetic group.
http://purl.obolibrary.org/obo/chebi.owl
COMe:PRX000008
hemoprotein
chebi_ontology
Haemoprotein
Haemprotein
haem protein
haemoprotein
heme protein
hemeproteins
hemoproteins
CHEBI:35137
hemoprotein
A substance that diminishes the rate of a chemical reaction.
http://purl.obolibrary.org/obo/chebi.owl
inhibitor
chebi_ontology
inhibidor
inhibiteur
inhibitors
CHEBI:35222
inhibitor
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:22721
benzofurans
chebi_ontology
CHEBI:35259
benzofurans
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
triazolobenzodiazepines
CHEBI:35501
triazolobenzodiazepine
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
.
carbon oxoacids
oxoacids of carbon
CHEBI:35605
carbon oxoacid
A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:23960
CHEBI:4859
KEGG COMPOUND:C00287
Ester
chebi_ontology
.
[*]OC([*])=O
esters
CHEBI:35701
ester
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
hydroxy acid
hydroxy monocarboxylic acids
CHEBI:35868
hydroxy monocarboxylic acid
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
dihydroxy monocarboxylic acids
CHEBI:35972
dihydroxy monocarboxylic acid
http://purl.obolibrary.org/obo/chebi.owl
COMe:PRX000150
chebi_ontology
haem-thiolate protein
heme-thiolate proteins
CHEBI:36074
heme-thiolate protein
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:13677
CHEBI:14911
proteins
chebi_ontology
CHEBI:36080
protein
Any molecular entity consisting of more than one atom.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
polyatomic entities
CHEBI:36357
polyatomic entity
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
http://purl.obolibrary.org/obo/chebi.owl
organochalcogen compound
chebi_ontology
.
organochalcogen compounds
CHEBI:36962
organochalcogen compound
An organochalcogen compound containing at least one carbon-oxygen bond.
http://purl.obolibrary.org/obo/chebi.owl
CiteXplore:17586126
organooxygen compound
chebi_ontology
.
organooxygen compounds
CHEBI:36963
organooxygen compound
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:25429
CHEBI:38075
chebi_ontology
.
multi-ring heterocyclic compounds
organic heteropolycyclic compounds
CHEBI:38166
organic heteropolycyclic compound
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
monocyclic heteroarenes
CHEBI:38179
monocyclic heteroarene
A dihydroxy monocarboxylic acid that is (6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl} hept-6-enoic acid carrying two hydroxy substituents at positions 3 and 5 (the 3R,5S-diastereomer).
http://purl.obolibrary.org/obo/chebi.owl
Beilstein:9670765
ChemIDplus:287714-41-4
CiteXplore:17970755
CiteXplore:18509206
CiteXplore:19724024
CiteXplore:19956889
CiteXplore:23806820
CiteXplore:23881596
CiteXplore:23944632
CiteXplore:24072337
CiteXplore:24076283
CiteXplore:24076297
CiteXplore:24156555
CiteXplore:24163149
CiteXplore:24230979
CiteXplore:24253250
CiteXplore:24259612
CiteXplore:24304551
CiteXplore:24333476
CiteXplore:24353409
CiteXplore:24410968
CiteXplore:24417785
CiteXplore:24434545
CiteXplore:24440231
CiteXplore:24440960
CiteXplore:24444439
CiteXplore:24452083
CiteXplore:24456217
CiteXplore:24467235
DrugBank:DB01098
HMDB:HMDB15230
KEGG DRUG:D08492
Patent:US2013035316
Reaxys:9670765
Wikipedia:Rosuvastatin
(3R,5S,6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid
chebi_ontology
(3R,5S,6E)-7-(4-(4-fluorophenyl)-6-(1-methylethyl)-2-(ethyl(methylsulfonyl)amino)-5-pyrimidinyl)-3,5-dihydroxy-6-heptenoic acid
(3R,5S,6E)-7-{4-(4-fluorophenyl)-6-isopropyl-2-[methyl(methylsulfonyl)amino]pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid
C22H28FN3O6S
CC(C)c1nc(nc(-c2ccc(F)cc2)c1\C=C\[C@@H](O)C[C@@H](O)CC(O)=O)N(C)S(C)(=O)=O
InChI=1S/C22H28FN3O6S/c1-13(2)20-18(10-9-16(27)11-17(28)12-19(29)30)21(14-5-7-15(23)8-6-14)25-22(24-20)26(3)33(4,31)32/h5-10,13,16-17,27-28H,11-12H2,1-4H3,(H,29,30)/b10-9+/t16-,17-/m1/s1
InChIKey=BPRHUIZQVSMCRT-VEUZHWNKSA-N
rosuvastatin
CHEBI:38545
rosuvastatin
http://purl.obolibrary.org/obo/chebi.owl
COMe:PRX000645
cytochrome P450
chebi_ontology
CYP
P450 protein
cytochrome P-450
CHEBI:38559
cytochrome P450
A racemate comprising equimolar amounts of (3R,5S)- and (3S,5R)-fluvastatin. An HMG-CoA reductase inhibitor, it is used (often as the corresponding sodium salt) to reduce triglycerides and LDL-cholesterol, and increase HDL-chloesterol, in the treatment of hyperlipidaemia.
http://purl.obolibrary.org/obo/chebi.owl
Beilstein:9168031
ChemIDplus:93957-54-1
CiteXplore:11273020
CiteXplore:12147804
CiteXplore:18410471
CiteXplore:18413661
CiteXplore:18452779
CiteXplore:18936176
CiteXplore:23212095
CiteXplore:23846727
DrugBank:DB01095
KEGG COMPOUND:93957-54-1
KEGG COMPOUND:C07014
KEGG DRUG:D07983
Patent:US4739073
Patent:WO8402131
Wikipedia:Fluvastatin
rac-(3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid
chebi_ontology
(+-)-fluvastatin
(6E)-erythro7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid
C24H26FNO4
Cranoc
erythro-(E)-3,5-dihydroxy-7-[3'-(4''-fluorophenyl)-1'-(1''-methylethyl)indol-2'-yl]hept-6-enoic acid
fluvastatin
fluvastatina
fluvastatine
fluvastatinum
rac-(3R,5S)-fluvastatin
rac-(3R,5S,6E)-7-(3-(4-fluorophenyl)-1-(1-methylethyl)-1H-indol-2-yl)-3,5-dihydroxy-6-heptenoic acid
CHEBI:38561
fluvastatin
http://purl.obolibrary.org/obo/chebi.owl
triazole
chebi_ontology
C2H3N3
CHEBI:38597
triazole
A member of the class of benzofurans consisting of a 1-benzofuran skeleton and its substituted derivatives thereof.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
CHEBI:38830
1-benzofurans
A dihydroxy monocarboxylic acid that is a member of the drug class known as statins, used primarily for lowering blood cholesterol and for preventing cardiovascular diseases.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:2910
CHEBI:39538
Beilstein:8373630
ChemIDplus:134523-00-5
CiteXplore:11693468
CiteXplore:15012735
CiteXplore:18720283
DrugBank:DB01076
HMDB:HMDB05006
KEGG COMPOUND:134523-00-5
KEGG COMPOUND:C06834
KEGG DRUG:D07474
PDBeChem:117
Patent:EP409281
Patent:US5273995
Reaxys:8373630
Wikipedia:Atorvastatin
(3R,5R)-7-[3-(anilinocarbonyl)-5-(4-fluorophenyl)-4-phenyl-2-(propan-2-yl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid
Atorvastatin
chebi_ontology
(3R,5R)-7-[2-(4-fluorophenyl)-5-(1-methylethyl)-3-phenyl-4-(phenylcarbamoyl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid
(R-(R*,R*))-2-(4-Fluorophenyl)-beta,delta-dihydroxy-5-(1-methylethyl)-3-phenyl-4-((phenylamino)carbonyl)-1H-pyrrole-1-heptanoic acid
7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID
7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]-3,5-DIHYDROXY-HEPTANOIC ACID
Atorlip
C33H35FN2O5
CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(O)=O
InChI=1S/C33H35FN2O5/c1-21(2)31-30(33(41)35-25-11-7-4-8-12-25)29(22-9-5-3-6-10-22)32(23-13-15-24(34)16-14-23)36(31)18-17-26(37)19-27(38)20-28(39)40/h3-16,21,26-27,37-38H,17-20H2,1-2H3,(H,35,41)(H,39,40)/t26-,27-/m1/s1
InChIKey=XUKUURHRXDUEBC-KAYWLYCHSA-N
atorvastatin
atorvastatina
atorvastatine
atorvastatinum
CHEBI:39548
atorvastatin
A fatty acid ester that is mevastatin carrying an additional methyl group on the carbobicyclic skeleton. It is used in as a antilipemic drug and has been found in fungal species such as Aspergillus terreus and Pleurotus ostreatus (oyster mushroom).
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:40299
CHEBI:6544
ChemIDplus:3631989
ChemIDplus:75330-75-5
CiteXplore:11375168
CiteXplore:11389707
CiteXplore:11483865
CiteXplore:18642339
CiteXplore:24093797
DrugBank:DB00227
HMDB:HMDB14372
KEGG COMPOUND:C07074
KEGG DRUG:75330-75-5
KEGG DRUG:D00359
KNApSAcK:C00000547
PDBeChem:803
Patent:CN103172602
Patent:WO2013090461
Reaxys:4720754
Wikipedia:Lovastatin
(1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxotetrahydro-2H-pyran-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl (2S)-2-methylbutanoate
LOVASTATIN
Lovastatin
chebi_ontology
(1S,3R,7S,8S,8aR)-1,2,3,7,8,8a-hexahydro-3,7-dimethyl-8-(2-(2R,4R)-(tetrahydro-4-hydroxy-6-oxo-2H-pyran-2-yl)ethyl)-1-naphthalenyl (S)-2-methyl-butyrate
2beta,6alpha-dimethyl-8alpha-(2-methyl-1-oxobutoxy)-mevinic acid lactone
6alpha-methylcompactin
C24H36O5
InChI=1S/C24H36O5/c1-5-15(3)24(27)29-21-11-14(2)10-17-7-6-16(4)20(23(17)21)9-8-19-12-18(25)13-22(26)28-19/h6-7,10,14-16,18-21,23,25H,5,8-9,11-13H2,1-4H3/t14-,15-,16-,18+,19+,20-,21-,23-/m0/s1
InChIKey=PCZOHLXUXFIOCF-BXMDZJJMSA-N
MK-803
ML-530B
Mevacor
Mevinolin
[H][C@]12[C@H](C[C@@H](C)C=C1C=C[C@H](C)[C@@H]2CC[C@@H]1C[C@@H](O)CC(=O)O1)OC(=O)[C@@H](C)CC
CHEBI:40303
lovastatin
A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It has been shown to exhibit antifungal activity.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:46079
CHEBI:5099
Beilstein:4269710
ChemIDplus:86386-73-4
CiteXplore:11366931
CiteXplore:16822276
CiteXplore:23171950
CiteXplore:23793863
DrugBank:DB00196
HMDB:HMDB14342
KEGG DRUG:D00322
PDBeChem:TPF
Patent:GB2099818
Patent:US4404216
Reaxys:7311650
Wikipedia:Fluconazole
2-(2,4-difluorophenyl)-1,3-bis-(1H-1,2,4-triazol-1-yl)propan-2-ol
chebi_ontology
2,4-difluoro-alpha,alpha-bis(1H-1,2,4-triazol-1-ylmethyl)benzyl alcohol
2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL
Biozole
C13H12F2N6O
Diflucan
Elazor
InChI=1S/C13H12F2N6O/c14-10-1-2-11(12(15)3-10)13(22,4-20-8-16-6-18-20)5-21-9-17-7-19-21/h1-3,6-9,22H,4-5H2
InChIKey=RFHAOTPXVQNOHP-UHFFFAOYSA-N
OC(Cn1cncn1)(Cn1cncn1)c1ccc(F)cc1F
Triflucan
fluconazol
fluconazole
fluconazolum
CHEBI:46081
fluconazole
A N-carbonylpiperazine that has formula C26H28Cl2N4O4.
http://purl.obolibrary.org/obo/chebi.owl
Beilstein:634785
DrugBank:DB01026
1-acetyl-4-(4-{[2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine
chebi_ontology
C26H28Cl2N4O4
CC(=O)N1CCN(CC1)c1ccc(OCC2COC(Cn3ccnc3)(O2)c2ccc(Cl)cc2Cl)cc1
InChI=1S/C26H28Cl2N4O4/c1-19(33)31-10-12-32(13-11-31)21-3-5-22(6-4-21)34-15-23-16-35-26(36-23,17-30-9-8-29-18-30)24-7-2-20(27)14-25(24)28/h2-9,14,18,23H,10-13,15-17H2,1H3
InChIKey=XMAYWYJOQHXEEK-UHFFFAOYSA-N
CHEBI:48339
ketoconazole
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
benzothiazepines
CHEBI:48684
benzothiazepine
Any molecular entity that contains carbon.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:25700
CHEBI:33244
chebi_ontology
.
organic compounds
organic entity
organic molecular entities
organic molecules
CHEBI:50860
organic molecular entity
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
Chemische Substanz
CHEBI:59999
chemical substance
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
Mischung
CHEBI:60004
mixture
A dioxolane that has formula C35H38Cl2N8O4.
http://purl.obolibrary.org/obo/chebi.owl
ChEMBL:17194821
ChemIDplus:84625-61-6
DrugBank:DB01167
KEGG DRUG:84625-61-6
KEGG DRUG:D00350
Wikipedia:Itraconazole
2-(butan-2-yl)-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one
Itraconazole
chebi_ontology
C35H38Cl2N8O4
CCC(C)n1ncn(-c2ccc(cc2)N2CCN(CC2)c2ccc(OC[C@H]3CO[C@@](Cn4cncn4)(O3)c3ccc(Cl)cc3Cl)cc2)c1=O
InChI=1S/C35H38Cl2N8O4/c1-3-25(2)45-34(46)44(24-40-45)29-7-5-27(6-8-29)41-14-16-42(17-15-41)28-9-11-30(12-10-28)47-19-31-20-48-35(49-31,21-43-23-38-22-39-43)32-13-4-26(36)18-33(32)37/h4-13,18,22-25,31H,3,14-17,19-21H2,1-2H3/t25?,31-,35-/m0/s1
InChIKey=VHVPQPYKVGDNFY-ZPGVKDDISA-N
Itrizole (TN)
Oriconazole
Sporanox (TN)
CHEBI:6076
itraconazole
A racemate is an equimolar mixture of a pair of enantiomers.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
melange racemique
racemates
racemic mixture
CHEBI:60911
racemate
Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen.
http://purl.obolibrary.org/obo/chebi.owl
Wikipedia:Azole
chebi_ontology
azoles
CHEBI:68452
azole
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
http://purl.obolibrary.org/obo/chebi.owl
chebi_ontology
organic molecules
CHEBI:72695
organic molecule
A lactam that is 2,3-dihydro-1,5-benzothiazepin-4(5H)-one in which positions 2 and 3 are substituted by 4-methoxyphenyl and acetoxy, respectively, while the hydrogen attached to the nitrogen is substituted by a 2-(dimethylamino)ethyl group.
http://purl.obolibrary.org/obo/chebi.owl
ChemIDplus:34933-06-7
Reaxys:25644899
5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate
chebi_ontology
3-acetoxy-5-(2-(dimethylamino)ethyl)-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one
C22H26N2O4S
COc1ccc(cc1)C1Sc2ccccc2N(CCN(C)C)C(=O)C1OC(C)=O
InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3
InChIKey=HSUGRBWQSSZJOP-UHFFFAOYSA-N
CHEBI:82814
5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate
A fatty acid ester comprising a dihydroxyheptanoic acid unit condensed into a lactone; a partially reduced naphthalene structure; and a 2,2-dimethylbutyric acyl substituent at C17. It is used as a cholesterol-lowering and anti-cardiovascular disease drug.
http://purl.obolibrary.org/obo/chebi.owl
CHEBI:45577
Beilstein:4768037
ChemIDplus:79902-63-9
CiteXplore:11336576
CiteXplore:12827636
CiteXplore:14561068
CiteXplore:14973129
CiteXplore:18199328
CiteXplore:18688862
CiteXplore:18936176
DrugBank:DB00641
KEGG DRUG:79902-63-9
KEGG DRUG:D00434
PDBeChem:SIM
Patent:EP33538
Patent:US4444784
Wikipedia:Simvastatin
(1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxotetrahydro-2H-pyran-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl 2,2-dimethylbutanoate
SIMVASTATIN
Simvastatin
chebi_ontology
(3R,5R)-7-{(1S,2S,6R,8S,8aR)-8-[(2,2-dimethylbutanoyl)oxy]-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl}-3,5-dihydroxyheptanoic acid
2,2-dimethylbutyric acid, 8-ester with (4R,6R)-6-(2-((1S,2S,6R,8S,8aR)-1,2,6,7,8,8a-hexahydro-8-hydroxy-2,6-dimethyl-1-naphthyl)ethyl)tetrahydro-4-hydroxy-2H-pyran-2-one
C25H38O5
CCC(C)(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@@H]12
InChI=1S/C25H38O5/c1-6-25(4,5)24(28)30-21-12-15(2)11-17-8-7-16(3)20(23(17)21)10-9-19-13-18(26)14-22(27)29-19/h7-8,11,15-16,18-21,23,26H,6,9-10,12-14H2,1-5H3/t15-,16-,18+,19+,20-,21-,23-/m0/s1
InChIKey=RYMZZMVNJRMUDD-HGQWONQESA-N
MK-733
Simvastatina
Simvastatine
Simvastatinum
Zocor
simvastatin
CHEBI:9150
simvastatin
A triazolobenzodiazepine that has formula C17H12Cl2N4.
http://purl.obolibrary.org/obo/chebi.owl
Beilstein:1226643
ChemIDplus:28911-01-5
DrugBank:DB00897
KEGG DRUG:D00387
Wikipedia:Triazolam
8-chloro-6-(2-chlorophenyl)-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine
chebi_ontology
C17H12Cl2N4
Cc1nnc2CN=C(c3ccccc3Cl)c3cc(Cl)ccc3-n12
Halcion
InChI=1S/C17H12Cl2N4/c1-10-21-22-16-9-20-17(12-4-2-3-5-14(12)19)13-8-11(18)6-7-15(13)23(10)16/h2-8H,9H2,1H3
InChIKey=JOFWLTCLBGQGBO-UHFFFAOYSA-N
CHEBI:9674
triazolam
The process of one material (absorbate) being retained by another (absorption).
http://purl.obolibrary.org/obo/chmo.owl
REX:0000188
CHMO:0002914
Gold Book, somewhat modified. It goes on "The process of one material (absorbate) being retained by another (absorbent); this may be the physical solution of a gas, liquid, or solid in a liquid, attachment of molecules of a gas, vapour, liquid, or dissolved substance to a solid surface by physical forces, etc."
absorption of material
He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene".
Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here:
http://code.google.com/p/clo-ontology/wiki/Cell_Lines
MB, SS, JZ, MAH, BP, CS, YH
The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.).
The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history. As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use.
cell line
A potential drug-drug interaction (PDDI) is an information content entity that specifies the possibility of a drug-drug interaction based on either reasonable extrapolation about drug-drug interaction mechanisms or a data item created by clinical studies, clinical observation or physiological experiment.
Mathias Brochhausen
potential drug-drug interaction
the DDI mechanism, the risk of it causing a clinical effect, the clinical effect brought about by that DDI, factor's that modify the probability of it occuring
An information content entity that is about a drug-drug interaction.
DDI description
drug-drug interaction description
Mathias Brochhausen
mechanistic assertion data item
A data item that is about a biological process
data item about biological process
A data item that is about a drug-drug interaction and the creation of which was triggered by an observation outside a controlled context (e.g. a clinical trial).
Mathias Brochhausen
observational data item about drug-drug interaction
A data item that is about a biological process and that is the specified output of a clinical study.
physiological observation from clinical study data item
A data item that is the output of a process of estimating, beyond the original observation range, the value of a variable on the basis of its relationship with another variable.
Mathias Brochhausen
https://en.wikipedia.org/w/index.php?title=Extrapolation&oldid=690284752
data item from extrapolation
A biological process that realizes the function of the gastrointestinal system (or any organ that is a part of it.). This includes digestion of ingested substances, absorption and eliminating waste.
Physiological activity and functions of the gastrointestinal system as a whole or of any of its parts, including digestion, absorption and eliminating waste.
gastrointestinal functioning
A plan specification that specifies processes to prevent or mitigate a drug-drug interaction
management option
An instance of this entity would represent an optional recommendation for the clinical management of patients who are exposed or about to be exposed to a potential DDI. Management options may be generated by expert opinion, consensus, and/or a review and synthesis of relevant evidence.
drug-drug interaction management option
A drug-drug interaction that has been the subject of a case report or study.
interaction occured
An instance of a drug-drug interaction that has been identified in case report or study.
reported drug-drug interaction
A data item that is the outcome of running a kinetic model and that states that drug A has some effects on the absorption, metabolism and elimination of drug B.
Evidence from a kinetic model that a drug-Y has some effect on the absorption, metabolism and elimination of drug-X.
pharmacokinetic interaction signal
Bioavailability is a disposition that is borne by a drug product and is realized by the process of a proportion of the active pharmaceutical ingredient in that drug product reaching systemic circulation.
Anuj Shah
Mathias Brochhausen
bioavailability
An information content entity that makes a statement about a drug product being an object drug in a drug interaction.
Mathias Brochhausen
object drug information
The role that inheres in a drug product or drug ingredient and that is realized by being affected by another drug pharmacokinetically or pharmacodynamically in a drug drug interaction.
Daniel C. Malone
Jodi Schneider
Mathias Brochhausen
Philip E. Empey
Richard D. Boyce
William R. Hogan
http://www.hanstenandhorn.com/article-d-i.html
object drug role
The role that inheres in a drug product or drug ingredient that is realized by affecting another drug pharmacokinetically or pharmacodynamically in a drug drug interaction.
Daniel C. Malone
Jodi Schneider
Mathias Brochhausen
Philip E. Empey
Richard C. Boyce
William R. Hogan
http://www.hanstenandhorn.com/article-d-i.html
precipitant drug role
An information content entity that makes a statement about a drug product being an precipitant drug in a drug interaction.
Mathias Brochhausen
precipitant drug information
A potential drug drug interaction that is about a drug metabolism.
Mathias Brochhausen
metabolic potential drug-drug interaction
A disposition inhering in a drug product that when realized is realized by processes that negatively affect the safety or the efficacy of the drug product, or increase its toxicity..
Mathias Brochhausen
narrow therapeutic index
A metabolism induction potential drug-drug interaction that is about an decrease of metabolic activity because of either a decreased expression of the enzyme or inference with how the enzyme contributes to the metabolic process.
Mathias Brochhausen
metabolism inhibition potential drug-drug interaction
A metabolism induction potential drug-drug interaction that is about an increase of an enzyme participating in the metabolic process.
Mathias Brochhausen
metabolism induction potential drug-drug interaction
A drug product or drug ingredient that participates in a drug-drug interaction.
Drug participant in drug-drug interaction
A drug entity that participate in a drug-drug interaction but for which its role is not assignable as a precipitant or object.
material entity participant in drug-drug interaction
A biological process that results in a clinically meaningful change to the response of at least one co-administrated drug.
DDI
A clinically meaningful alteration in the exposure and/or response to a drug (object drug) that has occurred as a result of the co-administration of another drug (precipitant drug)Oates JA. Chapter 5. Goodman and Gilman 11th ed (2006):117–36; Hines. Response can refer to either precipitating an adverse event or altering the therapeutic effect of the object drug. Although some DDIs may be used for therapeutic benefit, this paper focuses on those with adverse clinical consequences. (based on the 2013 DDI conference series) / has participant some mechanism.
drug-drug interaction
A planned process of administering more than one drug to the same individual over a specific time interval.
This class currently does not have a restriction. One candidate restriction is a necessary condition: 'has participant at some time' min 2 'drug product'. I was not able to find an OWL reasoner for Protege 5 that supports cardinality restrictions.
An instance of this occurs when at least two or more drugs are taken in a specific time interval and the individual time interval for each drug administration overlaps with the other drug's or drugs' time interval(s). (SG1)
drug co-administration
An information content entity that represents a drug interaction as a directional series of molecular processes.
An instance of this entity would represent the biochemical process by which pharmacokinetic or pharmacodynamic DDI is thought to occur.
drug interaction mechanism
An information content entity that is about a drug co-administration and is intended to be specified input into the assessment of whether a drug-drug interaction exists or not.
An instance of this type represents a information artifact used to establish knowledge for or against the existence of a drug-drug interaction.
drug-drug interaction evidence
A potential drug-drug interaction that is causally linked to an elevated risk of an adverse event that warrants a drug-drug interaction management option.
Alternative definitions use the risk of harm instead of the risk of an AE.
clinically relevant potential drug-drug interaction
A measurement datum that is the specified outcome of a drug bioavailability assay.
Anuj Shah
Mathias Brochhausen
F
bioavailability measurement datum
An assay with the objective to capture information about the bioavailability of an active ingredient in a drug product.
Anuj Shah
Mathias Brochhausen
drug bioavailability assay
An entity that is the result of a drug-drug interaction.
drug-drug interaction effect
Anuj Shah
Mathias Brochhausen
It is a disposition that is borne by drug product and is realized by the metabolism of the active pharmaceutical ingredient in that drug product before entering systemic circulation, when ingested.
first pass effect disposition
Anuj Shah
Mathias Brochhausen
An assay with the objective to capture information about the first pass metabolism of an active ingredient in a drug product.
drug first pass metabolism assay
Anuj Shah
Mathias Brochhausen
A measurement datum that is the specified outcome of a drug first pass metabolism assay.
first pass metabolism measurement datum
Anuj Shah
Mathias Brochhausen
Daintith J (ed.): A Dictionary of Chemistry. 2008. Oxford University Press, Oxford UK.
Absorbability is a disposition that is borne by a material entity that if realized is realized by the material entity taken up by another material entity in a different state of matter.
absorbability
An assay with the objective to capture information about the absorbability of an active ingredient in a drug product.
Anuj Shah
Mathias Brochhausen
drug absorbability assay
A measurement datum that is the specified outcome of an drug absorbability assay.
Anuj Shah
Mathias Brochhausen
AUC
absorbability measurement datum
Anuj Shah
Mathias Brochhausen
An assay that measures the maximum concentration of an active ingredient of a drug product in a specified compartment of the body of an organism after the first dose of the drug product has been administered.
drug maximum concentration assay
A measurement datum that is the specified outcome of a drug maximum concentration assay.
Anuj Shah
Mathias Brochhausen
Cmax
drug maximum concentration measurement datum
A role that is borne by the enzyme responsible for 50% or more of the active pharmaceutic ingredient or metabolite’s total clearance from the body. The role role is realized by the metabolic process of the active pharmaceutical ingredient or metabolite.
Anuj Shah
Mathias Brochhausen
primary total clearance enzyme role
Anuj Shah
Mathias Brochhausen
A role that is borne by the enzyme responsible for 50% or more of the active pharmaceutic ingredient or metabolite’s total metabolic clearance from the body.
primary metabolic clearance enzyme role
A drug-drug interaction description that is part of a drug package insert.
drug-drug interaction description from drug package insert
A drug-drug interaction description from a drug package insert for an FDA approved drug.
drug-drug interaction description from FDA label information
A document that is provided along with a medication and that gives additional information about that medication.
https://en.wikipedia.org/w/index.php?title=Package_insert&oldid=699801598
drug package insert
FDA drug label
http://www.fda.gov/forpatients/other/offlabel/default.htm
A drug package insert for FDA-approved drugs that gives information about the drug, including the approved doses and how it's to be given to treat the medical condition for which it was approved.
U.S. Food and Drug Administration drug label
An area under curve in a plot of concentration of granular part of a drug product in some matrix (medium) against time.
pharmacokinetic area under curve
An information content entity that is part of a drug package insert and that is about a pharmacokinetic area under the curve measurement result.
Mathias Brochhausen
drug package AUC information
Mathias Brochhausen
Standards Development Working Group of the "Addressing PDDI Evidence Gaps" porject.
An information content entity that provides statements or data that are used to support or refute an assertion.
obsolete_evidence information content entity
true
Mathias Brochhausen
AUC information
An information content entity that is about a pharmacokinetic area under curve.
pharmacokinetic area under curve information
2
A pharmacokinetic area under curve information that is about at least 2 area under curve measurments and the time series shows an increase of the area under curve.
Mathias Brochhausen
information about increase of pharmacokinetic area under the curve
2
A pharmacokinetic area under curve information that is about at least 2 area under curve measurments and the time series shows a decrease of the area under curve.
Mathias Brochhausen
information about decrease of pharmacokinetic area under the curve
A biological process that has as a participant a part of a drug product and includes absorption, distribution, metabolism and excretion of that substance.
Mathias Brochhausen
"Addressing PDDI Evidence Gaps" Standards Development Group.
pharmacokinetic process
An information content entity that is used to support or refute an assertion.
Mathias Brochhausen
"Addressing PDDI Evidence Gaps" Standards Development Group
evidence information content entity
An information content entity that is part of an evidence information content entity and mentions the specified input to an assay.
Mathias Brochhausen
"Addressing PDDI Evidence Gaps" Standards Development Group
evidence material information
Mathias Brochhausen
"Addressing PDDI Evidence Gaps" Standards Development Group
A data item that is part of an evidence information content entity and is the specified output of an assay.
evidence data item
An evidence information content entity that is about a clinical drug trial.
Mathias Brochhausen
EV_Clinical_Trial
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from clinical study
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process, as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from drug metabolism identification experiment
An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process, as it's specified input.
Mathias Brochhausen
EV_EX_Met_Enz_Inhibit
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from drug metabolism inhibition experiment
Mathias Brochhausen
EV_EX_Trans_Prot_ID
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
This is going to be a fully axiomatized class. The axiom is coming soon and will be based on the material found here: https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZGlrcmFuZGlyfGd4OjE3OWNhYzFmMDc0ZGNlYmE
evidence information from transport protein identification experiment
Mathias Brochhausen
EV_EX_Trans_Prot_Inhibit
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
This is going to be a fully axiomatized class. The axiom is coming soon and will be based on the material found here: https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZGlrcmFuZGlyfGd4OjE3OWNhYzFmMDc0ZGNlYmE
evidence information from transport protein inhibition experiment
An evidence information content entity that is about an assay that was triggered by an adverse drug event.
Mathias Brochhausen
EV_Case_Report_ADE
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from observation-based adverse drug event report
An evidence information content entity that is about an assay that realizes an observation design.
Mathias Brochhausen
EV_Observational
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from observational study
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID_Cyp450
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 drug metabolism identification experiment
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has a cell line as a specified input.
Mathias Brochhausen
EV_EX_Enz_ID_Cyp450_Hum_Recom
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 recombinant drug metabolism identification experiment
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has chemical inhibitors as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Chem
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 recombinant drug metabolism identification experiment using chemical inhibitors
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has antibody inhibitors as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Antibody
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 recombinant drug metabolism identification experiment using antibody inhibitors
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 human microsome drug metabolism identification experiment
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has chemical inhibitors as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome_Chem
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 human microsome drug metabolism identification experiment using chemical inhibitors
An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has antibody inhibitors as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome_Antibody
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 human microsome drug metabolism identification experiment using antibody inhibitors
An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input.
Mathias Brochhausen
EV_EX_Met_Enz_Inhibit_Cyp450
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 metabolic enzyme inhibition experiment
An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input.
Mathias Brochhausen
EV_CT_DDI
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from drug-drug interaction clinical trial
An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input and does not have group randomization as a part.
Mathias Brochhausen
EV_PK_DDI_NR
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from non-randomized drug-drug interaction clinical trial
An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input, and that does not have group randomization as a part, and that realizes a clinical study design that has parallel group design as a part.
Mathias Brochhausen
EV_PK_DDI_Par_Grps
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from parallel groups drug-drug interaction clinical trial'
An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input and does have group randomization as a part.
Mathias Brochhausen
EV_PK_DDI_RCT
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from randomized drug-drug interaction clinical trial
An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics.
Mathias Brochhausen
EV_CT_Pharmacokinetic
evidence information from pharmacokinetic trial
An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics and that has organisms as participants that participated in genotyping.
Mathias Brochhausen
EV_CT_PK_Genotype
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from genotyped pharmacokinetic trial
An evidence information content entity that is about an assay that was triggered by an occurrent.
Mathias Brochhausen
EV_Case_Report
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from observation-based report
An evidence information content entity that is about an assay that realizes an observation design and has a drug product as a specified input, and that focuses on pharmacokinetics in an organism.
Mathias Brochhausen
EV_PK_Observational
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from observational pharmacokinetic study
An evidence information content entity that is about an assay that realizes an observation design and has at least two drug products as a specified input, and that focuses on pharmacokinetics in an organism.
Mathias Brochhausen
EV_PK_DDI_Observational
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from observational drug-drug interaction study
An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input, and that has cell lines as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_Inhibit_Cyp450_Hum_Recom
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 recombinant drug metabolism inhibition experiment
An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input, and that has human tissue specimens as a specified input.
Mathias Brochhausen
EV_EX_Met_Enz_Inhibit_Cyp450_Hum_Microsome
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from CYP450 human microsome drug metabolism inhibition experiment
A data set that is structured and stored on a computer and that is publicly available and contains reports of adverse events.
Mathias Brochhausen
public adverse event reporting database
An evidence information content entity that is about an assay that was triggered by an adverse drug event, and that is part on a publicly accessible database for adverse event reporting.
Mathias Brochhausen
EV_Case_Report_ADE_Public_Reported
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from a publicly reported observation-based adverse drug event report
An evidence information content entity that is about an assay that was triggered by an adverse drug event following the administration of at least two drugs.
Mathias Brochhausen
EV_Case_Report_DI
https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html
evidence information from an observation-based case-report of a drug interaction
Mathias Brochhausen
A protocol that specifies methodology to assess the likelihood of a drug to be the cause for an adverse event by answering a set of questions about the drug reaction report.
adverse drug reaction causality evaluation protocol
An evidence information content entity that is about an assay that was triggered by an adverse drug event following the administration of at least two drugs, and that is the specified outcome of a adverse drug reaction causality evaluation.
Mathias Brochhausen
EV_Case_Report_DI_Evaluated
evidence information from an evaluated observation-based case-report of a drug interaction
Mathias Brochhausen
Cl
A measurement datum that is the specified output of measuring the volume of plasma that is completely cleared off of a substance per unit time.
clearance measurement datum
Mathias Brochhausen
A dimensionless ratio unit which describes the relation between the two numbers x and y by giving the multiplier necessary to make x equal to y.
fold
An information content entity that is part of a pharmacokinetic parameter ratio and that describes whether the relationship between the numbers of the ratio is a positive or a negative one.
Mathias Brochhausen
pharmacokinetic parameter ratio directionality
Mathias Brochhausen
AUC ratio
An information content entity that describes the relation between the mean (arithmetic and geometric) pharmacokinetic area under the curve (AUC) for a given active ingredient or metabolite in absence of another drug, and the mean (arithmetic and geometric) pharmacokinetic AUC for a given active ingredient or metabolite coadministered with another active ingredient or metabolite.
area under the curve ratio
An information content entity that describes the relation between the mean (arithmetic and geometric) of a measurement of the volume of plasma from which an active ingredient or metabolite is completely removed by the kidney in a given amount of time in absence of another drug, and the mean (arithmetic and geometric) of a measurement of the volume of plasma from which an active ingredient or metaboliteis completely removed by the kidney in a given amount of time when coadministered with another active ingredient or metabolite.
CL_R ratio
renal clearance ratio
An information content entity that describes the relationship between the mean (arithmetic and geometric) of measurements of a pharmacokintect parameter for a given drug A in absence of another drug and the mean (arithmetic and geometric) of measurements of a pharmacokintect parameter for a given drug A coadministrated with another drug B.
Mathias Brochhausen
pharmacokinetic parameter ratio
An pharmacokinetic parameter directionality that describes negative relationship between the numbers of the ratio.
Mathias Brochhausen
pharmacokinetic parameter ratio decrease
An pharmacokinetic parameter directionality that describes positive relationship between the numbers of the ratio.
Mathias Brochhausen
pharmacokinetic parameter ratio increase
An information content entity that describes the relation between the mean (arithmetic and geometric) of the drug maximum concentration measurements for a given active ingredient or metabolite in absence of another active ingredient or metabolite, and the mean (arithmetic and geometric) of the drug maximum concentration measurements for a given active ingredient or metabolite coadministered with another active ingredient or metabolite.
Mathias Brochhausen
Cmax ratio
drug maximum concentration ratio
An information content entity that describes the relation between the mean (arithmetic and geometric) time it takes for half of a given active ingredient or metabolite to be removed from the system in absence of another active ingredient or metabolite, and the mean (arithmetic and geometric) time it takes for half of a given active ingredient or metabolite to be removed from the system when coadministered with another active ingredient or metabolite.
Mathias Brochhausen
t1/2 ratio
half-life ratio
An information content entity that describes the relation between the mean (arithmetic and geometric) of a measurement of the volume of plasma from which an active ingredient or a metabolite is completely removed by the liver in a given amount of time in absence of another drug, and the mean (arithmetic and geometric) of a measurement of the volume of plasma from which an active ingredient or metabolite is completely removed by the liver in a given amount of time when coadministered with another active ingredient or metabolite.
Mathias Brochhausen
CL_H ratio
hepatic clearance ratio
a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role
William Hogan
http://purl.obolibrary.org/obo/dron.owl
William Hogan
drug product
active ingredient role
a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism
William R. Hogan
http://purl.obolibrary.org/obo/dron.owl
active ingredient
role of a scattered molecular aggregate
a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes
William R. Hogan
http://purl.obolibrary.org/obo/dron.owl
role of scattered molecular aggregate
administration of a drug product to an organism
a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism
William R. Hogan
http://purl.obolibrary.org/obo/dron.owl
drug administration
Body substance in liquid state contained in the lumen of arterial and venous trees, blood capillary and the cardiac chambers; constitutes the liquid phase of blood.
http://purl.obolibrary.org/obo/fma.owl
Blood plasma
fma
FMA:62970
Portion of plasma
Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures. Examples: saliva, semen, cerebrospinal fluid, respiratory air, urine, feces, blood, plasma, lymph.
http://purl.obolibrary.org/obo/fma.owl
Body substance
fma
FMA:9669
Portion of body substance
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
http://purl.obolibrary.org/obo/go.owl
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
molecular_function
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
http://purl.obolibrary.org/obo/go.owl
Wikipedia:Enzyme
enzyme activity
molecular_function
GO:0003824
catalytic activity
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
http://purl.obolibrary.org/obo/go.owl
GO:0008372
NIF_Subcellular:sao-1337158144
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
cellular_component
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
http://purl.obolibrary.org/obo/obi.owl
biological_process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
http://purl.obolibrary.org/obo/go.owl
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
biological_process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
http://purl.obolibrary.org/obo/go.owl
down regulation of metabolic process
down-regulation of metabolic process
downregulation of metabolic process
negative regulation of metabolism
inhibition of metabolic process
biological_process
GO:0009892
negative regulation of metabolic process
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
http://purl.obolibrary.org/obo/go.owl
cellular_component
GO:0019814
Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
immunoglobulin complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
http://purl.obolibrary.org/obo/go.owl
macromolecule complex
cellular_component
GO:0032991
macromolecular complex
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
http://purl.obolibrary.org/obo/go.owl
Wikipedia:Antibody
antibody
cellular_component
GO:0042571
Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
immunoglobulin complex, circulating
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
http://purl.obolibrary.org/obo/go.owl
Wikipedia:Protein_complex
protein-protein complex
cellular_component
GO:0043234
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
protein complex
The chemical reactions and pathways by which individual cells transform chemical substances.
http://purl.obolibrary.org/obo/go.owl
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
http://purl.obolibrary.org/obo/go.owl
GO:0043119
positive regulation of physiological process
up regulation of biological process
up-regulation of biological process
upregulation of biological process
activation of biological process
stimulation of biological process
biological_process
GO:0048518
positive regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
http://purl.obolibrary.org/obo/go.owl
GO:0043118
down regulation of biological process
down-regulation of biological process
downregulation of biological process
negative regulation of physiological process
inhibition of biological process
biological_process
GO:0048519
negative regulation of biological process
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
http://purl.obolibrary.org/obo/go.owl
GO:0050791
regulation of physiological process
biological_process
GO:0050789
regulation of biological process
Any process that modulates a measurable attribute of any biological process, quality or function.
http://purl.obolibrary.org/obo/go.owl
regulation
biological_process
GO:0065007
biological regulation
A role that inheres in a protein or a compound upon which enzyme catalyzes. It is realized in the enzymatic reaction processes, where the molecules at the beginning of the process, called substrates, are converted into different molecules, called products.
enzyme substrate role
Homo sapiens
human
human being
man
http://purl.obolibrary.org/obo/obi.owl
Homo sapiens
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
adverse event
an adverse event that occurs after a drug administration
adverse drug event
A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment.
http://en.wikipedia.org/wiki/Contraindication
contraindication
a drug adverse event that is caused by a drug adiministration. Here a causal effect is established between the drug administration and the adverse event.
causal adverse drug event
serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death.
severe adverse event
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
http://purl.obolibrary.org/obo/obi.owl
processed material
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
http://purl.obolibrary.org/obo/obi.owl
evaluant role
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
http://purl.obolibrary.org/obo/obi.owl
study assay
any method
assay
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
PlanAndPlannedProcess Branch
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
http://purl.obolibrary.org/obo/obi.owl
study protocol
protocol
enzyme
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything
that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
person: Melanie Courtot
GROUP:OBI
http://purl.obolibrary.org/obo/obi.owl
enzyme
scattered molecular aggregate
the sodium and chloride ions in a glass of salt water
A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
PERSON: Alan Ruttenberg
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
http://purl.obolibrary.org/obo/dron.owl
scattered molecular aggregate
specimen collection process
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
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.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Bjoern Peters
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
http://purl.obolibrary.org/obo/obi.owl
specimen collection process
in vitro design
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
Person: Chris Stoeckert, Jie Zheng
MO_347 in_vitro_design
http://purl.obolibrary.org/obo/obi.owl
in vitro design
tissue specimen
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
PERSON: Chris Stoeckert, Jie Zheng
MO_954 organism_part
http://purl.obolibrary.org/obo/obi.owl
tissue specimen
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
http://purl.obolibrary.org/obo/obi.owl
value specification
organism
animal
fungus
plant
virus
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.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
http://purl.obolibrary.org/obo/obi.owl
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
http://purl.obolibrary.org/obo/obi.owl
specimen
cultured cell population
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948).
A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
PERSON:Matthew Brush
cell culture sample
PERSON:Matthew Brush
http://purl.obolibrary.org/obo/obi.owl
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
cultured cell population
observation design
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
Philippe Rocca-Serra
OBI branch derived
http://purl.obolibrary.org/obo/obi.owl
observation design
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
PERSON: Chris Stoeckert
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
http://purl.obolibrary.org/obo/obi.owl
study design
clinical study design
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
The definition needs to be extended to other things than simply patients
PlanAndPlannedProcess Branch
Clinical Research Glossary Version 4.0 CDICS glossary group
http://purl.obolibrary.org/obo/obi.owl
clinical study design
parallel group design
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
Philippe Rocca-Serra
independent measure design
http://www.holah.karoo.net/experimentaldesigns.htm
http://purl.obolibrary.org/obo/obi.owl
parallel group design
group assignment
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
group assignment is a process which has an organism as specified input and during which a role is assigned
Philippe Rocca-Serra
cohort assignment
study assignment
OBI Plan
http://purl.obolibrary.org/obo/obi.owl
group assignment
Albert Goldfain
creation date: 2009-06-23T11:53:49Z
http://purl.obolibrary.org/obo/ogms.owl
bodily process
A bodily process that is clinically abnormal.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:54:29Z
http://purl.obolibrary.org/obo/ogms.owl
pathological bodily process
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=35
creation date: 2010-03-31T04:51:11Z
http://purl.obolibrary.org/obo/dron.owl
treatment
PMID:12892658 "Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change."
Area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph
PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch
Orlaith Burke, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran
area under curve
Anatomical entity that has mass.
http://purl.obolibrary.org/obo/uberon.owl
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.
http://purl.obolibrary.org/obo/uberon.owl
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
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
http://www.ebi.ac.uk/efo/efo.owl
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
digestive
AAO:0000129
BILA:0000082
BTO:0000058
CALOHA:TS-1293
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MAT:0000018
MA:0002431
MESH:A03
MIAA:0000018
NCI_Thesaurus:Digestive_System
SNOMEDCT:278859004
TADS:0000170
TAO:0000339
WBbt:0005748
Wikipedia:Digestive_system
XAO:0000125
ZFA:0000339
alimentary system
alimentary tract
gastrointestinal system
gut
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
galen:DigestiveSystem
uberon
UBERON:0001007
digestive system
A unit of measurement is a standardized quantity of a physical quality.
http://purl.obolibrary.org/obo/uo.owl
george gkoutos
unit.ontology
UO:0000000
unit
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
http://purl.obolibrary.org/obo/uo.owl
george gkoutos
unit.ontology
UO:0000186
dimensionless unit
A dimensionless ratio unit which denotes numbers as fractions of 100.
http://purl.obolibrary.org/obo/uo.owl
george gkoutos
%
unit.ontology
UO:0000187
percent
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
http://purl.obolibrary.org/obo/uo.owl
george gkoutos
unit.ontology
UO:0000190
ratio
http://purl.org/obo/owl/go_xp_all
GO:0005554
molecular_function
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
molecular_function
http://purl.org/obo/owl/go_xp_all
molecular_function
catalytic activity
http://purl.org/obo/owl/go_xp_all
GO:0008151
GO:0050875
biological_process
cellular process
http://purl.org/obo/owl/go_xp_all
biological_process
drug metabolic process
http://www.ebi.ac.uk/efo/efo.owl
Genotyping
NCIt:C45447
An assay in which variation in the genome is analysed
ArrayExpress production team
James Malone
genotyping
true
group randomization
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
group randomization
http://purl.obolibrary.org/obo/obi.owl
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.