Drug-drug Interaction and Drug-drug Interaction Evidence Ontology
Anuj Shah
Dan Malone
Jessica Tay-Sontheimer
Jingjing Yu
Jodi Schneider
Philip E. Empey
Richard D. Boyce
William R. Hogan
Mathias Brochhausen
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/).
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.
DIDEO
BFO OWL specification label
BFO CLIF specification label
Cell line LINCS ID
STR profile
editor preferred label
editor preferred term
editor preferred term~editor preferred label
example of usage
has curation status
definition
editor note
definition editor
term editor
alternative term
definition source
curator note
imported from
expand expression to
OBO foundry unique label
elucidation
has associated axiom(fol)
has literature mining keywords
MPIO user-centered definition
ISA alternative term
temporal interpretation
Unique Apollo Label
Creator
Source
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
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.
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
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
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.
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
begins_to_exist_during
[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
[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 )
organismally_begins_to_exist_during
there is some extended organism e & p1 occurs_in e & p2 occurs_in e & p1 immediately precedes p2
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.
is substrate of
realizes substrate role
involves substrate
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.
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.
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
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
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
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
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
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
Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process.
regulates
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
Chris Mungall
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.
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.
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)".
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.
capable of part of
x actively participates in y if and only if x participates in y and x realizes some active role
actively participates in
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.
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.
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.
ends with
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
consumes
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
produces
has output
a particular instances of akt-2 enables some instance of protein kinase activity
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
enabled by
regulated by
negatively regulated by
input of
output of
causally downstream of
directly inhibits
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
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
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.
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
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
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.
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.
An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected.
Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b
Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
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.
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
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
causally influences (material entity to material entity)
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.
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.
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).
has_proper_part
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
A measurement datum that is the output of counting.
count
An identifier that denotes a drug product.
drug identifier
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.
(2S,3S)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate
(+)-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
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
Abbreviation for nicotinamide-adenine dinucleotide when its oxidation state is unknown or unspecified. It is used in metabolic pathways like glycolysis and citric acid cycle.
A steroid glucosiduronic acid having 17alpha-estradiol as the steroid component.
17alpha-hydroxyestra-1,3,5(10)-trien-3-yl beta-D-glucopyranosiduronic acid
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
NADPH is the reduced form of NADP+; used in anabolic reactions, such as lipid and nucleic acid synthesis, which require NADPH as a reducing agent.
2'-O-phosphonoadenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate}
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Reduced nicotinamide adenine dinucleotide phosphate
dihydronicotinamide-adenine dinucleotide phosphate
reduced nicotinamide-adenine dinucleotide phosphate
A tripeptide compound consisting of glutamic acid attached via its side chain to the N-terminus of cysteinylglycine.
A coenzyme found in all living cells; consists of two nucleotides joined through their 5'-phosphate groups, with one nucleotide containing an adenine base and the other containing nicotinamide.
adenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate}
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Reduced nicotinamide adenine dinucleotide
nicotinamide adenine dinucleotide (reduced)
A UDP-sugar having alpha-D-glucuronic acid as the sugar component.
uridine 5'-[3-(alpha-D-glucopyranuronosyl) dihydrogen diphosphate]
An adenosine bisphosphate having monophosphate groups at the 3'- and 5'-positions and a sulfo group attached to the phosphate at position 5'.
A lactone having a six-membered lactone ring.
An organic heterocyclic compound containing a benzene ring fused to an imidazole ring.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable 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.
A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17.
chemical entity
A role played by the molecular entity or part thereof within a biological context.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
Any carboxylic acid with at least one hydroxy group.
A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.
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.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
An organoiodine compound that has formula C25H29I2NO3.
2-Butyl-3-benzofuranyl 4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl ketone
An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms.
An N-sulfonylurea that consists of 1-butylurea having a tosyl group attached at the 3-position.
A chromenone having the keto group located at the 2-position.
2-Propenoic acid, 3-(2-hydroxyphenyl)-, d-lactone
2-Propenoic acid, 3-(2-hydroxyphenyl)-, delta-lactone
A propanone that is propan-1-one substituted by a tert-butylamino group at position 2 and a 3-chlorophenyl group at position 1.
An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands).
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
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.
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.
A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.
A macromolecule formed by a living organism.
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.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
Any organic molecule that consists of atoms connected in the form of a ring.
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).
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.
A 17beta-hydroxy steroid that is testosterone bearing an additional hydroxy substituent at the 6beta-position.
Conjugated proteins containing heme as the prosthetic group.
A substance that diminishes the rate of a chemical reaction.
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.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Any molecular entity consisting of more than one atom.
A member of the class of 1,3-benzoxazoles that is 1,3-benzoxazol-2-ol in which the hydrogen atom at position 5 is substituted by chlorine. A centrally acting muscle relaxant with sedative properties, it is used for the symptomatic treatment of painful muscle spasm.
A coordination entity in which the central atom to which the ligands are attached comes from groups 1, 2, 13, 14, 15, 16, 17, or 18 of the periodic table.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
A molecular entity consisting of two or more chemical elements.
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).
(3R,5S,6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid
(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
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.
rac-(3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid
(6E)-erythro7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid
erythro-(E)-3,5-dihydroxy-7-[3'-(4''-fluorophenyl)-1'-(1''-methylethyl)indol-2'-yl]hept-6-enoic acid
rac-(3R,5S,6E)-7-(3-(4-fluorophenyl)-1-(1-methylethyl)-1H-indol-2-yl)-3,5-dihydroxy-6-heptenoic acid
A member of the class of benzofurans consisting of a 1-benzofuran skeleton and its substituted derivatives thereof.
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.
(3R,5R)-7-[3-(anilinocarbonyl)-5-(4-fluorophenyl)-4-phenyl-2-(propan-2-yl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid
(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
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).
(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
(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
An organic heterotetracyclic compound that is morphinan substituted by a methoxy group at position 3 and a methyl group at position 7. It is used as an antitussive drug for suppressing cough.
A tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia. It is a mitotic inhibitor used in cancer chemotherapy. Note that the use of the former generic name 'taxol' is now limited, as Taxol is a registered trade mark.
4alpha,10beta-bis(acetyloxy)-13alpha-[(2S,3S)-3-benzamido-2-hydroxy-3-phenylpropanoyloxy]-1,7beta-dihydroxy-9-oxo-5beta,20-epoxytax-11-en-2alpha-yl benzoate
(2aR-(2aalpha,4beta,4abeta,6beta,9alpha(alpha R*,betaS*),11alpha,12alpha,12balpha))-beta-(Benzoylamino)-alpha-hydroxybenzenepropanoic acid 6,12b-bis(acetyloxy)-12-(benzoyloxy)-2a,3,4,4a,5,6,9,10,11,12,12a,12b-dodecahydro-4,11-dihydroxy-4a,8,13,13-tetramethyl-5-oxo-7,11-methano-1H-cyclodeca(3,4)benz(1,2-b)oxet-9-yl ester
5beta,20-Epoxy-1,2-alpha,4,7beta,10beta,13alpha-hexahydroxytax-11-en-9-one 4,10-diacetate 2-benzoate 13-ester with (2R,3S)-N-benzoyl-3-phenylisoserine
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.
2,4-difluoro-alpha,alpha-bis(1H-1,2,4-triazol-1-ylmethyl)benzyl alcohol
A monocarboxylic acid consisting of phenylacetic acid having a (2,6-dichlorophenyl)amino group at the 2-position.
2-[(2,6-dichlorophenyl)amino]benzeneacetic acid
{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid
2-((2,6-dichlorophenyl)amino)benzeneacetic acid
[2-(2,6-dichloroanilino)phenyl]acetic acid
A N-carbonylpiperazine that has formula C26H28Cl2N4O4.
Any molecular entity that contains carbon.
A monocarboxylic acid that is the 4'-hydroxylated metabolite of diclofenac.
{2-[(2,6-dichloro-4-hydroxyphenyl)amino]phenyl}acetic acid
(o-(2,6-Dichloro-4-hydroxyanilino)phenyl)acetic acid
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A dioxolane that has formula C35H38Cl2N8O4.
A racemate is an equimolar mixture of a pair of enantiomers.
A urea that consists of 1-butylurea having a 4-hydroxymethylbenzenesulfonyl group attached at the 3-position.
A sulfoxide that is omeprazole in which one of the methyl hydrogens at position 5 on the pyridine ring is substituted by a hydroxy group.
A taxane diterpenoid that consists of paclitaxel bearing an additional hydroxy substituent at the 6alpha-position.
(2alpha,5beta,6alpha,7beta,10beta,13alpha)-4,10-diacetoxy-13-{[(2R,3S)-3-(benzoylamino)-2-hydroxy-3-phenylpropanoyl]oxy}-1,6,7-trihydroxy-9-oxo-5,20-epoxytax-11-en-2-yl benzoate
A magnesium salt comprising of two chlorine atoms bound to a magnesium atom.
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.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate
A racemate comprising equimolar amounts of (R)- and (S)-omeprazole.
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.
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.
(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
(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
A triazolobenzodiazepine that has formula C17H12Cl2N4.
A separation method where components of a sample are separated on the basis of their density in a centrifuge according to the centrifugal force they experience. Samples are spun at >5000 rpm.
The process of one material (absorbate) being retained by another (absorption).
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."
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.
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
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
WEB: http://web.expasy.org/cellosaurus/CVCL_0045
WEB: https://www.atcc.org/Products/All/CRL-1573.aspx
293-derived cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12
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.
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
A data item that is about a biological process
mechanistic assertion data item
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).
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.
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
"Use only if benefit outweighs risk: “When a systemic dose of epinephrine is given to a person on one of these nonselective beta-blockers, an acute hypertensive reaction is almost certain. Systolic BPs of 250 mm/Hg are not uncommon. Most people can probably withstand a short episode of such a hypertensive reaction without permanent sequelae, but strokes have occurred in susceptible patients. Thus, it is best to avoid this reaction if possible. If a patient is likely to receive systemic epinephrine, it would be prudent to use a cardioselective beta-blocker.” (Title: Individualized Drug Interaction Alerts; Authors: Daniel C. Malone , University of Arizona; John Horn, Philip Hansten, University of Washington)
No precaution: “If the NSAID is being used as an analgesic or antipyretic, it would be prudent to use an alternative such as acetaminophen. In some people, acetaminophen can increase the anticoagulant effect of warfarin, so monitor the INR if acetaminophen is used in doses over 2 g/day for a few days. For more severe pain consider short-term opioids in place of the NSAID.“ (Title: Individualized Drug Interaction Alerts; Authors: Daniel C. Malone , University of Arizona; John Horn, Philip Hansten, University of Washington)
A evidence-based plan specification that specifies processes to prevent or mitigate a drug-drug interaction
management option
Evidence-based strategy to mitigate the potential clinical consequences of a drug-drug interaction; e.g., use only if benefit outweighs risk, assess risk and take action if necessary, no special precautions.
recommended action
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.
bioavailability
An information content entity that makes a statement about a drug product being an object drug in a drug interaction.
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
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.
Richard C. Boyce
precipitant drug role
An information content entity that makes a statement about a drug product being an precipitant drug in a drug interaction.
precipitant drug information
A potential drug drug interaction that is about a drug metabolism.
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..
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.
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.
metabolism induction potential drug-drug interaction
A material entity that is either drug product or an ingredient thereof and 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
Non-steroidal anti-inflammatory drugs (NSAIDs) have antiplatelet effects which increase the bleeding risk when combined with oral anticoagulants such as warfarin. The antiplatelet effect of NSAIDs lasts only as long as the NSAID is present in the circulation, unlike aspirin’s antiplatelet effect, which lasts for up to 2 weeks after aspirin is discontinued.
Timolol is a nonselective beta-blocker, and timolol eye drops have been shown to produce systemic beta-blockade. Timolol is metabolized by CYP2D6, and patients who are deficient in CYP2D6 (PMs) have been shown to develop higher timolol plasma concentrations following timolol ophthalmic aqueous drops.
An information content entity that represents a drug interaction as a directional series of molecular processes.
This is an information content entity that is about a clinically measurable drug-drug interaction.
drug interaction mechanism
An assertion about the process or the processes by which a drug-drug interaction clinical consequence occurs.
An instance of this entity would represent the biochemical process by which pharmacokinetic or pharmacodynamic DDI is thought to occur.
mechanism of interaction information
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 scalar measurement datum that is the specified outcome of a drug bioavailability assay.
bioavailability measurement datum
An assay with the objective to capture information about the bioavailability of an active ingredient in a drug product.
drug bioavailability assay
An entity that is the result of a drug-drug interaction.
obsolete_drug-drug interaction effect
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
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
A scalar measurement datum that is the specified outcome of a drug first pass metabolism assay.
first pass metabolism measurement datum
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.
Daintith J (ed.): A Dictionary of Chemistry. 2008. Oxford University Press, Oxford UK.
absorbability
An assay with the objective to capture information about the absorbability of an active ingredient in a drug product.
drug absorbability assay
A a scalar measurement datum that is the specified outcome of an drug absorbability assay.
AUC
absorbability measurement datum
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 scalar measurement datum that is the specified outcome of a drug maximum concentration assay.
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.
primary total clearance enzyme role
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.
drug package insert
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.
FDA drug label
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.
drug package AUC information
An information content entity that provides statements or data that are used to support or refute an assertion.
Standards Development Working Group of the "Addressing PDDI Evidence Gaps" porject.
obsolete_evidence information content entity
An information content entity that is about a pharmacokinetic area under curve.
AUC information
pharmacokinetic area under curve information
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.
information about increase of pharmacokinetic area under the curve
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.
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.
"Addressing PDDI Evidence Gaps" Standards Development Group.
pharmacokinetic process
An information content entity that is used to support or refute an assertion.
"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.
evidence material information
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.
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.
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.
evidence information from drug metabolism inhibition experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes.
evidence information from transport protein identification experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of drug component transporter.
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.
evidence information from observation-based adverse drug event report
An evidence information content entity that is about an assay that realizes an observation design.
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.
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.
EV_EX_Enz_ID_Cyp450_Hum_Recom
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.
EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Chem
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.
EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Antibody
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.
evidence information from CYP450 human microsome drug metabolism identification experiment
evidence information from CYP450 human microsome drug metabolism identification experiment using chemical inhibitors
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.
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.
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.
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.
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.
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.
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.
evidence information from genotyped pharmacokinetic trial
An evidence information content entity that is about an assay that was triggered by an occurrent.
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.
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.
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.
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.
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.
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.
EV_Case_Report_ADE_Public_Reported
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.
EV_Case_Report_DI
evidence information from an observation-based case-report of a drug interaction
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.
EV_Case_Report_DI_Evaluated
evidence information from an evaluated observation-based case-report of a drug interaction
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
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.
pharmacokinetic parameter ratio directionality
A pharmacokinetic parameter ratio that describes the relation between the pharmacokinetic area under the curve (AUC) for a given active ingredient or metabolite in an organism with and without the inhibiting drug present in the organism.
AUC ratio
area under the curve ratio
A pharmacokinetic parameter ratio that describes the relation between the measurement of the volume of blood, serum, or plasma from which an active ingredient or a metabolite is completely removed by the kidney in a given amount of time in an organism with and without the inhibiting drug present in the organism.
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.
pharmacokinetic parameter ratio
An pharmacokinetic parameter directionality that describes negative relationship between the numbers of the ratio.
pharmacokinetic parameter ratio decrease
An pharmacokinetic parameter directionality that describes positive relationship between the numbers of the ratio.
pharmacokinetic parameter ratio increase
A pharmacokinetic parameter ratio that describes the relation between the drug maximum concentration measurements for a given active ingredient or metabolite in an organism with and without the inhibiting drug present in the organism.
Cmax ratio
drug maximum concentration ratio
A pharmacokinetic parameter ratio that describes the relation between the time it takes for half of a given active ingredient or metabolite to be removed from the system of an organism with and without the inhibiting drug present in the organism.
t1/2 ratio
half-life ratio
A pharmacokinetic parameter ratio that describes the relation between the measurement of the volume of blood, serum, or plasma from which an active ingredient or a metabolite is completely removed by the liver in a given amount of time in an organism with and without the inhibiting drug present in the organism.
CL_H ratio
hepatic clearance ratio
A pharmacokinetic parameter ratio that describes the relation between the measurement of the fraction of the administered dose of an unaltered drug that reaches systemic circulation in the abscene of another drug, and the the measurement of the fraction of the administered dose of an unaltered drug that reaches systemic circulation when coadministered with another drug.
F ratio
bioavailability ratio
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 phenotyping.
evidence information from phenotyped pharmacokinetic trial
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of P-Glycoprotein.
EV_EX_Trans_Prot_ID_P_Glycoprotein
evidence information from p-glycoprotein transport protein identification experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of P-Glycoprotein using bidirectional flux in Caco-2 cells.
EV_EX_Trans_Prot_ID_P_Glycoprotein_Caco_2
evidence information from p-glycoprotein transport protein identification experiment using Caco 2 cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of P-Glycoprotein using overexpressed cells.
EV_EX_Trans_Prot_ID_P_Glycoprotein_Overexpressed_Cells
evidence information from p-glycoprotein transport protein identification experiment using overexpressed cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B1.
EV_EX_Trans_Prot_ID_OATP1B1
evidence information from OATP1B1 transport protein identification experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B3.
EV_EX_Trans_Prot_ID_OATP1B3
evidence information from OATP1B3 transport protein identification experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B1 using overexpressed cells.
EV_EX_Trans_Prot_ID_OATP1B1_Overexpressed_Cells
evidence information from OATP1B1 transport protein identification experiment using overexpressed cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of drug components being imported across plasma membranes by involvement of OATP1B3 using overexpressed cells.
EV_EX_Trans_Prot_ID_OATP1B3_Overexpressed_Cells
evidence information from OATP1B3 transport protein identification experiment using overexpressed cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of P-Glycoprotein.
EV_EX_Trans_Prot_Inhibit_P_Glycoprotein
evidence information from p-glycoprotein inhibition experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of P-Glycoprotein, and that has Caco 2 cell lines as a specified input.
EV_EX_Trans_Prot_Inhibit_P_Glycoprotein_Caco_2
evidence information from p-glycoprotein inhibition experiment using Caco 2 cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of P-Glycoprotein, and that has overexpressed cell lines as a specified input.
EV_EX_Trans_Prot_Inhibit_P_Glycoprotein_Overexpressed_Cells
evidence information from p-glycoprotein inhibition experiment using overexpressed cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B1.
EV_EX_Trans_Prot_Inhibit_OATP1B1
evidence information from OATP1B1 inhibition experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B1, and that has overexpressed cell lines as a specified input.
EV_EX_Trans_Prot_Inhibit_OATP1B1_Overexpressed_Cells
evidence information from OATP1B1 inhibition experiment using overexpressed cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B3, and that has overexpressed cell lines as a specified input.
EV_EX_Trans_Prot_Inhibit_OATP1B3_Overexpressed_Cells
evidence information from OATP1B3 inhibition experiment using overexpressed cell lines
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the inhibition of OATP1B3.
EV_EX_Trans_Prot_Inhibit_OATP1B3
evidence information from OATP1B3 inhibition experiment
A pharmacokinetic parameter ratio that describes the theoretical volume that would be necessary to contain the total amount of an administered drug at the same concentration that it is observed in a bodily fluid for a given active ingredient or metabolite in an organism with and without the inhibiting drug present. It is expressed as a ratio of the volume of distribution with the inhibitor present as the numerator and absent as the denominator.
amended definition from Spruill WJ, Wade WE, DiPiro JT, Blouin RA, Pruemer JM: Concepts in Clinical Pharmacology. Bethesda, MA, 2014 based on a comment by Philip E. Empey.
volume of distribution ratio
A pharmacokinetic parameter ratio that describes the time from dose administration until a drug reaches its maximum concentration for a given active ingredient or metabolite in an organism with and without the inhibiting drug present in the organism. It is expressed as a ratio of the Tmax with the inhibitor present as the numerator and absent as the denominator.
Tmax ratio
time to maximum drug concentration ratio
A pharmacokinetic parameter ratio that describes the drug transmembrane transporter activity regarding an active ingredient or a metabolite in an in vitro bi-directional transport assay. It is expressed as a ratio of the apparent permeability in the basal to apical direction as the numerator and apparent permeability in the apical-to-basolateral direction as the denominator.
efflux ratio
A pharmacokinetic parameter ratio that describes the drug transmembrane transporter activity regarding an active ingredient or a metabolite in an in vitro bi-directional transport assay using transporter transfected cell model. It is expressed as a ratio of the efflux ratio in cells transfected with the transporter as the numerator and efflux ratio in cells not transfected with the transporter (wild type cells) as the denominator.
net flux ratio
A measurement data that gives the concentration of an inhibiting agent to reach half of the maximum inhibition of a meabolic or transport process.
inhibitory constant
The role that inheres in a chemical substance and that, if realized, is realized by a single, specified metabolic or transport reaction, which is being affected by another chemically substance pharmacokinetically in a drug-drug interaction experiment or natural product-drug interaction.
probe subtrate role
An assay that is the realization of a concretization of a clinical study design.
clinical study
A biological process that is the result of a drug-drug interaction.
drug-drug interaction effect
A value specification that specifies the relationship between two numbers.
ratio value specification
A ratio value specification where the relationship between to numbers is expressed as a fraction of 100.
percentage value specification
An identifier that denotes a set of drug identifiers.
Term and definition provided by Richard D. Boyce.
drug concept set identifier
a cultured cell population that is derived from hepatocytes isolated from a human being and that has undergone cryopreservation
John Judkins
Cells isolated from human liver that have been frozen and stored, usually in liquid nitrogen; an in vitro model system for human metabolism or transport; cells can be thawed and used in metabolism or transport assays
cryopreserved human hepatocyte population
a cultured cell population that is derived from hepatocytes freshly isolated from a human being
Cells isolated from human liver, never frozen; an in vitro model system for human metabolism or transport; cells can be used in metabolism or transport assays
freshly isolated human hepatocyte population
a cultured cell population that is derived from cells isolated from the liver of a transgenic organism
Cells isolated from livers of transgenic animals; an in vitro model system for human metabolism or transport
transgenic animal hepatocyte population
a cultured cell population derived from hepatocytes, in which, during the culturing process, the cells occupy a region bound by two parallel plates made of gelled collagen
sandwich cultured hepatocyte population
a cultured cell population derived from cells isolated from human intestinal epithelium
human intestinal epithelial cell population
an immortal human liver-derived cell line cell that is part of the HepaRG cell line
HepaRG cells are terminally differentiated human hepatocellular carcinoma cells that reproducibly express drug-metabolizing enzymes and transporters. They are commonly used for metabolism and transport evaluations in vitro, as they respond and function like primary human hepatocytes across a range of applications.
HepaRG cell
an immortal human liver-derived cell line cell that is part of the Fa2N-4 cell line
Fa2N-4 cell line was prepared by immortalizing hepatocytes from a 12 year-old Caucasian female donor with Simian virus 40 large T antigen. The donor was tested negative for CMV, HIV, HBV, and HCV. This cell line was mainly used for major CYP induction studies (including CYP3A4/5, 1A2, 2B6, and 2C9) with limitations. Hepatic transporter expression levels are low.
Fa2N-4 cell
an immortal human liver-derived cell line cell that is part of the HBG BC2 cell line
BC2 cell
An Immortalized human hepatoma cell line possesses the capacities of being reversibly differentiated in vitro, and of maintaining a relatviely higher mtabolic rate in the differentiated phase. It is mainly used for repeated toxicity evaluation in vitro.
HBG BC2 cell
a processed material that has a supernatant role resulting from high-speed centrifugation of a human liver S9 fraction
Cell cytosol obtained via centrifugation of human liver cells. It is commonly used to support in vitro DMPK studies related to liver cytsolic enzymes, especially non-CYP enzymes, such as phase I enzyme aldehyde oxidase (AO), phase II enzyme SULT.
human liver cytosolic fraction
a processed material that has a supernatant role resulting from high-speed centrifugation of a human intestine S9 fraction
Cell cytosol obtained via centrifugation of human enterocytes. It is commonly used to support in vitro evaluation of intestinal cytosolic enzymes in the first-pass metabolism of orally ingested xenobitotics.
human intestine cytosolic fraction
a processed material that has a supernatant role resulting from medium-speed centrifugation of a human liver homogenate
A mixture of cell cytosol and microsomes isolated by disruption and centrifugation of human liver cells. It contains a wide range of drug-metabolizing enzymes and is commonly used for in vitro DMPK studies, including both phase I and phase II xenobiotic metabolism.
human liver S9 fraction
a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a human intestine S9 fraction, which is derived from a single donor
individual human intestinal microsomes
Subcellular fractions, derived from endoplasmic reticulum that has been isolated from enterocytes from a single human donor. They contain a rich variety of metaboliz enzymes for assessing first-pass metabolism for orally ingested drugs.
individual human intestinal microsomal fraction
a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a pool of human liver S9 fractions, which is derived from multiple donors
pooled human liver microsomes
Subcellular fractions, derived from endoplasmic reticulum that has been isolated from liver cells from multiple human donors. They contain a rich variety of metaboliz enzymes (e.g. CYP, UGT, FMO) for assessing drug DMPK in vitro, such as metabolic stability, CYP inhibition, CYP phenotyping, metabolite charaterization, etc.
pooled human liver microsomal fraction
a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a human liver S9 fraction, which is derived from a single donor
individual human liver microsomes
Subcellular fractions, derived from endoplasmic reticulum that has been isolated from liver cells from a single human donor. They contain a rich variety of metaboliz enzymes (e.g. CYP, UGT, FMO) for assessing drug DMPK in vitro, such as metabolic stability, CYP inhibition, CYP phenotyping, metabolite charaterization, etc.
individual human liver microsomal fraction
a processed material that has a centrifuge pellet role resulting from high-speed centrifugation of a pool of human intestine S9 fractions, which is derived from multiple donors
pooled human intestinal microsomes
Subcellular fractions, derived from endoplasmic reticulum that has been isolated from enterocytes of multiple human donors. They contain a rich variety of metaboliz enzymes for assessing first-pass metabolism for orally ingested drugs.
pooled human intestinal microsomal fraction
a processed material that has a supernatant role resulting from medium-speed centrifugation of a human intestine homogenate
A mixture of cell cytosol and microsomes isolated by disruption and centrifugation of human enterocytes. It contains a wide range of drug-metabolizing enzymes and is commonly used for in vitro DMPK studies, including both phase I and phase II xenobiotic metabolism.
human intestine S9 fraction
a cultured cell that is part of a culture derived from an insect and has a recombinant protein production host role
baculovirus-insect cell
Insect cell-hosted viral system used to produce and express recombinant proteins/enzymes; these systems are used in metabolism studies
baculovirus-insect recombinant protein production host cell
a cultured cell of the species Escherichia coli that bears a recombinant protein production host role
Prokaryotic in vitro system used to produce and express recombinant proteins/enzymes; these systems are used in metabolism studies
E. coli recombinant protein production host cell
a measurement datum that describes the decrease in activity of a transporter or enzyme in the presence of a compound from activity in the control experiment
% inhibition
Percent inhibition: the percent decrease in activity of a transporter or enzyme in the presence of a compound from activity in the control experiment
percent inhibition
a hydroxylation that has midazolam as input and 1'-hydroxymidazolam as output
Hydroxylation of midazolam at the 1' position to form 1'-hydroxymidazolam;probe substrate of CYP3A4 activity (used to measure CYP3A4 activity)
midazolam 1'-hydroxylation
a deethylation that has 7-ethoxyresorufin as input and resorufin as output
O-deethylation of 7-Ethoxyresorufin to form resorufin; probe substrate of CYP1A activity
7-ethoxyresorufin O-deethylation
a dehydrogenation that has nifedipine as input and has dehydronifedipine as output
Dehydrogenation of nifedipine to dehydronifedipine;probe substrate of CYP3A4 activity (used to measure CYP3A4 activity)
nifedipine dehydrogenation
a hydroxylation that has bufuralol as input and 1'-hydroxybufurolol as output
1'-hydroxylation of bufuralol to form 1'-hydroxybufurolol; probe substrate of CYP2D6 activity
bufuralol 1'-hydroxylation
a hydroxylation that has omeprazole as input and has 5-hydroxyomeprazole as output
Hydroxylation of omeprazole at the 5 position to form 5-hydroxyomeprazole; probe substrate of CYP2C19 activity
omeprazole 5-hydroxylation
a hydroxylation that has bupropion as input and 1-hydroxybupropion as output
Hydroxylation of bupropion at the 1 position to form 1-hydroxybupropion; probe substrate of CYP2B6 activity
bupropion hydroxylation
a hydroxylation that has paclitaxel as input and 6-alpha-hydroxypaclitaxel as output
Hydroxylation of paclitaxel at the 6-alpha position to form 6-alpha-hydroxypaclitaxel; probe substrate of CYP2C8 activity
paclitaxel 6-alpha hydroxylation
a deethylation that has phenacetin as input and acetaminophen as output
O-deethylation of phenacetin to form acetaminophen; probe substrate of CYP1A2 activity
phenacetin O-deethylation
a hydroxylation that has coumarin as input and has 7-hydroxycoumarin as output
Hydroxylation of coumarin at the 7 position to form 7-hydroxycoumarin; probe substrate of CYP2A6 activity
coumarin 7-hydroxylation
a hydroxylation that has testosterone as input and 6-beta-hydroxytestosterone as output
Hydroxylation of testosterone at the 6-beta position to form 6-beta-hydroxytestosterone; probe substrate of CYP3A4 activity
testosterone 6-beta-hydroxylation
a demethylation that has dextromethorphan as input and has dextrorphan as output
O-demethylation of dextromethorphan to form dextrorphan;probe substrate of CYP2C9 activity
dextromethorphan O-demethylation
a hydroxylation that has diclofenac as input and 4'-hydroxydiclofenac as output
Hydroxylation of diclofenac to form 4'-hydroxydiclofenac; probe substrate of CYP2C9 activity
diclofenac 4'-hydroxylation
a target of material addition role that is borne by a cultured cell and, if realized, is realized in recombinant protein production
An in vitro system that uses a combination of genetic pieces typically in a plasmid that is incorporated into a host cell which is used to produce the protein of interest
recombinant protein production host role
a count of administrations of a substance to an organism over a duration of 24 hours
the frequency of administration of the precipitant during the day
number of doses in a day
an immortal human liver-derived cell line cell that is part of the Hep G2 cell line
HepG2 was derived from a liver hepatocellular carcinoma of a 15 year-old Caucasian male. HepG2 cells secrete a variety of major plasma proteins. They are a suitable in vitro model system for the study of polarized human hepatocytes, with high degree of morphological and functional differentiation in vitro. It can be used for hepatic metabolism, transport, and toxicity evaluations in vitro. It was tested negative for HBV.
Hep G2 cell
a CHO cell that is a specified output of a transfection
Chinese hamster ovary cells transfected with human transporter DNA; an in vitro model used to study transporters
CHO transfected cell
a Hep G2 cell that has a target of material addition role and is a specified input of a transfection
Well characterized immortalized human liver cancer cell line used as an in vitro model system of metabolism or transport
Hep G2 transfected cell
a Caco-2 cell that is a specified output of a gene knockout that has specified input siRNA
Caco-2 cells treated with siRNA designed to down-regulate specific enzymes or transporters
siRNA knockout Caco-2 cell
a 293-derived cell that is a specified output of a transfection
HEK293 transfected cell
Immortalized human kideny cells transfected/transduced with a transporter or enzyme; an in vitro model overexpressing transporter or enzyme of interest; used for transporter or metabolism assays
293 transfected cell
a count of human beings from whom originate hepatocytes to be used in an investigation
Number of Livers
Number of individual liver samples used
number of liver donors
a hydroxylation that has tolbutamide as input and 4-hydroxytolbutamide as output
Methyhydroxylation of tolbutamide to form hydroxytolbutamide;probe substrate of CYP2D6 activity
tolbutamide methylhydroxylation
a glucuronosylation that has estradiol as input and has estradiol-3-glucuronide as output
Glucuronidation of estradiol to estradiol-3-glucuronide; probe substrate of UGT1A1 activity (used to measure UGT1A1 activity)
estradiol glucuronosylation
an MDCK cell that is the specified output of a transfection
Dog cells transfected with human transporter; an in vitro model used to study transporters
MDCK transfected cell
a glucuronosylation that has lamotrigine as input and has lamotrigine glucoronide as output
lamotrigine glucuronidation
Glucuronidation of lamotrigine; probe substrate of UGT1A4 activity (used to measure UGT1A4 activity)
lamotrigine glucuronosylation
a hydroxylation that has chlorzoxazone as input and 6-hydroxychlorzoxazone as output
Hydroxylation of chlorzoxazone at the 6 position to form 6-hydroxychlorzoxazone; probe substrate of CYP2E1 activity
chlorzoxazone 6-hydroxylation
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 POSITIVE regulation of a metabolic process, as its specified input.
Eric Chou
evidence information from drug metabolism induction experiment
An evidence information content entity that is about an assay that realizes an ex vivo design, and that has chemical substances as its specific input, which are the outcome of the INDUCTION of drug component transporter.
evidence information from drug transport protein induction experiment
An evidence information content entity that is about an assay that has chemical substances as its specific input an that has as its specified output the identification and quantification of chemical constituents
evidence information from chemical analytic characterization of material
An evidence information content entity that is about an assay that has as its specific input the identity and quantity of chemical constituents of two or more chemical substances, and has is its specified output an assessment of the similarity of the input chemical substances.
evidence information from chemical analytic metabolomics of material
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
clinical drug role
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
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
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
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
drug administration
Reagent that is a polymer comprised of nucleotides, each of which consists of three components: a nitrogenous heterocyclic base, which is either a purine or a pyrimidine; a pentose sugar; and a phosphate group.
Placeholder for class to be imported from the Reagent Ontology (ReO).
Characterization of the phenotype is often done in transgenic or knockout mice.
An organismal assay that involves characterization of a phenotype; any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two.
A reagent that is a polymer comprised of RNA nucleotides.
An RNA reagent consisting of a short, linear RNA polymer, typically with 100 or fewer bases.
An RNA interference reagent used to silence expression of a target gene in cells, through the RNA interference pathway.
An RNA interference oligonucleotide capable of silencing expression of a target gene through the RNAi pathway. siRNAs are synthesized as single-stranded molecules, typically 19-25 nucleotides in length, and paired with complementary sequences to form duplexes that serve as substrates for cellular RNAi processing machinery.
MHB, http://www.sigmaaldrich.com/life-science/custom-oligos/sirna-oligos.html
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.
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.
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.
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.
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.
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.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.
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.
metabolic process resulting in cell growth
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
negative regulation of metabolic process
cellular process
drug 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.
Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
Any process that modulates the activity of a transporter.
Any process that stops or reduces the activity of a transporter.
negative regulation of transporter activity
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
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.
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.
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.
The chemical reactions and pathways by which individual cells transform chemical substances.
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.
positive regulation of physiological process
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.
negative regulation of physiological process
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.
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
Any process that modulates a measurable attribute of any biological process, quality or function.
The directed movement of some substance from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis.
The directed movement of some substance from outside of a cell, across the plasma membrane and into the cytosol.
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
proper name
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
identifier
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.
a biological interaction that uses the information from a gene to synthesize a functional gene product.
express, expressed, expresses, expressing, expression, expressions
a gene expression that has increased volume.
hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression
Formation of a covalent bond between a substrate and a glucuronosyl group.
A process in which at least one of the participants is a molecule.
TODO: needs work, formal definition, etc.
An oxidation process that involves the removal of adjacent hydrogen atoms, resulting in an increase of bond order.
Formation of a covalent bond between a substrate and a hydroxy group.
Breaking of a covalent bond between a substrate and a methyl group.
Breaking of a covalent bond between a substrate and an ethyl group.
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.
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.
centrifuge pellet role
Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..
9Mar09 after discussion with process branch changed definition to include use of centrifuge;
supernatant role
Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
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
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")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
PERSON: Bjoern Peters
material transformation
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
Melanie Courtot
microplate
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.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
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.
target of material addition role
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
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
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
scattered molecular aggregate
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/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
a protocol specifying to administer 1 ml of vaccine to a mouse
a directive information entity that describes the dose that will be administered to a target
gene knock out
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
PERSON: Chris Stoeckert, Jie Zheng
MO_771 gene_knock_out
transfection
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
half maximal effective concentration (EC50)
Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
half maximal inhibitory concentration (IC50)
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
ex vivo design
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
MO_808 ex_vivo_design
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.
MO_347 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).
A value specification that specifies the mass of some thing.
A value specification that consists of two parts: a numeral and a unit label
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.
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.
WEB: http://en.wikipedia.org/wiki/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.
GROUP: OBI Biomaterial Branch
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.
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.
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
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
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.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
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
Clinical Research Glossary Version 4.0 CDICS glossary group
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
independent measure design
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
Bjoern Peters
IEDB
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
OBI Plan
genetic transformation
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
the introduction. alteration or integration of genetic material into a cell or organism
PERSON:Kevin Clancy
genetic modification
cell pellet
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
PERSON: Helen Parkinson
GROUP: CEBS
A bodily process that is clinically abnormal.
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
p-glycoprotein
multidrug resistance protein 1
A protein that is a translation product of the human POR gene or a 1:1 ortholog thereof.
A solute carrier organic anion transporter family member that is a translation product of the human SLCO1B1 gene or a 1:1 ortholog thereof.
liver-specific organic anion transporter 1
sodium-independent organic anion-transporting polypeptide 2
solute carrier organic anion transporter family member 1B1
A solute carrier organic anion transporter family member that is a translation product of the human SLCO1B3 gene or a 1:1 ortholog thereof.
liver-specific organic anion transporter 2
organic anion-transporting polypeptide 8
solute carrier organic anion transporter family member 1B3
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
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
A unit of measurement is a standardized quantity of a physical quality.
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
A dimensionless ratio unit which denotes numbers as fractions of 100.
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
An information content entity that specifies how a dose is quantified in a dose administration.
This part of a prescription usually specifies a fixed amount (like '50 mg' or '500 mL'), but may instead specify a rate in some situations, e.g., in ongiong IV perfusions, where the total dose that will be administered in a single dose is unkown until the administration has ended. In either situation, the dose quantification specification is what enables the calculation of the quantity of active ingredient or drug product in the dose that is administered
A dose quantification specification that quantifies a dose by referring to the quantity of active ingredient administered in a dose administration.
active ingredient quantification specification
A dose quantification specification that quantifies a dose by referring to the quantity of drug product administered in a dose administration.
drug product quantification specification
An assay in which variation in the genome is analysed
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
group randomization
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.