Philip E. Empey Dan Malone Drug-drug Interaction and Drug-drug Interaction Evidence Ontology Anuj Shah Mathias Brochhausen http://creativecommons.org/licenses/by/4.0/ Jodi Schneider Richard D. Boyce William R. Hogan release version 2019-01-30 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/). Jingjing Yu DIDEO The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. Jessica Tay-Sontheimer BFO OWL specification label BFO CLIF specification label Cell line LINCS ID Cell line LINCS ID STR profile editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage has curation status has curation status definition definition textual definition editor note editor note definition editor definition editor term editor term editor alternative term alternative term definition source definition source curator note curator note imported from expand expression to OBO foundry unique label elucidation elucidation has associated axiom(fol) has literature mining keywords MPIO user-centered definition ISA alternative term IEDB alternative term temporal interpretation is direct form of is indirect form of external_definition has_relational_adjective Unique Apollo Label has_rank Creator Source Source alternative_term definition has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset label see also is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of http://purl.obolibrary.org/obo/ro.owl part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part http://purl.obolibrary.org/obo/obi.owl has part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by Optional.of(http://purl.obolibrary.org/obo/obi.owl) http://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/ro.owl precedes continuant(c) and process(p) and first_time_point(p,t1) and last_time_point(p,t2) and not(exists_at(c,t1)) and exists_at(c,t2) Alan Ruttenberg https://code.google.com/p/bfo/issues/detail?id=50&colspec=ID%20Type%20Status%20Owner%20Summary%20Reporter%20Modified begins_to_exist_during o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent http://purl.obolibrary.org/obo/bfo.owl http://purl.obolibrary.org/obo/dideo/release/2017-11-17/dideo.owl [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part there is some extended organism e & there is some temporal region tr & p occupies temporal region tr & p occurs_in e & c begins to exist during p & there is some t ( t part-of tr & c located-in e at t ) Alan Ruttenberg Mathias Brochhausen William R. Hogan organismally_begins_to_exist_during there is some extended organism e & p1 occurs_in e & p2 occurs_in e & p1 immediately precedes p2 Mathias Brochhausen for immediatly precedes please see: http://krr.meraka.org.za/~aow2010/Trentelman-etal.pdf organismally immediately precedes is organismally immediately preceded by A pharmaeutic ingredient or a metabolite X is the substrate of an enzyme E, iff E catalyzes X to M. Mathias Brochhausen is substrate of realizes substrate role true involves substrate true inhibits-catalyzes metabolism of catalyzes a Phase I or Phase II enzymatic reaction involving is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl is_specified_input_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl is_specified_output_of specifies value of A relation between a value specification and an entity which the specification is about. Optional.of(http://purl.obolibrary.org/obo/obi.owl) specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI http://purl.obolibrary.org/obo/obi.owl has value specification process is result of 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 IEDB PERSON:Bjoern Peters Optional.of(http://purl.obolibrary.org/obo/obi.owl) process is result of inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in http://purl.obolibrary.org/obo/obi.owl inheres in participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in http://purl.obolibrary.org/obo/ro.owl participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://purl.obolibrary.org/obo/dron.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant David Osumi-Sutherland http://purl.obolibrary.org/obo/ro.owl X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of Optional.of(http://purl.obolibrary.org/obo/obi.owl) X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets http://purl.obolibrary.org/obo/ro.owl X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. http://purl.obolibrary.org/obo/ro.owl regulates (processual) false regulates x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall http://purl.obolibrary.org/obo/ro.owl negatively regulates (process to process) negatively regulates 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. Chris Mungall http://purl.obolibrary.org/obo/ro.owl has prototype mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". http://purl.obolibrary.org/obo/ro.owl RO_0000053 some (RO_0000054 only ?Y) capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in http://purl.obolibrary.org/obo/ro.owl RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in http://purl.obolibrary.org/obo/ro.owl actively participates in Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. http://purl.obolibrary.org/obo/ro.owl https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by http://purl.obolibrary.org/obo/ro.owl starts with x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by http://purl.obolibrary.org/obo/ro.owl ends with 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. Chris Mungall 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. Chris Mungall produces has output a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. http://purl.obolibrary.org/obo/ro.owl enables Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function http://purl.obolibrary.org/obo/ro.owl functionally related to inverse of enables Chris Mungall http://purl.obolibrary.org/obo/ro.owl enabled by inverse of regulates Chris Mungall http://purl.obolibrary.org/obo/ro.owl regulated by (processual) regulated by Chris Mungall http://purl.obolibrary.org/obo/ro.owl negatively regulated by inverse of has input Chris Mungall Optional.of(http://purl.obolibrary.org/obo/ro.owl) input of inverse of has output Chris Mungall Optional.of(http://purl.obolibrary.org/obo/ro.owl) output of inverse of upstream of Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally downstream of Chris Mungall directly negatively regulates http://purl.obolibrary.org/obo/ro.owl directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates http://purl.obolibrary.org/obo/ro.owl indirectly inhibits This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall http://purl.obolibrary.org/obo/ro.owl immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) http://purl.obolibrary.org/obo/ro.owl causally upstream of or within Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally downstream of or within A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. http://purl.obolibrary.org/obo/ro.owl in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://code.google.com/p/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. Chris Mungall binds molecularly binds with http://purl.obolibrary.org/obo/ro.owl molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b Chris Mungall http://purl.obolibrary.org/obo/ro.owl molecularly controls Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. Chris Mungall inhibits http://purl.obolibrary.org/obo/ro.owl molecularly decreases activity of A relationship between a material entity and a process where the material entity has some causal role that influences the process http://purl.obolibrary.org/obo/ro.owl causal agent in p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall https://docs.google.com/document/d/1WxocTXZaGVhEV1n7NB86pCF3SUcBJh8bq4vQrVCkjSU/edit# Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causal relation between processes The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl causal relation between material entities Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall http://purl.obolibrary.org/obo/ro.owl causally influences (material entity to material entity) causally influences A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall http://purl.obolibrary.org/obo/ro.owl causal relation between material entity and a process A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro.owl related via dependence to DIDEO uses this object property from the old (depracted) RO, since we need to infer parts of drug products as represented by DRON (and DRON [along with many other OBO Foundry candidate ontologies] uses this object property). http://purl.obolibrary.org/obo/ido.owl OBO_REL:0000007 relationship has_proper_part DIDEO uses this object property from the old (depracted) RO, since we need to infer parts of drug products as represented by DRON (and DRON [along with many other OBO Foundry candidate ontologies] uses this object property). http://purl.obolibrary.org/obo/ido.owl OBO_REL:0000006 relationship proper_part_of has specified value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified value A measurement datum that is the output of counting. Mathias Brochhausen http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl A measurement datum that is the output of counting. count count An identifier that denotes a drug product. Matthew Diller William R. Hogan http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl An identifier that denotes a drug product. drugId 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. http://purl.obolibrary.org/obo/chebi.owl CHEBI:4602 Beilstein:3573079 ChemIDplus:42399-41-7 CiteXplore:11937779 CiteXplore:16651034 CiteXplore:19167257 CiteXplore:23687551 CiteXplore:24261918 CiteXplore:25122162 CiteXplore:8369596 DrugBank:DB00343 HMDB:HMDB14487 KEGG COMPOUND:42399-41-7 KEGG COMPOUND:C06958 KEGG DRUG:D07845 NIST Chemistry WebBook:42399-41-7 Patent:DE1805714 Patent:DE3415035 Patent:US3562257 Patent:US4552695 Reaxys:3573079 Wikipedia:Diltiazem (2S,3S)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate DILTIAZEM Diltiazem chebi_ontology (+)-cis-5-[2-(dimethylamino)ethyl]-2,3-dihydro-3-hydroxy-2-(p-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one acetate ester (2S,3S)-5-(2-(dimethylamino)ethyl)-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]thiazepin-3-yl acetate (2S-cis)-3-(acetyloxy)-5-[2-(dimethylamino)ethyl]-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one Acetic acid (2S,3S)-5-(2-dimethylamino-ethyl)-2-(4-methoxy-phenyl)-4-oxo-2,3,4,5-tetrahydro-benzo[b][1,4]thiazepin-3-yl ester C22H26N2O4S COc1ccc(cc1)[C@@H]1Sc2ccccc2N(CCN(C)C)C(=O)[C@@H]1OC(C)=O D-cis-diltiazem InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3/t20-,21+/m1/s1 InChIKey=HSUGRBWQSSZJOP-RTWAWAEBSA-N d-cis-diltiazem diltiazem diltiazemum CHEBI:101278 diltiazem 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. http://purl.obolibrary.org/obo/chebi.owl HMDB:HMDB00902 Wikipedia:Nicotinamide_adenine_dinucleotide NAD chebi_ontology nicotinamide-adenine dinucleotide CHEBI:13389 NAD A steroid glucosiduronic acid having 17alpha-estradiol as the steroid component. http://purl.obolibrary.org/obo/chebi.owl CHEBI:14218 CHEBI:23962 CHEBI:4863 KEGG:C04300 17alpha-hydroxyestra-1,3,5(10)-trien-3-yl beta-D-glucopyranosiduronic acid chebi_ontology 0 17alpha-estradiol 3-glucuronide 448.210 448.50610 C24H32O8 Estradiol-17alpha 3-D-glucuronoside InChI=1S/C24H32O8/c1-24-9-8-14-13-5-3-12(10-11(13)2-4-15(14)16(24)6-7-17(24)25)31-23-20(28)18(26)19(27)21(32-23)22(29)30/h3,5,10,14-21,23,25-28H,2,4,6-9H2,1H3,(H,29,30)/t14-,15-,16+,17-,18+,19+,20-,21+,23-,24+/m1/s1 MUOHJTRCBBDUOW-FNUZHIFDSA-N [H][C@]12CC[C@]3(C)[C@H](O)CC[C@@]3([H])[C@]1([H])CCc1cc(O[C@@H]3O[C@@H]([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)ccc21 CHEBI:15822 17alpha-estradiol 3-glucosiduronic acid A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13672 CHEBI:14859 CHEBI:8312 KEGG COMPOUND:C00419 Polynucleotide chebi_ontology C10H17O10PR2(C5H8O6PR)n polynucleotides CHEBI:15986 polynucleotide 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. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13399 CHEBI:13400 CHEBI:21904 CHEBI:44286 CHEBI:7425 Beilstein:77911 CAS:53-57-6 COMe:MOL000028 ECMDB:ECMDB04111 HMDB:HMDB00221 KEGG:C00005 KNApSAcK:C00019545 PDBeChem:NDP PMID:16884311 PMID:17371809 PMID:8627598 YMDB:YMDB00426 2'-O-phosphonoadenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} NADPH chebi_ontology 0 745.091 745.42116 ACFIXJIJDZMPPO-NNYOXOHSSA-N C21H30N7O17P3 InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE NC(=O)C1=CN(C=CC1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](OP(O)(O)=O)[C@@H]2O)n2cnc3c(N)ncnc23)[C@@H](O)[C@H]1O Reduced nicotinamide adenine dinucleotide phosphate TPNH dihydronicotinamide-adenine dinucleotide phosphate reduced nicotinamide-adenine dinucleotide phosphate CHEBI:16474 NADPH A tripeptide compound consisting of glutamic acid attached via its side chain to the N-terminus of cysteinylglycine. http://purl.obolibrary.org/obo/chebi.owl CHEBI:12402 CHEBI:14327 CHEBI:24334 CHEBI:42873 CHEBI:43049 CHEBI:5437 CAS:70-18-8 DrugBank:DB00143 Drug_Central:1312 HMDB:HMDB00125 KEGG:C00051 KEGG:D00014 KNApSAcK:C00001518 MetaCyc:GLUTATHIONE PDBeChem:GSH PMID:17439666 PMID:4200890 PMID:4745654 Reaxys:1729812 Wikipedia:Glutathione Glutathione L-gamma-glutamyl-L-cysteinylglycine chebi_ontology 0 307.084 307.32300 5-L-Glutamyl-L-cysteinylglycine C10H17N3O6S GSH Glutathione-SH InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1 N-(N-gamma-L-Glutamyl-L-cysteinyl)glycine N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(O)=O)C(O)=O RWSXRVCMGQZWBV-WDSKDSINSA-N Reduced glutathione gamma-L-Glutamyl-L-cysteinyl-glycine CHEBI:16856 glutathione 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. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13395 CHEBI:13396 CHEBI:21902 CHEBI:44216 CHEBI:7423 Beilstein:79324 CAS:58-68-4 COMe:MOL000027 DrugBank:DB00157 Gmelin:544241 HMDB:HMDB01487 KEGG:C00004 KNApSAcK:C00019343 PDBeChem:NAI PMID:11259315 PMID:19459318 Reaxys:79324 Wikipedia:Nicotinamide_adenine_dinucleotide NADH adenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} chebi_ontology 0 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE 665.125 665.44126 BOPGDPNILDQYTO-NNYOXOHSSA-N C21H29N7O14P2 DPNH InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 NC(=O)C1=CN(C=CC1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n2cnc3c(N)ncnc23)[C@@H](O)[C@H]1O Reduced nicotinamide adenine dinucleotide nicotinamide adenine dinucleotide (reduced) CHEBI:16908 NADH A UDP-sugar having alpha-D-glucuronic acid as the sugar component. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13489 CHEBI:13506 CHEBI:22104 CHEBI:46309 CHEBI:9846 Beilstein:78881 CAS:2616-64-0 HMDB:HMDB00935 KEGG:C00167 KEGG:G10612 KNApSAcK:C00007238 PDBeChem:UGA PMID:11420884 PMID:13984680 PMID:14351193 Reaxys:78881 Wikipedia:Uridine_diphosphate_glucuronic_acid uridine 5'-[3-(alpha-D-glucopyranuronosyl) dihydrogen diphosphate] chebi_ontology 0 580.034 580.28538 C15H22N2O18P2 HDYANYHVCAPMJV-LXQIFKJMSA-N InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1 O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)O[C@H]2O[C@@H]([C@@H](O)[C@H](O)[C@H]2O)C(O)=O)O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1=O UDP-D-glucuronate UDP-alpha-D-glucuronate UDP-glucuronate UDPglucuronate URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID uridine diphosphate glucuronic acid CHEBI:17200 UDP-alpha-D-glucuronic acid An adenosine bisphosphate having monophosphate groups at the 3'- and 5'-positions and a sulfo group attached to the phosphate at position 5'. http://purl.obolibrary.org/obo/chebi.owl CHEBI:11679 CHEBI:11680 CHEBI:1353 CHEBI:19857 CAS:482-67-7 KEGG:C00053 KNApSAcK:C00007446 PDBeChem:PPS 3'-O-phosphono-5'-adenylyl sulfate 3'-Phospho-5'-adenylyl sulfate 3'-phospho-5'-adenylyl sulfate chebi_ontology 0 3'-Phosphoadenosine 5'-phosphosulfate 3'-Phosphoadenylyl sulfate 3'-phosphoadenosine 5'-phosphosulfate 506.986 507.26552 C10H15N5O13P2S GACDQMDRPRGCTN-KQYNXXCUSA-N InChI=1S/C10H15N5O13P2S/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-30(20,21)28-31(22,23)24/h2-4,6-7,10,16H,1H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)(H,22,23,24)/t4-,6-,7-,10-/m1/s1 Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP(O)(=O)OS(O)(=O)=O)[C@@H](OP(O)(O)=O)[C@H]1O PAPS CHEBI:17980 3'-phospho-5'-adenylyl sulfate A lactone having a six-membered lactone ring. http://purl.obolibrary.org/obo/chebi.owl delta-lactone chebi_ontology . 1,5-lactone 1,5-lactones delta-lactona delta-lactonas delta-lactones CHEBI:18946 delta-lactone An organic heterocyclic compound containing a benzene ring fused to an imidazole ring. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology CHEBI:22715 benzimidazoles Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/chebi.owl molecular entity chebi_ontology . entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology diazoles CHEBI:23677 diazole A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. http://purl.obolibrary.org/obo/chebi.owl CHEBI:42364 PMID:10696569 PMID:24084694 Wikipedia:Estradiol estra-1,3,5(10)-triene-3,17-diol chebi_ontology 0 272.178 272.38196 C18H24O2 InChI=1S/C18H24O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-17,19-20H,2,4,6-9H2,1H3/t14-,15-,16+,17?,18+/m1/s1 VOXZDWNPVJITMN-WKUFJEKOSA-N [H][C@]12CC[C@]3(C)C(O)CC[C@@]3([H])[C@]1([H])CCc1cc(O)ccc21 oestradiol CHEBI:23965 estradiol chemical entity A role played by the molecular entity or part thereof within a biological context. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology biological function grouped_by_functions CHEBI:24432 biological role A cyclic compound having as ring members atoms of carbon and at least of one other element. http://purl.obolibrary.org/obo/chebi.owl ChEBI:C03123 chebi_ontology . organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound Any carboxylic acid with at least one hydroxy group. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology hydroxy carboxylic acids hydroxyacids CHEBI:24669 hydroxy carboxylic acid A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton. http://purl.obolibrary.org/obo/chebi.owl imidazoles chebi_ontology CHEBI:24780 imidazoles Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. http://purl.obolibrary.org/obo/chebi.owl lactone lactones chebi_ontology . Lacton Lakton Laktone lactona lactonas CHEBI:25000 lactone Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. http://purl.obolibrary.org/obo/chebi.owl CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite http://purl.obolibrary.org/obo/chebi.owl chebi_ontology phenoxazines CHEBI:25970 phenoxazine An organoiodine compound that has formula C25H29I2NO3. http://purl.obolibrary.org/obo/chebi.owl Beilstein:1271711 ChemIDplus:1951-25-3 DrugBank:DB01118 KEGG COMPOUND:1951-25-3 KEGG COMPOUND:C06823 KEGG DRUG:D02910 Wikipedia:Amiodarone (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone Amiodarone chebi_ontology 2-Butyl-3-(3,5-diiodo-4-(2-diethylaminoethoxy)benzoyl)benzofuran 2-Butyl-3-benzofuranyl 4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl ketone 2-n-Butyl-3',5'-diiodo-4'-N-diethylaminoethoxy-3-benzoylbenzofuran C25H29I2NO3 CCCCc1oc2ccccc2c1C(=O)c1cc(I)c(OCCN(CC)CC)c(I)c1 InChI=1S/C25H29I2NO3/c1-4-7-11-22-23(18-10-8-9-12-21(18)31-22)24(29)17-15-19(26)25(20(27)16-17)30-14-13-28(5-2)6-3/h8-10,12,15-16H,4-7,11,13-14H2,1-3H3 InChIKey=IYIKLHRQXLHMJQ-UHFFFAOYSA-N CHEBI:2663 amiodarone An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . heterotricyclic compounds organic heterotricyclic compounds CHEBI:26979 organic heterotricyclic compound http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . heterobicyclic compounds organic heterobicyclic compounds two-ring heterocyclic compounds CHEBI:27171 organic heterobicyclic compound An N-sulfonylurea that consists of 1-butylurea having a tosyl group attached at the 3-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:27019 CHEBI:9616 CAS:64-77-7 DrugBank:DB01124 Drug_Central:2696 KEGG:C07148 KEGG:D00380 LINCS:LSM-3907 PMID:11835228 PMID:11840346 PMID:11911494 PMID:12042355 PMID:12355256 PMID:15207658 PMID:15317941 PMID:15620874 PMID:15655519 PMID:16290322 PMID:16426753 PMID:19059420 PMID:20880646 PMID:21178111 PMID:21193530 PMID:21471135 PMID:21535124 PMID:21712613 PMID:21757329 PMID:21827497 PMID:21831467 PMID:22028182 PMID:22079696 Patent:DE1066575 Patent:GB808071 Patent:US2968158 Reaxys:1984428 Wikipedia:Tolbutamide N-[(butylamino)carbonyl]-4-methylbenzenesulfonamide Tolbutamide chebi_ontology 0 1-Butyl-3-(p-methylphenylsulfonyl)urea 1-Butyl-3-(p-tolylsulfonyl)urea 1-Butyl-3-tosylurea 1-p-Toluenesulfonyl-3-butylurea 270.104 270.34800 3-(p-Tolyl-4-sulfonyl)-1-butylurea C12H18N2O3S CCCCNC(=O)NS(=O)(=O)c1ccc(C)cc1 InChI=1S/C12H18N2O3S/c1-3-4-9-13-12(15)14-18(16,17)11-7-5-10(2)6-8-11/h5-8H,3-4,9H2,1-2H3,(H2,13,14,15) JLRGJRBPOGGCBT-UHFFFAOYSA-N N-(4-Methylbenzenesulfonyl)-N'-butylurea N-(4-Methylphenylsulfonyl)-N'-butylurea N-(Sulfonyl-p-methylbenzene)-N'-N-butylurea N-(p-Methylbenzenesulfonyl)-N'-butylurea N-Butyl-N'-(4-methylphenylsulfonyl)urea N-Butyl-N'-(p-tolylsulfonyl)urea N-Butyl-N'-p-toluenesulfonylurea N-n-Butyl-N'-tosylurea Orinase (TN) Tolylsulfonylbutylurea tolbutamida tolbutamide tolbutamidum CHEBI:27999 tolbutamide A chromenone having the keto group located at the 2-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:101256 CHEBI:23402 CHEBI:3906 CHEBI:41552 Beilstein:383644 CAS:91-64-5 DrugBank:DB04665 Drug_Central:738 Gmelin:165222 HMDB:HMDB01218 KEGG:C05851 KEGG:D07751 KNApSAcK:C00002460 LINCS:LSM-2519 MetaCyc:COUMARIN PMID:17988284 PMID:19025869 PMID:21046436 PMID:21462332 PMID:21798343 PMID:8735869 Reaxys:383644 Wikipedia:Coumarin 2H-chromen-2-one chebi_ontology 0 1,2-Benzopyrone 146.037 146.14270 146.143 2-Propenoic acid, 3-(2-hydroxyphenyl)-, d-lactone 2-Propenoic acid, 3-(2-hydroxyphenyl)-, delta-lactone 2H-1-Benzopyran-2-one 2H-benzo[b]pyran-2-one 5,6-Benzo-2-pyrone Benzo-a-pyrone Benzo-alpha-pyrone C9H6O2 C=1C=CC=C2C1C=CC(=O)O2 Coumarine Coumarinic anhydride Cumarin InChI=1S/C9H6O2/c10-9-6-5-7-3-1-2-4-8(7)11-9/h1-6H Rattex Tonka bean camphor ZYGHJZDHTFUPRJ-UHFFFAOYSA-N cis-o-Coumarinic acid lactone o-Hydroxycinnamic acid lactone o-hydroxycinnamic acid delta-lactone CHEBI:28794 coumarin http://purl.obolibrary.org/obo/chebi.owl Beilstein:88093 CAS:125-73-5 LINCS:LSM-36603 17-methyl-9alpha,13alpha,14alpha-morphinan-3-ol chebi_ontology (+)-3-hydroxy-N-methylmorphinan 0 257.178 257.37066 C17H23NO InChI=1S/C17H23NO/c1-18-9-8-17-7-3-2-4-14(17)16(18)10-12-5-6-13(19)11-15(12)17/h5-6,11,14,16,19H,2-4,7-10H2,1H3/t14-,16+,17+/m1/s1 JAQUASYNZVUNQP-PVAVHDDUSA-N [H][C@]12CCCC[C@]11CCN(C)[C@H]2Cc2ccc(O)cc12 d-3-hydroxy-N-methylmorphinan dextrorphan dextrorphane dextrorphanum CHEBI:29133 dextrorphan A propanone that is propan-1-one substituted by a tert-butylamino group at position 2 and a 3-chlorophenyl group at position 1. http://purl.obolibrary.org/obo/chebi.owl Beilstein:2101062 CAS:34841-39-9 CAS:34911-55-2 DrugBank:DB01156 Drug_Central:435 HMDB:HMDB01510 KEGG:C06860 KEGG:D07591 LINCS:LSM-1267 MetaCyc:CPD-3481 PMID:12826985 PMID:15876900 Reaxys:2101062 Wikipedia:Bupropion 2-(tert-butylamino)-1-(3-chlorophenyl)propan-1-one Bupropion chebi_ontology 0 239.108 239.74086 C13H18ClNO CC(NC(C)(C)C)C(=O)c1cccc(Cl)c1 InChI=1S/C13H18ClNO/c1-9(15-13(2,3)4)12(16)10-6-5-7-11(14)8-10/h5-9,15H,1-4H3 SNPPWIUOZRMYNY-UHFFFAOYSA-N CHEBI:3219 bupropion An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands). http://purl.obolibrary.org/obo/chebi.owl coordination entities coordination entity chebi_ontology coordination compounds CHEBI:33240 coordination entity A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG COMPOUND:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology CO2R2 [*]C(=O)O[*] a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13428 CHEBI:13627 CHEBI:23027 CiteXplore:17147560 CiteXplore:18433345 carboxylic acid carboxylic acids chebi_ontology CHO2R Carbonsaeure Carbonsaeuren Karbonsaeure OC([*])=O RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . main group compounds main group molecular entities CHEBI:33579 main group molecular entity http://purl.obolibrary.org/obo/chebi.owl carbon group molecular entity chebi_ontology . carbon group molecular entities CHEBI:33582 carbon group molecular entity A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity A macromolecule formed by a living organism. http://purl.obolibrary.org/obo/chebi.owl biopolymer chebi_ontology Biopolymere biomacromolecules biopolymers CHEBI:33694 biomacromolecule http://purl.obolibrary.org/obo/chebi.owl chebi_ontology genetically encoded biomacromolecules genetically encoded biopolymers information biomacromolecules information biopolymers information macromolecule information macromolecules CHEBI:33695 information biomacromolecule A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. http://purl.obolibrary.org/obo/chebi.owl nucleic acids chebi_ontology NA Nukleinsaeure Nukleinsaeuren acide nucleique acides nucleiques acido nucleico acidos nucleicos CHEBI:33696 nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. http://purl.obolibrary.org/obo/chebi.owl ChemIDplus:63231-63-0 ribonucleic acid ribonucleic acids chebi_ontology RNA RNS Ribonukleinsaeure pentosenucleic acids ribonucleic acids ribose nucleic acid yeast nucleic acid CHEBI:33697 ribonucleic acid Any organic molecule that consists of atoms connected in the form of a ring. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . organic cyclic compounds CHEBI:33832 organic cyclic compound A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). http://purl.obolibrary.org/obo/chebi.owl heteroarenes chebi_ontology . hetarenes CHEBI:33833 heteroarene A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/chebi.owl Wikipedia:Macromolecule macromolecule chebi_ontology macromolecules polymer polymer molecule polymers CHEBI:33839 macromolecule http://purl.obolibrary.org/obo/chebi.owl magnesium coordination entity chebi_ontology magnesium coordination compounds magnesium coordination entities CHEBI:33976 magnesium coordination entity A 17beta-hydroxy steroid that is testosterone bearing an additional hydroxy substituent at the 6beta-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:63819 CAS:62-99-7 HMDB:HMDB06259 KEGG:C14497 LIPID_MAPS_instance:LMST02020054 PMID:10574192 PMID:15203039 PMID:22822673 Reaxys:2625776 6beta,17beta-dihydroxyandrost-4-en-3-one 6beta-Hydroxytestosterone chebi_ontology (6beta,17beta)-6,17-dihydroxyandrost-4-en-3-one 0 304.204 304.42380 4-androsten-6beta,17beta-diol-3-one 6beta,17beta-Dihydroxyandrost-4-en-3-one 6beta,17beta-dihydroxy-4-androsten-3-one 6beta,17beta-dihydroxyandrost-4-en-3-one C19H28O3 InChI=1S/C19H28O3/c1-18-7-5-11(20)9-15(18)16(21)10-12-13-3-4-17(22)19(13,2)8-6-14(12)18/h9,12-14,16-17,21-22H,3-8,10H2,1-2H3/t12-,13-,14-,16+,17-,18+,19-/m0/s1 XSEGWEUVSZRCBC-ZVBLRVHNSA-N [H][C@@]12C[C@@H](O)C3=CC(=O)CC[C@]3(C)[C@@]1([H])CC[C@]1(C)[C@@H](O)CC[C@@]21[H] CHEBI:34477 6beta-hydroxytestosterone http://purl.obolibrary.org/obo/chebi.owl Beilstein:225973 CAS:5725-91-7 KEGG:C13630 7-Ethoxyresorufin 7-ethoxy-3H-phenoxazin-3-one chebi_ontology 0 241.074 241.24208 7-Ethoxyphenoxazone C14H11NO3 CCOc1ccc2nc3ccc(=O)cc3oc2c1 CRCWUBLTFGOMDD-UHFFFAOYSA-N Ethoxyresorufin InChI=1S/C14H11NO3/c1-2-17-10-4-6-12-14(8-10)18-13-7-9(16)3-5-11(13)15-12/h3-8H,2H2,1H3 Resorufin ethyl ether CHEBI:34480 7-ethoxyresorufin http://purl.obolibrary.org/obo/chebi.owl CAS:54340-62-4 Drug_Central:424 KEGG:C13769 Bufuralol chebi_ontology (+/-)-Bufuralol 0 261.173 261.360 C16H23NO2 CCc1cccc2cc(oc12)C(O)CNC(C)(C)C InChI=1S/C16H23NO2/c1-5-11-7-6-8-12-9-14(19-15(11)12)13(18)10-17-16(2,3)4/h6-9,13,17-18H,5,10H2,1-4H3 SSEBTPPFLLCUMN-UHFFFAOYSA-N dl-Bufuralol CHEBI:34593 Bufuralol http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000002 metalloprotein chebi_ontology metalloproteine metalloproteins CHEBI:35134 metalloprotein http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000004 iron protein chebi_ontology iron proteins iron-containing proteins CHEBI:35136 iron protein Conjugated proteins containing heme as the prosthetic group. http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000008 hemoprotein chebi_ontology Haemoprotein Haemprotein haem protein haemoprotein heme protein hemeproteins hemoproteins CHEBI:35137 hemoprotein http://purl.obolibrary.org/obo/chebi.owl alkaline earth coordination entity chebi_ontology alkaline earth coordination compounds alkaline earth coordination entities CHEBI:35217 alkaline earth coordination entity A substance that diminishes the rate of a chemical reaction. http://purl.obolibrary.org/obo/chebi.owl inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor http://purl.obolibrary.org/obo/chebi.owl CHEBI:22721 benzofurans chebi_ontology CHEBI:35259 benzofurans http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . triazolobenzodiazepines CHEBI:35501 triazolobenzodiazepine http://purl.obolibrary.org/obo/chebi.owl chebi_ontology . carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. http://purl.obolibrary.org/obo/chebi.owl CHEBI:23960 CHEBI:4859 KEGG COMPOUND:C00287 Ester chebi_ontology . [*]OC([*])=O esters CHEBI:35701 ester http://purl.obolibrary.org/obo/chebi.owl chebi_ontology hydroxy acid hydroxy monocarboxylic acids CHEBI:35868 hydroxy monocarboxylic acid http://purl.obolibrary.org/obo/chebi.owl chebi_ontology dihydroxy monocarboxylic acids CHEBI:35972 dihydroxy monocarboxylic acid http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000150 chebi_ontology haem-thiolate protein heme-thiolate proteins CHEBI:36074 heme-thiolate protein A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. http://purl.obolibrary.org/obo/chebi.owl CHEBI:13677 CHEBI:14911 proteins chebi_ontology CHEBI:36080 protein Any molecular entity consisting of more than one atom. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity 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. http://purl.obolibrary.org/obo/chebi.owl CHEBI:47330 Beilstein:638882 CAS:95-25-0 DrugBank:DB00356 Drug_Central:626 HMDB:HMDB14500 KEGG:C07931 KEGG:D00771 LINCS:LSM-6011 PDBeChem:CLW PMID:10640318 PMID:11727787 PMID:12437348 PMID:16763012 PMID:16859676 PMID:17621748 PMID:21195386 PMID:23975871 PMID:24210069 PMID:25815637 PMID:6631711 Patent:US2895877 Reaxys:638882 Wikipedia:Chlorzoxazone 5-chloro-1,3-benzoxazol-2-ol CHLORZOXAZONE Chlorzoxazone chebi_ontology 0 168.993 169.56500 2-hydroxy-5-chlorobenzoxazole 5-chloro-2(3H)-benzoxazolone 5-chloro-2-benzoxazolinone 5-chloro-2-benzoxazolol 5-chloro-2-benzoxazolone 5-chloro-2-hydroxybenzoxazole 5-chlorobenzoxazolidone 5-chlorobenzoxazolin-2-one C7H4ClNO2 InChI=1S/C7H4ClNO2/c8-4-1-2-6-5(3-4)9-7(10)11-6/h1-3H,(H,9,10) Oc1nc2cc(Cl)ccc2o1 TZFWDZFKRBELIQ-UHFFFAOYSA-N chlorzoxane chlorzoxazona chlorzoxazone chlorzoxazonum CHEBI:3655 chlorzoxazone 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. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology main group coordination compounds main-group coordination entities CHEBI:36562 main-group coordination entity An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. http://purl.obolibrary.org/obo/chebi.owl organochalcogen compound chebi_ontology . organochalcogen compounds CHEBI:36962 organochalcogen compound An organochalcogen compound containing at least one carbon-oxygen bond. http://purl.obolibrary.org/obo/chebi.owl CiteXplore:17586126 organooxygen compound chebi_ontology . organooxygen compounds CHEBI:36963 organooxygen compound A molecular entity consisting of two or more chemical elements. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity http://purl.obolibrary.org/obo/chebi.owl chebi_ontology organic heterotetracyclic compounds CHEBI:38163 organic heterotetracyclic compound http://purl.obolibrary.org/obo/chebi.owl CHEBI:25429 CHEBI:38075 chebi_ontology . multi-ring heterocyclic compounds organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound http://purl.obolibrary.org/obo/chebi.owl chebi_ontology monocyclic heteroarenes CHEBI:38179 monocyclic heteroarene A dihydroxy monocarboxylic acid that is (6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl} hept-6-enoic acid carrying two hydroxy substituents at positions 3 and 5 (the 3R,5S-diastereomer). http://purl.obolibrary.org/obo/chebi.owl Beilstein:9670765 ChemIDplus:287714-41-4 CiteXplore:17970755 CiteXplore:18509206 CiteXplore:19724024 CiteXplore:19956889 CiteXplore:23806820 CiteXplore:23881596 CiteXplore:23944632 CiteXplore:24072337 CiteXplore:24076283 CiteXplore:24076297 CiteXplore:24156555 CiteXplore:24163149 CiteXplore:24230979 CiteXplore:24253250 CiteXplore:24259612 CiteXplore:24304551 CiteXplore:24333476 CiteXplore:24353409 CiteXplore:24410968 CiteXplore:24417785 CiteXplore:24434545 CiteXplore:24440231 CiteXplore:24440960 CiteXplore:24444439 CiteXplore:24452083 CiteXplore:24456217 CiteXplore:24467235 DrugBank:DB01098 HMDB:HMDB15230 KEGG DRUG:D08492 Patent:US2013035316 Reaxys:9670765 Wikipedia:Rosuvastatin (3R,5S,6E)-7-{4-(4-fluorophenyl)-2-[methyl(methylsulfonyl)amino]-6-(propan-2-yl)pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid chebi_ontology (3R,5S,6E)-7-(4-(4-fluorophenyl)-6-(1-methylethyl)-2-(ethyl(methylsulfonyl)amino)-5-pyrimidinyl)-3,5-dihydroxy-6-heptenoic acid (3R,5S,6E)-7-{4-(4-fluorophenyl)-6-isopropyl-2-[methyl(methylsulfonyl)amino]pyrimidin-5-yl}-3,5-dihydroxyhept-6-enoic acid C22H28FN3O6S CC(C)c1nc(nc(-c2ccc(F)cc2)c1\C=C\[C@@H](O)C[C@@H](O)CC(O)=O)N(C)S(C)(=O)=O InChI=1S/C22H28FN3O6S/c1-13(2)20-18(10-9-16(27)11-17(28)12-19(29)30)21(14-5-7-15(23)8-6-14)25-22(24-20)26(3)33(4,31)32/h5-10,13,16-17,27-28H,11-12H2,1-4H3,(H,29,30)/b10-9+/t16-,17-/m1/s1 InChIKey=BPRHUIZQVSMCRT-VEUZHWNKSA-N rosuvastatin CHEBI:38545 rosuvastatin http://purl.obolibrary.org/obo/chebi.owl COMe:PRX000645 cytochrome P450 chebi_ontology CYP P450 protein cytochrome P-450 CHEBI:38559 cytochrome P450 A racemate comprising equimolar amounts of (3R,5S)- and (3S,5R)-fluvastatin. An HMG-CoA reductase inhibitor, it is used (often as the corresponding sodium salt) to reduce triglycerides and LDL-cholesterol, and increase HDL-chloesterol, in the treatment of hyperlipidaemia. http://purl.obolibrary.org/obo/chebi.owl Beilstein:9168031 ChemIDplus:93957-54-1 CiteXplore:11273020 CiteXplore:12147804 CiteXplore:18410471 CiteXplore:18413661 CiteXplore:18452779 CiteXplore:18936176 CiteXplore:23212095 CiteXplore:23846727 DrugBank:DB01095 KEGG COMPOUND:93957-54-1 KEGG COMPOUND:C07014 KEGG DRUG:D07983 Patent:US4739073 Patent:WO8402131 Wikipedia:Fluvastatin rac-(3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid chebi_ontology (+-)-fluvastatin (6E)-erythro7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid C24H26FNO4 Cranoc erythro-(E)-3,5-dihydroxy-7-[3'-(4''-fluorophenyl)-1'-(1''-methylethyl)indol-2'-yl]hept-6-enoic acid fluvastatin fluvastatina fluvastatine fluvastatinum rac-(3R,5S)-fluvastatin rac-(3R,5S,6E)-7-(3-(4-fluorophenyl)-1-(1-methylethyl)-1H-indol-2-yl)-3,5-dihydroxy-6-heptenoic acid CHEBI:38561 fluvastatin http://purl.obolibrary.org/obo/chebi.owl triazole chebi_ontology C2H3N3 CHEBI:38597 triazole A member of the class of benzofurans consisting of a 1-benzofuran skeleton and its substituted derivatives thereof. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology CHEBI:38830 1-benzofurans A dihydroxy monocarboxylic acid that is a member of the drug class known as statins, used primarily for lowering blood cholesterol and for preventing cardiovascular diseases. http://purl.obolibrary.org/obo/chebi.owl CHEBI:2910 CHEBI:39538 Beilstein:8373630 ChemIDplus:134523-00-5 CiteXplore:11693468 CiteXplore:15012735 CiteXplore:18720283 DrugBank:DB01076 HMDB:HMDB05006 KEGG COMPOUND:134523-00-5 KEGG COMPOUND:C06834 KEGG DRUG:D07474 PDBeChem:117 Patent:EP409281 Patent:US5273995 Reaxys:8373630 Wikipedia:Atorvastatin (3R,5R)-7-[3-(anilinocarbonyl)-5-(4-fluorophenyl)-4-phenyl-2-(propan-2-yl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid Atorvastatin chebi_ontology (3R,5R)-7-[2-(4-fluorophenyl)-5-(1-methylethyl)-3-phenyl-4-(phenylcarbamoyl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoic acid (R-(R*,R*))-2-(4-Fluorophenyl)-beta,delta-dihydroxy-5-(1-methylethyl)-3-phenyl-4-((phenylamino)carbonyl)-1H-pyrrole-1-heptanoic acid 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]-3,5-DIHYDROXY-HEPTANOIC ACID Atorlip C33H35FN2O5 CC(C)c1c(C(=O)Nc2ccccc2)c(-c2ccccc2)c(-c2ccc(F)cc2)n1CC[C@@H](O)C[C@@H](O)CC(O)=O InChI=1S/C33H35FN2O5/c1-21(2)31-30(33(41)35-25-11-7-4-8-12-25)29(22-9-5-3-6-10-22)32(23-13-15-24(34)16-14-23)36(31)18-17-26(37)19-27(38)20-28(39)40/h3-16,21,26-27,37-38H,17-20H2,1-2H3,(H,35,41)(H,39,40)/t26-,27-/m1/s1 InChIKey=XUKUURHRXDUEBC-KAYWLYCHSA-N atorvastatin atorvastatina atorvastatine atorvastatinum CHEBI:39548 atorvastatin A fatty acid ester that is mevastatin carrying an additional methyl group on the carbobicyclic skeleton. It is used in as a antilipemic drug and has been found in fungal species such as Aspergillus terreus and Pleurotus ostreatus (oyster mushroom). http://purl.obolibrary.org/obo/chebi.owl CHEBI:40299 CHEBI:6544 ChemIDplus:3631989 ChemIDplus:75330-75-5 CiteXplore:11375168 CiteXplore:11389707 CiteXplore:11483865 CiteXplore:18642339 CiteXplore:24093797 DrugBank:DB00227 HMDB:HMDB14372 KEGG COMPOUND:C07074 KEGG DRUG:75330-75-5 KEGG DRUG:D00359 KNApSAcK:C00000547 PDBeChem:803 Patent:CN103172602 Patent:WO2013090461 Reaxys:4720754 Wikipedia:Lovastatin (1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxotetrahydro-2H-pyran-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl (2S)-2-methylbutanoate LOVASTATIN Lovastatin chebi_ontology (1S,3R,7S,8S,8aR)-1,2,3,7,8,8a-hexahydro-3,7-dimethyl-8-(2-(2R,4R)-(tetrahydro-4-hydroxy-6-oxo-2H-pyran-2-yl)ethyl)-1-naphthalenyl (S)-2-methyl-butyrate 2beta,6alpha-dimethyl-8alpha-(2-methyl-1-oxobutoxy)-mevinic acid lactone 6alpha-methylcompactin C24H36O5 InChI=1S/C24H36O5/c1-5-15(3)24(27)29-21-11-14(2)10-17-7-6-16(4)20(23(17)21)9-8-19-12-18(25)13-22(26)28-19/h6-7,10,14-16,18-21,23,25H,5,8-9,11-13H2,1-4H3/t14-,15-,16-,18+,19+,20-,21-,23-/m0/s1 InChIKey=PCZOHLXUXFIOCF-BXMDZJJMSA-N MK-803 ML-530B Mevacor Mevinolin [H][C@]12[C@H](C[C@@H](C)C=C1C=C[C@H](C)[C@@H]2CC[C@@H]1C[C@@H](O)CC(=O)O1)OC(=O)[C@@H](C)CC CHEBI:40303 lovastatin 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. http://purl.obolibrary.org/obo/chebi.owl CAS:125-71-3 DrugBank:DB00514 HMDB:HMDB01920 KEGG:C06947 KEGG:D03742 PMID:17461892 PMID:18198471 PMID:24269965 Reaxys:88549 Wikipedia:Dextromethorphan 3-methoxy-17-methylmorphinan Dextromethorphan chebi_ontology 0 271.194 271.39724 C18H25NO DXM InChI=1S/C18H25NO/c1-19-10-9-18-8-4-3-5-15(18)17(19)11-13-6-7-14(20-2)12-16(13)18/h6-7,12,15,17H,3-5,8-11H2,1-2H3/t15-,17+,18+/m0/s1 MKXZASYAUGDDCJ-CGTJXYLNSA-N [H][C@@]12CCCC[C@@]11CCN(C)[C@@H]2Cc2ccc(OC)cc12 d-Methorphan delta-Methorphan CHEBI:4470 dextromethorphan 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. http://purl.obolibrary.org/obo/chebi.owl CHEBI:45862 CHEBI:7887 CAS:33069-62-4 DrugBank:DB01229 Drug_Central:2044 KEGG:C07394 KEGG:D00491 KNApSAcK:C00002365 PDBeChem:TA1 Wikipedia:Paclitaxel 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 Paclitaxel chebi_ontology (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 0 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 853.331 853.90618 C47H51NO14 InChI=1S/C47H51NO14/c1-25-31(60-43(56)36(52)35(28-16-10-7-11-17-28)48-41(54)29-18-12-8-13-19-29)23-47(57)40(61-42(55)30-20-14-9-15-21-30)38-45(6,32(51)22-33-46(38,24-58-33)62-27(3)50)39(53)37(59-26(2)49)34(25)44(47,4)5/h7-21,31-33,35-38,40,51-52,57H,22-24H2,1-6H3,(H,48,54)/t31-,32-,33+,35-,36+,37+,38-,40-,45+,46-,47+/m0/s1 RCINICONZNJXQF-MZXODVADSA-N TAXOL Taxol A [H][C@]12[C@H](OC(=O)c3ccccc3)[C@]3(O)C[C@H](OC(=O)[C@H](O)[C@@H](NC(=O)c4ccccc4)c4ccccc4)C(C)=C([C@@H](OC(C)=O)C(=O)[C@]1(C)[C@@H](O)C[C@H]1OC[C@@]21OC(C)=O)C3(C)C taxol CHEBI:45863 paclitaxel A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It has been shown to exhibit antifungal activity. http://purl.obolibrary.org/obo/chebi.owl CHEBI:46079 CHEBI:5099 Beilstein:4269710 ChemIDplus:86386-73-4 CiteXplore:11366931 CiteXplore:16822276 CiteXplore:23171950 CiteXplore:23793863 DrugBank:DB00196 HMDB:HMDB14342 KEGG DRUG:D00322 PDBeChem:TPF Patent:GB2099818 Patent:US4404216 Reaxys:7311650 Wikipedia:Fluconazole 2-(2,4-difluorophenyl)-1,3-bis-(1H-1,2,4-triazol-1-yl)propan-2-ol chebi_ontology 2,4-difluoro-alpha,alpha-bis(1H-1,2,4-triazol-1-ylmethyl)benzyl alcohol 2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL Biozole C13H12F2N6O Diflucan Elazor InChI=1S/C13H12F2N6O/c14-10-1-2-11(12(15)3-10)13(22,4-20-8-16-6-18-20)5-21-9-17-7-19-21/h1-3,6-9,22H,4-5H2 InChIKey=RFHAOTPXVQNOHP-UHFFFAOYSA-N OC(Cn1cncn1)(Cn1cncn1)c1ccc(F)cc1F Triflucan fluconazol fluconazole fluconazolum CHEBI:46081 fluconazole A monocarboxylic acid consisting of phenylacetic acid having a (2,6-dichlorophenyl)amino group at the 2-position. http://purl.obolibrary.org/obo/chebi.owl CHEBI:4507 CHEBI:47380 Beilstein:2146636 CAS:15307-86-5 DrugBank:DB00586 Drug_Central:865 HMDB:HMDB14724 KEGG:C01690 KEGG:D07816 LINCS:LSM-2160 PDBeChem:DIF PMID:11322639 PMID:1502708 PMID:23777257 PMID:7838674 Patent:NL6604752 Patent:US3558690 Reaxys:2146636 Wikipedia:Diclofenac 2-[(2,6-dichlorophenyl)amino]benzeneacetic acid Diclofenac {2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid chebi_ontology 0 2-((2,6-dichlorophenyl)amino)benzeneacetic acid 296.14900 353.022 C16H13Cl2NO4 DCOPUUMXTXDBNB-UHFFFAOYSA-N InChI=1S/C14H11Cl2NO2/c15-10-5-3-6-11(16)14(10)17-12-7-2-1-4-9(12)8-13(18)19/h1-7,17H,8H2,(H,18,19) OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl [2-(2,6-dichloroanilino)phenyl]acetic acid diclofenac diclofenac acid diclofenaco diclofenacum CHEBI:47381 diclofenac A N-carbonylpiperazine that has formula C26H28Cl2N4O4. http://purl.obolibrary.org/obo/chebi.owl Beilstein:634785 DrugBank:DB01026 1-acetyl-4-(4-{[2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine chebi_ontology C26H28Cl2N4O4 CC(=O)N1CCN(CC1)c1ccc(OCC2COC(Cn3ccnc3)(O2)c2ccc(Cl)cc2Cl)cc1 InChI=1S/C26H28Cl2N4O4/c1-19(33)31-10-12-32(13-11-31)21-3-5-22(6-4-21)34-15-23-16-35-26(36-23,17-30-9-8-29-18-30)24-7-2-20(27)14-25(24)28/h2-9,14,18,23H,10-13,15-17H2,1H3 InChIKey=XMAYWYJOQHXEEK-UHFFFAOYSA-N CHEBI:48339 ketoconazole http://purl.obolibrary.org/obo/chebi.owl chebi_ontology benzothiazepines CHEBI:48684 benzothiazepine Any molecular entity that contains carbon. http://purl.obolibrary.org/obo/chebi.owl CHEBI:25700 CHEBI:33244 chebi_ontology . organic compounds organic entity organic molecular entities organic molecules CHEBI:50860 organic molecular entity http://purl.obolibrary.org/obo/chebi.owl chebi_ontology magnesium halides CHEBI:51234 magnesium halide http://purl.obolibrary.org/obo/chebi.owl Beilstein:174850 CAS:635-78-9 7-hydroxy-3H-phenoxazin-3-one chebi_ontology 0 213.043 213.18892 7-Hydroxy-3H-phenoxazin-3-one 7-Hydroxyphenoxazin-3-one C12H7NO3 HSSLDCABUXLXKM-UHFFFAOYSA-N InChI=1S/C12H7NO3/c14-7-1-3-9-11(5-7)16-12-6-8(15)2-4-10(12)13-9/h1-6,14H Oc1ccc2nc3ccc(=O)cc3oc2c1 Resorufine CHEBI:51602 resorufin A monocarboxylic acid that is the 4'-hydroxylated metabolite of diclofenac. http://purl.obolibrary.org/obo/chebi.owl Beilstein:4198042 CAS:64118-84-9 PMID:10027798 PMID:10709153 PMID:10807502 PMID:12966366 PMID:14609740 PMID:15139759 PMID:15265128 PMID:15455182 PMID:17123753 PMID:18548238 PMID:2118185 PMID:9226412 PMID:9862754 Reaxys:4198042 {2-[(2,6-dichloro-4-hydroxyphenyl)amino]phenyl}acetic acid chebi_ontology (o-(2,6-Dichloro-4-hydroxyanilino)phenyl)acetic acid 0 311.012 312.14800 4'-OH DCF 4'-hydroxy diclofenac C14H11Cl2NO3 InChI=1S/C14H11Cl2NO3/c15-10-6-9(18)7-11(16)14(10)17-12-4-2-1-3-8(12)5-13(19)20/h1-4,6-7,17-18H,5H2,(H,19,20) KGVXVPRLBMWZLG-UHFFFAOYSA-N OC(=O)Cc1ccccc1Nc1c(Cl)cc(O)cc1Cl CHEBI:59613 4'-hydroxydiclofenac A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology Chemische Substanz CHEBI:59999 chemical substance A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology Mischung CHEBI:60004 mixture A dioxolane that has formula C35H38Cl2N8O4. http://purl.obolibrary.org/obo/chebi.owl ChEMBL:17194821 ChemIDplus:84625-61-6 DrugBank:DB01167 KEGG DRUG:84625-61-6 KEGG DRUG:D00350 Wikipedia:Itraconazole 2-(butan-2-yl)-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one Itraconazole chebi_ontology C35H38Cl2N8O4 CCC(C)n1ncn(-c2ccc(cc2)N2CCN(CC2)c2ccc(OC[C@H]3CO[C@@](Cn4cncn4)(O3)c3ccc(Cl)cc3Cl)cc2)c1=O InChI=1S/C35H38Cl2N8O4/c1-3-25(2)45-34(46)44(24-40-45)29-7-5-27(6-8-29)41-14-16-42(17-15-41)28-9-11-30(12-10-28)47-19-31-20-48-35(49-31,21-43-23-38-22-39-43)32-13-4-26(36)18-33(32)37/h4-13,18,22-25,31H,3,14-17,19-21H2,1-2H3/t25?,31-,35-/m0/s1 InChIKey=VHVPQPYKVGDNFY-ZPGVKDDISA-N Itrizole (TN) Oriconazole Sporanox (TN) CHEBI:6076 itraconazole A racemate is an equimolar mixture of a pair of enantiomers. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology melange racemique racemates racemic mixture CHEBI:60911 racemate A urea that consists of 1-butylurea having a 4-hydroxymethylbenzenesulfonyl group attached at the 3-position. http://purl.obolibrary.org/obo/chebi.owl CAS:5719-85-7 HMDB:HMDB06408 PMID:16493553 Reaxys:2867981 N-(butylcarbamoyl)-4-(hydroxymethyl)benzenesulfonamide chebi_ontology 0 1-Butyl-3-(4-hydroxymethylphenyl)sulfonylurea 286.099 286.34700 C12H18N2O4S CCCCNC(=O)NS(=O)(=O)c1ccc(CO)cc1 Hydroxymethyltolbutamide Hydroxytolbutamide InChI=1S/C12H18N2O4S/c1-2-3-8-13-12(16)14-19(17,18)11-6-4-10(9-15)5-7-11/h4-7,15H,2-3,8-9H2,1H3,(H2,13,14,16) Methylhydroxytolbutamide SJRHYONYKZIRPM-UHFFFAOYSA-N CHEBI:63799 4-hydroxytolbutamide 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. http://purl.obolibrary.org/obo/chebi.owl CAS:92340-57-3 PMID:19166730 PMID:21546194 PMID:7781266 PMID:8550990 PMID:9916309 Reaxys:8439890 (4-methoxy-6-{[(5-methoxy-1H-benzimidazol-2-yl)sulfinyl]methyl}-5-methylpyridin-3-yl)methanol chebi_ontology 0 361.110 361.41500 5-Methoxy-2-(((4-methoxy-3-methyl-5-hydroxymethyl-2-pyridinyl)methyl)sulfinyl)-1H-benzimidazole C17H19N3O4S CMZHQFXXAAIBKE-UHFFFAOYSA-N COc1ccc2[nH]c(nc2c1)S(=O)Cc1ncc(CO)c(OC)c1C Hydroxyomeprazole InChI=1S/C17H19N3O4S/c1-10-15(18-7-11(8-21)16(10)24-3)9-25(22)17-19-13-5-4-12(23-2)6-14(13)20-17/h4-7,21H,8-9H2,1-3H3,(H,19,20) CHEBI:63840 5'-hydroxyomeprazole A taxane diterpenoid that consists of paclitaxel bearing an additional hydroxy substituent at the 6alpha-position. http://purl.obolibrary.org/obo/chebi.owl CAS:153212-75-0 Reaxys:8105272 (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 chebi_ontology 0 6-hydroxytaxol 6alpha-hydroxypaclitaxel 6alpha-hydroxytaxol 869.326 869.90550 C47H51NO15 InChI=1S/C47H51NO15/c1-24-30(61-43(57)33(51)32(27-16-10-7-11-17-27)48-41(55)28-18-12-8-13-19-28)22-47(58)40(62-42(56)29-20-14-9-15-21-29)36-45(6,38(54)35(60-25(2)49)31(24)44(47,4)5)37(53)34(52)39-46(36,23-59-39)63-26(3)50/h7-21,30,32-37,39-40,51-53,58H,22-23H2,1-6H3,(H,48,55)/t30-,32-,33+,34-,35+,36-,37-,39+,40-,45-,46+,47+/m0/s1 NDCWHEDPSFRTDA-FJMWQILYSA-N [H][C@]12[C@H](OC(=O)c3ccccc3)[C@]3(O)C[C@H](OC(=O)[C@H](O)[C@@H](NC(=O)c4ccccc4)c4ccccc4)C(C)=C([C@@H](OC(C)=O)C(=O)[C@]1(C)[C@@H](O)[C@H](O)[C@H]1OC[C@@]21OC(C)=O)C3(C)C CHEBI:63859 6-hydroxypaclitaxel A magnesium salt comprising of two chlorine atoms bound to a magnesium atom. http://purl.obolibrary.org/obo/chebi.owl CAS:7786-30-3 Gmelin:9305 KEGG:C07755 MolBase:1868 Reaxys:8128169 magnesium dichloride chebi_ontology 0 93.923 95.21040 Cl2Mg InChI=1S/2ClH.Mg/h2*1H;/q;;+2/p-2 Magnesium chloride Magnesium chloride anhydrous Magnesiumchlorid MgCl2 TWRXJAOTZQYOKJ-UHFFFAOYSA-L [Mg++].[Cl-].[Cl-] [MgCl2] CHEBI:6636 magnesium dichloride Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. http://purl.obolibrary.org/obo/chebi.owl Wikipedia:Azole chebi_ontology azoles CHEBI:68452 azole http://purl.obolibrary.org/obo/chebi.owl CAS:59467-70-8 Drug_Central:1802 KEGG:C07524 KEGG:D00550 LINCS:LSM-5200 Midazolam chebi_ontology 0 325.078 325.768 C18H13ClFN3 Cc1ncc2CN=C(c3ccccc3F)c3cc(Cl)ccc3-n12 DDLIGBOFAVUZHB-UHFFFAOYSA-N InChI=1S/C18H13ClFN3/c1-11-21-9-13-10-22-18(14-4-2-3-5-16(14)20)15-8-12(19)6-7-17(15)23(11)13/h2-9H,10H2,1H3 buccolam mezolam midazolam HCl midazolam hydrochloride CHEBI:6931 Midazolam Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. http://purl.obolibrary.org/obo/chebi.owl chebi_ontology organic molecules CHEBI:72695 organic molecule http://purl.obolibrary.org/obo/chebi.owl Beilstein:497773 CAS:21829-25-4 DrugBank:DB01115 Drug_Central:1922 KEGG:C07266 KEGG:D00437 LINCS:LSM-4176 Wikipedia:Nifedipine Nifedipine dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate chebi_ontology 0 346.116 346.33460 4-(2'-Nitrophenyl)-2,6-dimethyl-1,4-dihydropyridin-3,5-dicarbonsaeuredimethylester Adalat Adapine C17H18N2O6 COC(=O)C1=C(C)NC(C)=C(C1c1ccccc1[N+]([O-])=O)C(=O)OC Coracten HYIMSNHJOBLJNT-UHFFFAOYSA-N InChI=1S/C17H18N2O6/c1-9-13(16(20)24-3)15(14(10(2)18-9)17(21)25-4)11-7-5-6-8-12(11)19(22)23/h5-8,15,18H,1-4H3 Nifecard Nifecor Nifedipres Procardia nifedipine nifedipino nifedipinum CHEBI:7565 nifedipine A racemate comprising equimolar amounts of (R)- and (S)-omeprazole. http://purl.obolibrary.org/obo/chebi.owl Beilstein:3628192 CAS:73590-58-6 DrugBank:DB00338 KEGG:C07324 KEGG:D00455 PMID:11060758 PMID:11208500 PMID:11210716 PMID:11304936 PMID:11321383 PMID:11395292 PMID:11404722 PMID:11459434 PMID:11568514 PMID:11700946 PMID:11774962 PMID:11807212 PMID:11851112 PMID:11903739 PMID:11962536 PMID:12072663 PMID:12135028 PMID:12235248 PMID:12495367 PMID:12683615 PMID:13680386 PMID:14616415 PMID:14708212 PMID:14725575 PMID:15004262 PMID:15125696 PMID:15586641 PMID:15598025 PMID:15684503 PMID:15707461 PMID:15774534 PMID:16080278 PMID:16129922 PMID:16259581 PMID:16276979 PMID:16380990 PMID:16386527 PMID:16397810 PMID:16440530 PMID:16998872 PMID:17049542 PMID:17384694 PMID:17532167 PMID:18294333 PMID:18366242 PMID:18416943 PMID:18448060 PMID:18498918 PMID:18520598 PMID:18571645 PMID:18616070 PMID:18793272 PMID:18818790 PMID:19150046 PMID:19166730 PMID:19176055 PMID:19236757 PMID:19327607 PMID:19383986 PMID:19434360 PMID:19470853 PMID:19517893 PMID:19746659 PMID:19796313 PMID:19801857 PMID:19937171 Patent:EP5129 Patent:US4255431 Patent:US5693818 Reaxys:3628192 Wikipedia:Omeprazole rac-5-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl}-1H-benzimidazole chebi_ontology 5-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl}-1H-benzimidazole Antra Audazol Belmazol Ceprandal Danlox Desec Elgam Emeproton Gasec Gastrimut Indurgan Inhibitron Losec OMEP OMP OMZ Olit Omapren Omebeta Prazidec Procelac Sanamidol Ulceral Ulcesep Ultop omeprazol omeprazole omeprazolum CHEBI:7772 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. http://purl.obolibrary.org/obo/chebi.owl ChemIDplus:34933-06-7 Reaxys:25644899 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate chebi_ontology 3-acetoxy-5-(2-(dimethylamino)ethyl)-2,3-dihydro-2-(4-methoxyphenyl)-1,5-benzothiazepin-4(5H)-one C22H26N2O4S COc1ccc(cc1)C1Sc2ccccc2N(CCN(C)C)C(=O)C1OC(C)=O InChI=1S/C22H26N2O4S/c1-15(25)28-20-21(16-9-11-17(27-4)12-10-16)29-19-8-6-5-7-18(19)24(22(20)26)14-13-23(2)3/h5-12,20-21H,13-14H2,1-4H3 InChIKey=HSUGRBWQSSZJOP-UHFFFAOYSA-N CHEBI:82814 5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate A fatty acid ester comprising a dihydroxyheptanoic acid unit condensed into a lactone; a partially reduced naphthalene structure; and a 2,2-dimethylbutyric acyl substituent at C17. It is used as a cholesterol-lowering and anti-cardiovascular disease drug. http://purl.obolibrary.org/obo/chebi.owl CHEBI:45577 Beilstein:4768037 ChemIDplus:79902-63-9 CiteXplore:11336576 CiteXplore:12827636 CiteXplore:14561068 CiteXplore:14973129 CiteXplore:18199328 CiteXplore:18688862 CiteXplore:18936176 DrugBank:DB00641 KEGG DRUG:79902-63-9 KEGG DRUG:D00434 PDBeChem:SIM Patent:EP33538 Patent:US4444784 Wikipedia:Simvastatin (1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxotetrahydro-2H-pyran-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl 2,2-dimethylbutanoate SIMVASTATIN Simvastatin chebi_ontology (3R,5R)-7-{(1S,2S,6R,8S,8aR)-8-[(2,2-dimethylbutanoyl)oxy]-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl}-3,5-dihydroxyheptanoic acid 2,2-dimethylbutyric acid, 8-ester with (4R,6R)-6-(2-((1S,2S,6R,8S,8aR)-1,2,6,7,8,8a-hexahydro-8-hydroxy-2,6-dimethyl-1-naphthyl)ethyl)tetrahydro-4-hydroxy-2H-pyran-2-one C25H38O5 CCC(C)(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@@H]12 InChI=1S/C25H38O5/c1-6-25(4,5)24(28)30-21-12-15(2)11-17-8-7-16(3)20(23(17)21)10-9-19-13-18(26)14-22(27)29-19/h7-8,11,15-16,18-21,23,26H,6,9-10,12-14H2,1-5H3/t15-,16-,18+,19+,20-,21-,23-/m0/s1 InChIKey=RYMZZMVNJRMUDD-HGQWONQESA-N MK-733 Simvastatina Simvastatine Simvastatinum Zocor simvastatin CHEBI:9150 simvastatin A triazolobenzodiazepine that has formula C17H12Cl2N4. http://purl.obolibrary.org/obo/chebi.owl Beilstein:1226643 ChemIDplus:28911-01-5 DrugBank:DB00897 KEGG DRUG:D00387 Wikipedia:Triazolam 8-chloro-6-(2-chlorophenyl)-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine chebi_ontology C17H12Cl2N4 Cc1nnc2CN=C(c3ccccc3Cl)c3cc(Cl)ccc3-n12 Halcion InChI=1S/C17H12Cl2N4/c1-10-21-22-16-9-20-17(12-4-2-3-5-14(12)19)13-8-11(18)6-7-15(13)23(10)16/h2-8H,9H2,1H3 InChIKey=JOFWLTCLBGQGBO-UHFFFAOYSA-N CHEBI:9674 triazolam 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. http://purl.obolibrary.org/obo/chmo.owl burchh 2009-06-19T02:03:14Z high speed centrifugation CHMO:0002013 high-speed centrifugation The process of one material (absorbate) being retained by another (absorption). http://purl.obolibrary.org/obo/chmo.owl REX:0000188 CHMO:0002914 Gold Book, somewhat modified. It goes on "The process of one material (absorbate) being retained by another (absorbent); this may be the physical solution of a gas, liquid, or solid in a liquid, attachment of molecules of a gas, vapour, liquid, or dissolved substance to a solid surface by physical forces, etc." absorption of material cell line cell 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 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 http://purl.obolibrary.org/obo/clo.owl 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. cell line cell He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here: http://code.google.com/p/clo-ontology/wiki/Cell_Lines MB, SS, JZ, MAH, BP, CS, YH The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. cell line LCL-1170 Caco-2 http://purl.obolibrary.org/obo/clo.owl disease: colorectal adenocarcinoma Caco-2 cell ATCC: HTB-37 CHEMBL: CHEMBL3307519 CVCL: CVCL_0025 EFO: EFO_0001099 HyperCLDB: cl618 MeSH: D018938 CHO Chinese Hamster Ovary cell http://purl.obolibrary.org/obo/clo-merged.owl CHO cell HyperCLDB: cl721 MeSH: D016466 LLC-PK subscript(1) http://purl.obolibrary.org/obo/clo.owl LLC-PK subscript(1) cell ATCC: CL-101 HyperCLDB: cl3221 MeSH: D018374 MDCK http://purl.obolibrary.org/obo/clo.owl MDCK cell HyperCLDB: cl5078 Amelogenin: X; CSF1PO: 11,12; D13S317: 12; D16S539: 9; D18S51: 18; D21S11: 28,30.2; D3S1358: 15,17; D5S818: 8,9; D7S820: 11,12; D8S1179: 12,14; FGA: 23; Penta D: 9,10; Penta E: 7,15; TH01: 7,9.3; TPOX: 11; vWA: 16,19 293 293 HEK HEK 293 HEK-293 HEK293 WEB: http://hek293.com/ WEB: http://web.expasy.org/cellosaurus/CVCL_0045 WEB: https://www.atcc.org/Products/All/CRL-1573.aspx http://purl.obolibrary.org/obo/clo-merged.owl 293-derived cell ATCC: CRL-1573 RRID: CVCL_0045 cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. http://purl.obolibrary.org/obo/clo.owl cell 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. cultured cell experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. http://purl.obolibrary.org/obo/clo.owl cell 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 experimentally modified cell in vitro A potential drug-drug interaction (PDDI) is an information content entity that specifies the possibility of a drug-drug interaction based on either reasonable extrapolation about drug-drug interaction mechanisms or a data item created by clinical studies, clinical observation or physiological experiment. Mathias Brochhausen potential drug-drug interaction the DDI mechanism, the risk of it causing a clinical effect, the clinical effect brought about by that DDI, factor's that modify the probability of it occuring An information content entity that is about a drug-drug interaction. DDI description drug-drug interaction description A data item that is about a biological process Mathias Brochhausen 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). Mathias Brochhausen observational data item about drug-drug interaction A data item that is about a biological process and that is the specified output of a clinical study. physiological observation from clinical study data item A data item that is the output of a process of estimating, beyond the original observation range, the value of a variable on the basis of its relationship with another variable. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Extrapolation&oldid=690284752 data item from extrapolation A biological process that realizes the function of the gastrointestinal system (or any organ that is a part of it.). This includes digestion of ingested substances, absorption and eliminating waste. Physiological activity and functions of the gastrointestinal system as a whole or of any of its parts, including digestion, absorption and eliminating waste. gastrointestinal functioning "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. Anuj Shah Mathias Brochhausen bioavailability An information content entity that makes a statement about a drug product being an object drug in a drug interaction. Mathias Brochhausen object drug information The role that inheres in a drug product or drug ingredient and that is realized by being affected by another drug pharmacokinetically or pharmacodynamically in a drug drug interaction. Daniel C. Malone Jodi Schneider Mathias Brochhausen Philip E. Empey Richard D. Boyce William R. Hogan http://www.hanstenandhorn.com/article-d-i.html object drug role The role that inheres in a drug product or drug ingredient that is realized by affecting another drug pharmacokinetically or pharmacodynamically in a drug drug interaction. Daniel C. Malone Jodi Schneider Mathias Brochhausen Philip E. Empey Richard C. Boyce William R. Hogan http://www.hanstenandhorn.com/article-d-i.html precipitant drug role An information content entity that makes a statement about a drug product being an precipitant drug in a drug interaction. Mathias Brochhausen precipitant drug information A potential drug drug interaction that is about a drug metabolism. Mathias Brochhausen metabolic potential drug-drug interaction A disposition inhering in a drug product that when realized is realized by processes that negatively affect the safety or the efficacy of the drug product, or increase its toxicity.. Mathias Brochhausen narrow therapeutic index A metabolism induction potential drug-drug interaction that is about an decrease of metabolic activity because of either a decreased expression of the enzyme or inference with how the enzyme contributes to the metabolic process. Mathias Brochhausen metabolism inhibition potential drug-drug interaction A metabolism induction potential drug-drug interaction that is about an increase of an enzyme participating in the metabolic process. Mathias Brochhausen metabolism induction potential drug-drug interaction A 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. Anuj Shah Mathias Brochhausen F bioavailability measurement datum An assay with the objective to capture information about the bioavailability of an active ingredient in a drug product. Anuj Shah Mathias Brochhausen drug bioavailability assay An entity that is the result of a drug-drug interaction. obsolete_drug-drug interaction effect true 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. Anuj Shah Mathias Brochhausen 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. Anuj Shah Mathias Brochhausen drug first pass metabolism assay A scalar measurement datum that is the specified outcome of a drug first pass metabolism assay. Anuj Shah Mathias Brochhausen 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. Anuj Shah Mathias Brochhausen 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. Anuj Shah Mathias Brochhausen drug absorbability assay A a scalar measurement datum that is the specified outcome of an drug absorbability assay. Anuj Shah Mathias Brochhausen 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. Anuj Shah Mathias Brochhausen drug maximum concentration assay A scalar measurement datum that is the specified outcome of a drug maximum concentration assay. Anuj Shah Mathias Brochhausen Cmax drug maximum concentration measurement datum A role that is borne by the enzyme responsible for 50% or more of the active pharmaceutic ingredient or metabolite’s total clearance from the body. The role role is realized by the metabolic process of the active pharmaceutical ingredient or metabolite. Anuj Shah Mathias Brochhausen primary total clearance enzyme role 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. Anuj Shah Mathias Brochhausen primary metabolic clearance enzyme role A drug-drug interaction description that is part of a drug package insert. drug-drug interaction description from drug package insert A drug-drug interaction description from a drug package insert for an FDA approved drug. drug-drug interaction description from FDA label information A document that is provided along with a medication and that gives additional information about that medication. https://en.wikipedia.org/w/index.php?title=Package_insert&oldid=699801598 drug package insert 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 http://www.fda.gov/forpatients/other/offlabel/default.htm U.S. Food and Drug Administration drug label An area under curve in a plot of concentration of granular part of a drug product in some matrix (medium) against time. pharmacokinetic area under curve An information content entity that is part of a drug package insert and that is about a pharmacokinetic area under the curve measurement result. Mathias Brochhausen drug package AUC information An information content entity that provides statements or data that are used to support or refute an assertion. Mathias Brochhausen Standards Development Working Group of the "Addressing PDDI Evidence Gaps" porject. obsolete_evidence information content entity true An information content entity that is about a pharmacokinetic area under curve. Mathias Brochhausen AUC information pharmacokinetic area under curve information 2 A pharmacokinetic area under curve information that is about at least 2 area under curve measurments and the time series shows an increase of the area under curve. Mathias Brochhausen information about increase of pharmacokinetic area under the curve 2 A pharmacokinetic area under curve information that is about at least 2 area under curve measurments and the time series shows a decrease of the area under curve. Mathias Brochhausen information about decrease of pharmacokinetic area under the curve A biological process that has as a participant a part of a drug product and includes absorption, distribution, metabolism and excretion of that substance. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group. pharmacokinetic process An information content entity that is used to support or refute an assertion. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group evidence information content entity An information content entity that is part of an evidence information content entity and mentions the specified input to an assay. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group evidence material information A data item that is part of an evidence information content entity and is the specified output of an assay. Mathias Brochhausen "Addressing PDDI Evidence Gaps" Standards Development Group evidence data item An evidence information content entity that is about a clinical drug trial. Mathias Brochhausen EV_Clinical_Trial https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from clinical study An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process, as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from drug metabolism identification experiment An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process, as it's specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from drug metabolism inhibition experiment 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. Mathias Brochhausen EV_EX_Trans_Prot_ID https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from transport protein inhibition experiment An evidence information content entity that is about an assay that was triggered by an adverse drug event. Mathias Brochhausen EV_Case_Report_ADE https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observation-based adverse drug event report An evidence information content entity that is about an assay that realizes an observation design. Mathias Brochhausen EV_Observational https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observational study An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 drug metabolism identification experiment An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has a cell line as a specified input. Mathias Brochhausen EV_EX_Enz_ID_Cyp450_Hum_Recom https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism identification experiment An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has chemical inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Chem https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism identification experiment using chemical inhibitors An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has antibody inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Recom_Antibody https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism identification experiment using antibody inhibitors An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism identification experiment An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has chemical inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome_Chem https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism identification experiment using chemical inhibitors An evidence information content entity that is about an in vitro assay that has a part of a drug or a drug metabolite, which participate in a metabolic process that has CYP 450 as a participant, as a specified input, and that has human tissue specimen as a specified input, and that has antibody inhibitors as a specified input. Mathias Brochhausen EV_EX_Met_Enz_ID_Cyp450_Hum_Microsome_Antibody https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism identification experiment using antibody inhibitors An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit_Cyp450 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 metabolic enzyme inhibition experiment An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input. Mathias Brochhausen EV_CT_DDI https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from drug-drug interaction clinical trial An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input and does not have group randomization as a part. Mathias Brochhausen EV_PK_DDI_NR https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from non-randomized drug-drug interaction clinical trial An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input, and that does not have group randomization as a part, and that realizes a clinical study design that has parallel group design as a part. Mathias Brochhausen EV_PK_DDI_Par_Grps https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from parallel groups drug-drug interaction clinical trial' An evidence information content entity that is about a clinical drug trial that has at least two drugs as its specified input and does have group randomization as a part. Mathias Brochhausen EV_PK_DDI_RCT https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from randomized drug-drug interaction clinical trial An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics. Mathias Brochhausen EV_CT_Pharmacokinetic https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from pharmacokinetic trial An evidence information content entity that is about a clinical drug trial that focusses on pharmacokinetics and that has organisms as participants that participated in genotyping. Mathias Brochhausen EV_CT_PK_Genotype https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from genotyped pharmacokinetic trial An evidence information content entity that is about an assay that was triggered by an occurrent. Mathias Brochhausen EV_Case_Report https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observation-based report An evidence information content entity that is about an assay that realizes an observation design and has a drug product as a specified input, and that focuses on pharmacokinetics in an organism. Mathias Brochhausen EV_PK_Observational https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observational pharmacokinetic study An evidence information content entity that is about an assay that realizes an observation design and has at least two drug products as a specified input, and that focuses on pharmacokinetics in an organism. Mathias Brochhausen EV_PK_DDI_Observational https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from observational drug-drug interaction study An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input, and that has cell lines as a specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit_Cyp450_Hum_Recom https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 recombinant drug metabolism inhibition experiment An evidence information content entity that is about an in vitro assay and that has parts of a drug or drug metabolites, which participate in a negative regulation of a metabolic process that also involves CYP 450, as it's specified input, and that has human tissue specimens as a specified input. Mathias Brochhausen EV_EX_Met_Enz_Inhibit_Cyp450_Hum_Microsome https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from CYP450 human microsome drug metabolism inhibition experiment A data set that is structured and stored on a computer and that is publicly available and contains reports of adverse events. Mathias Brochhausen public adverse event reporting database An evidence information content entity that is about an assay that was triggered by an adverse drug event, and that is part on a publicly accessible database for adverse event reporting. Mathias Brochhausen EV_Case_Report_ADE_Public_Reported https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from a publicly reported observation-based adverse drug event report An evidence information content entity that is about an assay that was triggered by an adverse drug event following the administration of at least two drugs. Mathias Brochhausen EV_Case_Report_DI https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html evidence information from an observation-based case-report of a drug interaction 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. Mathias Brochhausen adverse drug reaction causality evaluation protocol An evidence information content entity that is about an assay that was triggered by an adverse drug event following the administration of at least two drugs, and that is the specified outcome of a adverse drug reaction causality evaluation. Mathias Brochhausen EV_Case_Report_DI_Evaluated https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen Cl 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. Mathias Brochhausen fold An information content entity that is part of a pharmacokinetic parameter ratio and that describes whether the relationship between the numbers of the ratio is a positive or a negative one. Mathias Brochhausen pharmacokinetic parameter ratio directionality 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. Mathias Brochhausen 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. Mathias Brochhausen pharmacokinetic parameter ratio An pharmacokinetic parameter directionality that describes negative relationship between the numbers of the ratio. Mathias Brochhausen pharmacokinetic parameter ratio decrease An pharmacokinetic parameter directionality that describes positive relationship between the numbers of the ratio. Mathias Brochhausen pharmacokinetic parameter ratio increase 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. Mathias Brochhausen 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. Mathias Brochhausen 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. Mathias Brochhausen 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. Mathias Brochhausen 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. Mathias Brochhausen EV_CT_PK_Phenotype https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_P_Glycoprotein https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_P_Glycoprotein_Caco_2 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_P_Glycoprotein_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B1 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B3 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B1_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_ID_OATP1B3_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_P_Glycoprotein https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_P_Glycoprotein_Caco_2 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B1 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B1_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B3_Overexpressed_Cells https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen EV_EX_Trans_Prot_Inhibit_OATP1B3 https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html 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. Mathias Brochhausen Philip E. Empey 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. Mathias Brochhausen Philip E. Empey 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. Mathias Brochhausen Philip E. Empey 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. Mathias Brochhausen Philip E. Empey 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. Mathias Brochhausen ki 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. Mathias Brochhausen probe subtrate role An assay that is the realization of a concretization of a clinical study design. Mathias Brochhausen clinical study A biological process that is the result of a drug-drug interaction. Mathias Brochhausen drug-drug interaction effect A value specification that specifies the relationship between two numbers. Mathias Brochhausen ratio value specification A ratio value specification where the relationship between to numbers is expressed as a fraction of 100. Mathias Brochhausen percentage value specification An identifier that denotes a set of drug identifiers. Mathias Brochhausen 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 John Judkins 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 John Judkins 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 John Judkins sandwich cultured hepatocyte population a cultured cell population derived from cells isolated from human intestinal epithelium John Judkins human intestinal epithelial cell population an immortal human liver-derived cell line cell that is part of the HepaRG cell line John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins % 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins Number of Livers Number of individual liver samples used number of liver donors 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 hydroxylation that has tolbutamide as input and 4-hydroxytolbutamide as output John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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 John Judkins 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. Mathias Brochhausen Eric Chou Richard D. Boyce 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. Mathias Brochhausen Eric Chou Richard D. Boyce 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 Mathias Brochhausen Eric Chou Richard D. Boyce 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. Mathias Brochhausen Eric Chou Richard D. Boyce 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 William Hogan http://purl.obolibrary.org/obo/dron.owl William Hogan 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 http://purl.obolibrary.org/obo/dron.owl William Hogan drug product active ingredient role a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism William R. Hogan http://purl.obolibrary.org/obo/dron.owl active ingredient role of a scattered molecular aggregate a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes William R. Hogan http://purl.obolibrary.org/obo/dron.owl role of scattered molecular aggregate administration of a drug product to an organism a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism William R. Hogan http://purl.obolibrary.org/obo/dron.owl drug administration A primer. 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. PERSON: Melissa Haendel http://en.wikipedia.org/wiki/Nucleic_acid http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). nucleic acid reagent 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. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Phenotype http://purl.obolibrary.org/obo/ero.owl phenotype characterization A riboprobe. A reagent that is a polymer comprised of RNA nucleotides. PERSON: Matthew Brush PERSON: Matthew Brush http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). RNA reagent An RNA reagent consisting of a short, linear RNA polymer, typically with 100 or fewer bases. PERSON: Matthew Brush RNA oligo PERSON: Matthew Brush http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). RNA oligonucleotide An RNA interference reagent used to silence expression of a target gene in cells, through the RNA interference pathway. PERSON: Matthew Brush RNAi oligonucleotide PERSON: Matthew Brush http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). RNA interference oligonucleotide 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. PERSON: Matthew Brush siRNA oligo MHB, http://www.sigmaaldrich.com/life-science/custom-oligos/sirna-oligos.html http://purl.obolibrary.org/obo/ero.owl Placeholder for class to be imported from the Reagent Ontology (ReO). siRNA oligonucleotide Body substance in liquid state contained in the lumen of arterial and venous trees, blood capillary and the cardiac chambers; constitutes the liquid phase of blood. http://purl.obolibrary.org/obo/fma.owl Blood plasma fma FMA:62970 Portion of plasma Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures. Examples: saliva, semen, cerebrospinal fluid, respiratory air, urine, feces, blood, plasma, lymph. http://purl.obolibrary.org/obo/fma.owl Body substance fma FMA:9669 Portion of body substance Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. http://purl.obolibrary.org/obo/go.owl GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. molecular_function Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. http://purl.obolibrary.org/obo/go.owl Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. http://purl.obolibrary.org/obo/go.owl GO:0008372 NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. cellular_component 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. http://purl.obolibrary.org/obo/go.owl GO:0015457 GO:0015460 small molecule transport solute:solute exchange biological_process auxiliary transport protein activity transport accessory protein activity GO:0006810 transport biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. http://purl.obolibrary.org/obo/obi.owl biological_process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. http://purl.obolibrary.org/obo/go.owl Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth biological_process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. http://purl.obolibrary.org/obo/go.owl down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism inhibition of metabolic process biological_process GO:0009892 negative regulation of metabolic process A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/go.owl cellular_component GO:0019814 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex Any process that modulates the activity of a transporter. http://purl.obolibrary.org/obo/go.owl biological_process GO:0032409 regulation of transporter activity Any process that stops or reduces the activity of a transporter. http://purl.obolibrary.org/obo/go.owl down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process GO:0032410 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. http://purl.obolibrary.org/obo/go.owl regulation of localisation biological_process GO:0032879 regulation of localization A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. http://purl.obolibrary.org/obo/go.owl macromolecule complex cellular_component GO:0032991 macromolecular complex An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. http://purl.obolibrary.org/obo/go.owl Wikipedia:Antibody antibody cellular_component GO:0042571 Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available. immunoglobulin complex, circulating A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical. http://purl.obolibrary.org/obo/go.owl Wikipedia:Protein_complex protein-protein complex cellular_component GO:0043234 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein complex The chemical reactions and pathways by which individual cells transform chemical substances. http://purl.obolibrary.org/obo/go.owl cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. http://purl.obolibrary.org/obo/go.owl GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates 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. http://purl.obolibrary.org/obo/go.owl biological_process GO:0051049 regulation of transport 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. http://purl.obolibrary.org/obo/go.owl down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport 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. http://purl.obolibrary.org/obo/go.owl establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process GO:0051179 localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. http://purl.obolibrary.org/obo/go.owl establishment of localisation biological_process GO:0051234 establishment of localization Any process that modulates a measurable attribute of any biological process, quality or function. http://purl.obolibrary.org/obo/go.owl regulation biological_process GO:0065007 biological regulation 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. http://purl.obolibrary.org/obo/go.owl uptake biological_process GO:0098657 import into cell The directed movement of some substance from outside of a cell, across the plasma membrane and into the cytosol. http://purl.obolibrary.org/obo/go.owl biological_process GO:0098739 import across plasma membrane 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. Mathias Brochhausen proper name http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl name Mathias Brochhausen 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. enzyme substrate role a biological interaction that uses the information from a gene to synthesize a functional gene product. YH, ZX http://purl.obolibrary.org/obo/in/ino.owl express, expressed, expresses, expressing, expression, expressions gene expression a gene expression that has increased volume. YH, ZX increased gene expression overexpression http://purl.obolibrary.org/obo/in/ino.owl hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression overexpression Formation of a covalent bond between a substrate and a glucuronosyl group. http://purl.obolibrary.org/obo/mop.owl glucuronosylation MOP:0000156 has_participant: CHEBI:24303 glucuronosylation A process in which at least one of the participants is a molecule. http://purl.obolibrary.org/obo/mop.owl MOP:0000543 TODO: needs work, formal definition, etc. molecular process An oxidation process that involves the removal of adjacent hydrogen atoms, resulting in an increase of bond order. http://purl.obolibrary.org/obo/mop.owl batchelorc 2009-06-05T04:54:48Z MOP:0000590 dehydrogenation Formation of a covalent bond between a substrate and a hydroxy group. http://purl.obolibrary.org/obo/mop.owl MOP:0000673 hydroxylation http://purl.obolibrary.org/obo/mop.owl MOP:0000779 formation of covalent bond http://purl.obolibrary.org/obo/mop.owl MOP:0000780 breaking of covalent bond Breaking of a covalent bond between a substrate and a methyl group. http://purl.obolibrary.org/obo/mop.owl MOP:0001364 has_participant: CHEBI:32875 demethylation Breaking of a covalent bond between a substrate and an ethyl group. http://purl.obolibrary.org/obo/mop.owl de-ethylation MOP:0001385 has_participant: CHEBI:37807 deethylation http://purl.obolibrary.org/obo/doid.owl Dikarya http://purl.obolibrary.org/obo/vo.owl NCBITaxon:1637691 NCBITaxon:662101 NCBITaxon:662104 GC_ID:11 PMID:10319482 E. coli Escherichia/Shigella coli ncbi_taxonomy Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherchia coli Eschericia coli Escherichia coli African clawed frog Bufo laevis Xenopus laevis (Daudin, 1802) Xenopus leavis clawed frog common platanna platanna http://purl.obolibrary.org/obo/ero.owl Xenopus laevis Homo sapiens human human being man http://purl.obolibrary.org/obo/obi.owl Homo sapiens a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. adverse event an adverse event that occurs after a drug administration adverse drug event A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment. http://en.wikipedia.org/wiki/Contraindication contraindication a drug adverse event that is caused by a drug adiministration. Here a causal effect is established between the drug administration and the adverse event. causal adverse drug event serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death. severe adverse event 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.. GROUP: Role branch OBI 9Mar09 after discussion with process branch changed definition to include use of centrifuge; http://purl.obolibrary.org/obo/obi.owl centrifuge pellet role 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. GROUP: Role branch OBI http://purl.obolibrary.org/obo/obi.owl supernatant role processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg http://purl.obolibrary.org/obo/obi.owl processed material evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. http://purl.obolibrary.org/obo/obi.owl evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived http://purl.obolibrary.org/obo/obi.owl study assay any method assay 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 PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived http://purl.obolibrary.org/obo/obi.owl material processing 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 http://en.wikipedia.org/wiki/Microtiter_plate http://purl.obolibrary.org/obo/obi.owl microtiter plate protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) http://purl.obolibrary.org/obo/obi.owl study protocol protocol enzyme (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. person: Melanie Courtot GROUP:OBI http://purl.obolibrary.org/obo/obi.owl enzyme 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. GROUP: Role Branch OBI http://purl.obolibrary.org/obo/obi.owl target of material addition role manufacturer 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. GROUP: Role Branch OBI http://purl.obolibrary.org/obo/obi.owl manufacturer role scattered molecular aggregate the sodium and chloride ions in a glass of salt water A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates PERSON: Alan Ruttenberg Collective Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 http://purl.obolibrary.org/obo/dron.owl scattered molecular aggregate specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop http://purl.obolibrary.org/obo/obi.owl specimen collection process container 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?) PERSON: Bjoern Peters http://purl.obolibrary.org/obo/obi.owl container device 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. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. http://purl.obolibrary.org/obo/obi.owl device dose specification 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 http://purl.obolibrary.org/obo/obi.owl dose specification 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 http://purl.obolibrary.org/obo/obi.owl 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 PERSON: Chris Stoeckert, Jie Zheng MO_366 transfection http://purl.obolibrary.org/obo/obi.owl transfection 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. Bjoern Peters; Randi Vita wikipedia http://purl.obolibrary.org/obo/obi.owl half maximal effective concentration (EC50) 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. Bjoern Peters; Randi Vita wikipedia http://purl.obolibrary.org/obo/obi.owl half maximal inhibitory concentration (IC50) 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. Person: Chris Stoeckert, Jie Zheng MO_808 ex_vivo_design http://purl.obolibrary.org/obo/obi.owl 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. Person: Chris Stoeckert, Jie Zheng MO_347 in_vitro_design http://purl.obolibrary.org/obo/obi.owl in vitro design tissue specimen A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng MO_954 organism_part http://purl.obolibrary.org/obo/obi.owl tissue specimen mass value specification A value specification that specifies the mass of some thing. PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl mass value specification scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl scalar value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters http://purl.obolibrary.org/obo/obi.owl value specification organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism http://purl.obolibrary.org/obo/obi.owl organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch http://purl.obolibrary.org/obo/obi.owl specimen cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush http://purl.obolibrary.org/obo/obi.owl The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population observation design PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. Philippe Rocca-Serra OBI branch derived http://purl.obolibrary.org/obo/obi.owl observation design 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 Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm http://purl.obolibrary.org/obo/obi.owl centrifugation study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. http://purl.obolibrary.org/obo/obi.owl study design clinical study design PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] The definition needs to be extended to other things than simply patients PlanAndPlannedProcess Branch Clinical Research Glossary Version 4.0 CDICS glossary group http://purl.obolibrary.org/obo/obi.owl clinical study design parallel group design PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment Philippe Rocca-Serra independent measure design http://www.holah.karoo.net/experimentaldesigns.htm http://purl.obolibrary.org/obo/obi.owl parallel group design 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 http://purl.obolibrary.org/obo/obi.owl material component separation group assignment Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation group assignment is a process which has an organism as specified input and during which a role is assigned Philippe Rocca-Serra cohort assignment study assignment OBI Plan http://purl.obolibrary.org/obo/obi.owl group assignment 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 OBI branch derived http://purl.obolibrary.org/obo/obi.owl genetic transformation 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 PERSON: Philippe Rocca-Serra GROUP: CEBS GROUP: OBI Biomaterial Branch http://purl.obolibrary.org/obo/obi.owl cell pellet Albert Goldfain creation date: 2009-06-23T11:53:49Z http://purl.obolibrary.org/obo/ogms.owl bodily process A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z http://purl.obolibrary.org/obo/ogms.owl pathological bodily process A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z http://purl.obolibrary.org/obo/dron.owl treatment p-glycoprotein multidrug resistance protein 1 A protein that is a translation product of the human POR gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr.owl P450R POR protein CPR CYPOR PR:000013030 Category=gene. NADPH--cytochrome P450 reductase A solute carrier organic anion transporter family member that is a translation product of the human SLCO1B1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/pr/pr-non-classified.owl LST-1 liver-specific organic anion transporter 1 OATP-2 OATP-C SLCO1B1 solute carrier family 21 member 6 protein LST1 OATP2 OATPC SLC21A6 sodium-independent organic anion-transporting polypeptide 2 PR:000015223 Category=gene. 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. http://purl.obolibrary.org/obo/pr/pr-non-classified.owl PR:000015969 LST-1 liver-specific organic anion transporter 1 LST-2 OATP-8 SLC21A6 SLCO1B3 liver-specific organic anion transporter 2 organic anion transporter 8 organic anion-transporting polypeptide 8 solute carrier family 21 member 10 solute carrier family 21 member 8 protein LST2 OATP8 SLC21A8 Slc21a10 Slco1b2 PR:000015224 Category=gene. 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 Anatomical entity that has mass. http://purl.obolibrary.org/obo/uberon.owl AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. http://purl.obolibrary.org/obo/uberon.owl system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system http://www.ebi.ac.uk/efo/efo.owl An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MAT:0000018 MA:0002431 MESH:A03 MIAA:0000018 NCI_Thesaurus:Digestive_System SNOMEDCT:278859004 TADS:0000170 TAO:0000339 WBbt:0005748 Wikipedia:Digestive_system XAO:0000125 ZFA:0000339 alimentary system alimentary tract gastrointestinal system gut Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. galen:DigestiveSystem uberon UBERON:0001007 digestive system A unit of measurement is a standardized quantity of a physical quality. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000000 unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000186 dimensionless unit A dimensionless ratio unit which denotes numbers as fractions of 100. http://purl.obolibrary.org/obo/uo.owl george gkoutos % unit.ontology UO:0000187 percent A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. http://purl.obolibrary.org/obo/uo.owl george gkoutos unit.ontology UO:0000190 ratio An information content entity that specifies how a dose is quantified in a dose administration. http://purl.obolibrary.org/obo/PDRO/PDRO.owl 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 dose quantification specification A dose quantification specification that quantifies a dose by referring to the quantity of active ingredient administered in a dose administration. http://purl.obolibrary.org/obo/PDRO/PDRO.owl 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. http://purl.obolibrary.org/obo/PDRO/PDRO.owl drug product quantification specification http://purl.org/obo/owl/go_xp_all GO:0005554 molecular_function Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. molecular_function http://purl.org/obo/owl/go_xp_all molecular_function catalytic activity http://purl.org/obo/owl/go_xp_all GO:0008151 GO:0050875 biological_process cellular process http://purl.org/obo/owl/go_xp_all biological_process drug metabolic process http://www.ebi.ac.uk/efo/efo.owl Genotyping NCIt:C45447 An assay in which variation in the genome is analysed ArrayExpress production team James Malone genotyping true group randomization Philippe Rocca-Serra group randomization adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] http://purl.obolibrary.org/obo/obi.owl PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.