Minimum PDDI (Potential Drug-Drug Interaction) Information Ontology
type: Ontology
version IRI: mpio.owl
imports: ontology-metadata.owl
contributor: Sarah Bost
contributor: Richard D. Boyce
creator: Maria Herrero-Zazo
creator: Mathias Brochhausen
license: http://creativecommons.org/licenses/by/4.0/
version info: 2023-10-17

Definition
type: AnnotationProperty

Synonym
type: AnnotationProperty

BFO OWL specification label
type: AnnotationProperty

BFO CLIF specification label
type: AnnotationProperty

editor preferred label
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage

has curation status

definition
label: textual definition

editor note

definition editor
label: term editor

alternative term

definition source

curator note

imported from
type: AnnotationProperty

elucidation

has associated axiom(nl)

has associated axiom(fol)

has axiom label

MPIO user-centered definition
type: AnnotationProperty

temporal interpretation
type: AnnotationProperty

Unique Apollo Label
type: AnnotationProperty

Source
type: AnnotationProperty

label

has part
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: has_part
imported from: http://purl.obolibrary.org/obo/obi.owl
temporal interpretation: RO_0001901

preceded by
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: preceded by
editor note: 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.
alternative term: is preceded by
alternative term: preceded_by
imported from: Optional.of(http://purl.obolibrary.org/obo/obi.owl)
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

has occurrent part
type: ObjectProperty
sub property of: topObjectProperty
BFO OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
example of usage: [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: [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.
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: [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.
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
imported from: http://purl.obolibrary.org/obo/dideo/release/2017-11-17/dideo.owl
elucidation: [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])
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]

is about
type: ObjectProperty
sub property of: topObjectProperty
example of usage: This document is about information artifacts and their representations
has curation status: IAO_0000125
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: http://purl.obolibrary.org/obo/iao.owl

has_specified_input
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
definition: 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.
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: http://purl.obolibrary.org/obo/obi.owl

is_specified_output_of
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: is_specified_output_of
has curation status: IAO_0000122
definition: 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: http://purl.obolibrary.org/obo/obi.owl

process is result of
type: ObjectProperty
sub property of: immediately preceded by
editor preferred label: process is result of
example of usage: The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
has curation status: IAO_0000123
definition: is a relationship between a process and a preceding occurrent that directly caused the later one to occur
definition editor: IEDB
definition editor: PERSON:Bjoern Peters
imported from: Optional.of(http://purl.obolibrary.org/obo/obi.owl)

bearer of
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer of
alternative term: bearer_of
alternative term: is bearer of
imported from: http://purl.obolibrary.org/obo/obib.owl
temporal interpretation: RO_0001901
label: bearer_of
label: is bearer of

participates in
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: http://purl.obolibrary.org/obo/obi.owl

has participant
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative term: has_participant
imported from: http://purl.obolibrary.org/obo/ro/releases/2018-10-19/ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

immediately preceded by
type: ObjectProperty
sub property of: preceded by
definition editor: David Osumi-Sutherland
alternative term: starts_at_end_of
imported from: Optional.of(http://purl.obolibrary.org/obo/obi.owl)
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

has member
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: has member
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
imported from: http://purl.obolibrary.org/obo/obib.owl
temporal interpretation: RO_0001901

is member of
type: ObjectProperty
sub property of: topObjectProperty
imported from: http://semanticscience.org/ontology/sio.owl
description: is member of is a mereological relation between a item and a collection.

count
type: Class
subclass of: measurement datum
definition: A measurement datum that is the output of counting.
definition editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl
elucidation: A measurement datum that is the output of counting.
Unique Apollo Label: count

counting
type: Class
subclass of: planned process
definition: The planned process of finding the number of elements in a finite set of objects.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Counting
imported from: http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl
elucidation: The planned process of finding the number of elements in a finite set of objects.

drug identifier
type: Class
subclass of: IAO_0000030
definition: An identifier that denotes a drug product.
definition editor: Matthew Diller
definition editor: William R. Hogan
imported from: http://purl.obolibrary.org/obo/apollo_sv/v4.1.1./apollo_sv.owl
elucidation: An identifier that denotes a drug product.
Unique Apollo Label: drugId

material entity
type: Class
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: http://purl.obolibrary.org/obo/bfo/2.0/bfo.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

potential drug-drug interaction
type: Class
subclass of: IAO_0000030
subclass of: Restriction
  on property: has part
  some values from: drug identifier
definition: 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.
definition editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/dideo.owl

drug-drug interaction
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: has occurrent part
  some values from: drug co-administration
definition: A biological process that results in a clinically meaningful change to the response of at least one co-administrated drug.
alternative term: DDI
imported from: http://purl.obolibrary.org/obo/dideo.owl
comment: 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 co-administration
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: bearer of
      some values from: clinical drug role
definition: A planned process of administering more than one drug to the same individual over a specific time interval.
curator note: 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.
imported from: http://purl.obolibrary.org/obo/dideo/release/2017-11-17/dideo.owl
comment: 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)

obsolete_drug-drug interaction effect
type: Class
subclass of: Obsolete Class
definition: An entity that is the result of a drug-drug interaction.
IAO_0000231: IAO_0000226
imported from: http://purl.obolibrary.org/obo/dideo.owl
IAO_0100001: drug-drug interaction effect
deprecated: true

evidence information content entity
type: Class
subclass of: IAO_0000030
definition: An information content entity that is used to support or refute an assertion.
definition editor: Mathias Brochhausen
definition source: "Addressing PDDI Evidence Gaps" Standards Development Group
imported from: http://purl.obolibrary.org/obo/dideo.owl

drug-drug interaction effect
type: Class
equivalent class: Restriction
  on property: process is result of
  some values from: drug-drug interaction
subclass of: biological_process
definition: A biological process that is the result of a drug-drug interaction.
definition editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/dideo.owl

drug concept set identifier
type: Class
subclass of: IAO_0000030
definition: An identifier that denotes a set of drug identifiers.
definition editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/dideo/dev/dideo.owl
comment: Term and definition provided by Richard D. Boyce.

DDI mechanism
type: Class
Definition: The process or processes by which one drug B alters the disposition and/or effect of another drug A.
imported from: http://purl.obolibrary.org/obo/DINTO.owl

clinically relevant DDI effect
type: Class
subclass of: drug-drug interaction effect
Definition: A clinically relevant DDI effect is a DDI Effect that has clinical relevance for the patient clinical status or therapeutic outcome.
Synonym: significant DDI effect
imported from: http://purl.obolibrary.org/obo/DINTO.owl

clinical drug role
type: Class
definition: the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
definition editor: William Hogan
imported from: http://purl.obolibrary.org/obo/dron.owl
creator: William Hogan

biological_process
type: Class
editor preferred label: biological_process
definition: 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.
imported from: http://purl.obolibrary.org/obo/dideo.owl

directive information entity
type: Class
subclass of: IAO_0000030
has curation status: IAO_0000122
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: http://purl.obolibrary.org/obo/iao.owl

plan specification
type: Class
subclass of: directive information entity
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000122
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: http://purl.obolibrary.org/obo/iao.owl
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: IAO_0000027
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: IAO_0000125
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: http://purl.obolibrary.org/obo/iao.owl

medical context information
type: Class
subclass of: IAO_0000030
example of usage: “A number of factors have been associated with an increased risk of hyperkalemia. These include impaired renal function, diabetes mellitus, infrequent serum potassium monitoring, baseline serum potassium level, angiotensin converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs)." (Henz S et al. Nephrol Dial Transplant. 2008;23:3939-45; Eschmann E et al. Eur J Clin Pharmacol. 2014;70:215-23; Indermitte J et al. Drug Safety. 2007;30:71-80.)”
example of usage: “Both corticosteroids and aldosterone antagonists have been shown to substantially increase the risk of UGIB in patients on NSAIDs, with relative risks of 12.8 and 11 respectively compared to a risk of 4.3 with NSAIDs alone (Masclee et al. Gastroenterology. 2014;147:784-92.)”
definition: An information content entity that is about factors known to affect the pharmacodynamics or pharmacokinetics of a drug.
alternative term: contextual information/modifying factors
alternative term: modifying factors information
definition source: https://docs.google.com/viewer
MPIO user-centered definition: Factors such as patient age, patient health conditions, treatment dosage form, or concurrent medications that might alter the risk of a drug-drug interaction clinical consequence or its seriousness.

clinical consequences information
type: Class
subclass of: IAO_0000030
subclass of: Restriction
  on property: is about
  some values from: clinical history
definition: An information content entity that is about changes in the patient health status from baseline that can be observed or measured by a clinician or be reported by the patient.
definition source: https://docs.google.com/viewer
MPIO user-centered definition: Changes in patient health status from baseline that can be observed or measured by a clinician or reported by a patient.

information about clinical consequences suspected to be the result of a drug-drug interaction
type: Class
subclass of: clinical consequences information
subclass of: Restriction
  on property: is about
  some values from: drug-drug interaction effect
subclass of: Restriction
  on property: is about
  some values from: clinically relevant DDI effect
example of usage: An acute hypertensive reaction may be a clinical consequence of epinephrine given in the presence of beta-blockade.
example of usage: An acute upper gastrointestinal bleed or other bleeding event may be a clinical consequence of NSAIDs taken in conjunction with warfarin.
example of usage: Boosting of the antiretroviral effect of darunavir is a clinical consequence of co-administration with cobicistat.
definition: An information content entity that is about changes in patient health status from baseline that can be observed or measured by a clinician or reported by a patient and that may be the result of co-administration of two or more drugs that may interact.
definition source: https://docs.google.com/viewer
MPIO user-centered definition: Changes in patient health status from baseline that can be observed or measured by a clinician or reported by a patient and that may be the result of co-administration of two or more drugs that may interact.

suspected drug-drug interaction evidence
type: Class
subclass of: IAO_0000030
example of usage: "Both corticosteroids and aldosterone antagonists have been shown to substantially increase the risk of UGIB in patients on NSAIDs, with relative risks of 12.8 and 11 respectively compared to a risk of 4.3 with NSAIDs alone."
example of usage: “A crossover study in 36 healthy subjects found that aspirin 325 mg daily for two doses had no effect on the pharmacokinetics of a single 80-mg dose of tapentadol”
example of usage: “Colestyramine and colestipol do not appear to have any clinically important effects on the absorption of aspirin.”
definition: An information content entity that provides support for or refutation of a drug-drug interaction statement.
MPIO user-centered definition: The support for or refutation of a drug-drug interaction in humans; it may be data resulting from clinical studies, clinical observation or physiological experiments, or it may be an extrapolation based on drug-drug interaction mechanisms.

mechanism of interaction information
type: Class
subclass of: IAO_0000030
subclass of: Restriction
  on property: is about
  some values from: DDI mechanism
example of usage: 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.
example of usage: 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.
definition: An information content entity that is about the process or processes by which a drug-drug interaction clinical consequence occurs
MPIO user-centered definition: An assertion about the process or the processes by which a drug-drug interaction clinical consequence occurs.

frequency of harm information
type: Class
subclass of: IAO_0000030
subclass of: Class
  intersection of: IAO_0000030
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: Class
example of usage: Among 2,427 patients co-prescribed either clarithromycin or erythromycin and a statin metabolized by CYP3A4, 47 had a clinical consequence of hospitalization for acute kidney injury, for a frequency of harm of 1.9%.
definition: An information content entity that mentions both the number of individuals within a cohort that are experience a clinically relevant DDI effect over a specified time period and the total number of individuals in the cohort.
MPIO user-centered definition: The number of individuals within a cohort that experience a drug-drug interaction clinical consequence divided by the total number of individuals co-exposed to the drugs that are involved in the interaction.

frequency of exposure information
type: Class
subclass of: IAO_0000030
subclass of: Class
  intersection of: IAO_0000030
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: Class
example of usage: Among 2712 patients age 65 or older recruited at hospital admission and exposed to at least one potential drug drug interaction, 1642 patients were exposed to at least one potentially moderate drug drug interaction, for a frequency of exposure of 60.5%.
definition: An information content entity that mentions both the number of individuals within a cohort that are exposed to a drug-drug interaction over a specified time period and the total number of individuals in the cohort.
MPIO user-centered definition: The number of individuals within a cohort that are exposed to a drug-drug interaction over a specified time period divided by the total number of individuals in the cohort.

recommended action for potential drug-drug interaction
type: Class
subclass of: plan specification
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: potential drug-drug interaction
  intersection of: Restriction
    on property: is about
    some values from: evidence information content entity
example of usage: "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."
example of usage: "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)
example of usage: 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)
definition: An information content entity that describes an evidence-based strategy that should be adopted to mitigate the potential clinical consequences of a drug-drug interaction.
alternative term: recommended action
MPIO user-centered definition: 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.

seriousness information
type: Class
subclass of: IAO_0000030
example of usage: Atorvastatin is subject to drug-drug interactions with cytochrome P450 3A4 (CYP3A4) inhibitors. Increased exposure due to CYP3A4 inhibition may lead to serious adverse events (AEs), including rhabdomyolysis Khalilieh, Sauzanne, et al. "Results of a doravirine-atorvastatin drug-drug interaction study." Antimicrobial Agents and Chemotherapy (2016): AAC-01364.
example of usage: Drug-drug interactions with insulin secretagogues are associated with increased risk of serious hypoglycemia in patients with type 2 diabetes Han, Xu, et al. "Biomedical Informatics Approaches to Identifying Drug-Drug Interactions: Application to Insulin Secretagogues." Epidemiology (2017).
example of usage: Nevertheless, long-term combination therapy with immunomodulators and anti-TNFα agents may be associated with increased risks of serious infections and malignancies. Xu, Zhenhua, Hugh M. Davis, and Honghui Zhou. "Clinical impact of concomitant immunomodulators on biologic therapy: pharmacokinetics, immunogenicity, efficacy and safety." The Journal of Clinical Pharmacology 55.S3 (2015): S60-S74.
example of usage: Twenty-four healthy volunteers (11 males) were enrolled. All but 1 subject completed the trial, and no serious adverse events were reported Blonk, Maren, et al. "Pharmacokinetic Drug–Drug Interaction Study Between Raltegravir and Atorvastatin 20 mg in Healthy Volunteers." JAIDS Journal of Acquired Immune Deficiency Syndromes 69.1 (2015): 44-51.
definition: An information content entity that reports the degree to which a clinical consequence of a drug-drug interaction results in harm determining the type and speed of clinician intervention needed.
MPIO user-centered definition: The degree to which a drug-drug interaction clinical consequence may result in harm and that will determine the type and speed of clinician intervention.
comment: An event is serious when the patient outcome is: Death, Life-threatening Hospitalization (initial or prolonged), disability or permanent damage, congenital anomaly/birth Defect, required intervention to prevent permanent impairment or damage, in involved other important medical events. Source: U.S. Food and Drug Administration. “What is a Serious Adverse Event?” https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fda.gov_Safety_MedWatch_HowToReport_ucm053087.htm&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=_AhKSLG63uT9j7OK4dL0o2DAco1lYASNsYomMJX92ng&m=akNLTN3AxpBiAQmCa5kBvV98eEf8Pl2M-D5MBaU5ANI&s=i_7V5GfnXHZV_wJ4fPZCRVM66e0ZhKlG86F0WWSbxSY&e= (accessed August 19, 2016)

severity information
type: Class
subclass of: Obsolete Class
example of usage: All the treatment-emergent adverse events were mild. Mirabegron 50 mg was considered to be safe and well tolerated when coadministered with tolterodine 4 mg in healthy postmenopausal female volunteers. Nomura, Yuki, et al. "Pharmacokinetic drug interaction study between overactive bladder drugs mirabegron and tolterodine in Japanese healthy postmenopausal females." Drug Metabolism and Pharmacokinetics 31.6 (2016): 411-416.
example of usage: By a cumulative dose of 1500 mg paclitaxel, 35% of the patients had developed severe neuropathy. The overall hazard ratio between clopidogrel use and severe paclitaxel neuropathy was 1.7 (95% CI, 0.9-3.0). Agergaard, K., et al. "Clopidogrel paclitaxel drug‐drug interaction: A pharmacoepidemiologic study." Clinical Pharmacology & Therapeutics (2017).
example of usage: Combination lithium, a mood stabilizer, and risperidone, an atypical antipsychotic drug, is widely used for treatment of psychotic disorders. Rare reports concern severe adverse drug reaction in multiple organic systems with their combined use. We report two episodes of neurotoxicity and nephrotoxicity in a patient following the combined use of lithium and risperidone. Hsu, Chih-Wei, et al. "Neurotoxicity and nephrotoxicity caused by combined use of lithium and risperidone: a case report and literature review." BMC Pharmacology and Toxicology 17.1 (2016): 59.
example of usage: In 2015, European and U.S. health agencies issued warning letters in response to 9 reported clinical cases of severe bradycardia/bradyarrhythmia in hepatitis C virus (HCV)-infected patients treated with sofosbuvir (SOF) in combination with other direct acting antivirals (DAAs) and the antiarrhythmic drug, amiodarone (AMIO) Regan, Christopher P., et al. "Assessment of the clinical cardiac drug‐drug interaction associated with the combination of hepatitis C virus nucleotide inhibitors and amiodarone in guinea pigs and rhesus monkeys." Hepatology 64.5 (2016): 1430-1441.
definition: An information content entity about the intensity of a clinical consequence of a drug-drug interaction.
IAO_0000231: IAO_0000103
MPIO user-centered definition: The intensity of a drug-drug interaction clinical consequence.
comment: Severity is a term that is too similar to seriousness possibly causing confusion when communicating with clinicians. Moreover, seriousness (like the related term criticality) describes a POTENTIAL impact, whereas severity characterizes a reaction that has been realized in an individual. Since MPIO focuses on potential drug-drug interactions, it cannot include an attribute (severity) that is describing a realized reaction because you are then no longer in the realm of the potential. Finally, the W3C community workgroup that worked on the minimum information model for potential drug-drug interactions greatly preferred the use of an operational classification of risk to a severity rating. Hence, it was obsoleted as a failed exploratory term for the MPIO domain.
deprecated: true

operational classification statement
type: Class
subclass of: IAO_0000030
example of usage: Risk assessment based upon clinical management of drug interactions rather than clinical significance alone. Example using ORCA (see below for more about ORCA): Warfarin - NSAIDs The NSAIDs is topical diclofenac: Recommended Action: No special precautions The NSAID is NOT topical diclofenac but the patient is concomitantly taking a proton pump inhibitor or misoprostol: Recommended Action: Assess risk and take action if necessary The NSAID is NOT topical diclofenac, the patient is NOT concomitantly taking a proton pump inhibitor or misoprostol, and the patient has one or more of the following risk factors: History of upper gastrointestinal bleeding (UGIB) or peptic ulcer or age > 65 years old Recommended Action: Use only if benefit outweighs risk Concomitantly taking systemic corticosteroids, aldosterone antagonists, or high dose or multiple NSAID Recommended Action: Use only if benefit outweighs risk Example Operational Classification Criteria: Avoid Combination (Risk of combination outweighs benefit) Usually Avoid Combination (Use only under special circumstances) - Interactions for which there are clearly preferable alternatives for one or both drugs. - Interactions to avoid by using an alternative drug or other therapy unless the benefit is judged to outweigh the increased risk. Minimize Risk (Assess risk and take one or more of the following actions if needed) - Consider alternatives: Alternatives may be available that are less likely to interact. - Circumvent: Take action to minimize the interaction (without avoiding combination). Monitor: Early detection can minimize the risk of an adverse
definition: An information content entity that is about some risk management (http://purl.obolibrary.org/obo/ERO_0000715) that has as a specified input an instance of a potential drug-drug interaction (http://purl.obolibrary.org/obo/DIDEO_00000000).
definition editor: Mathias Brochhausen
MPIO user-centered definition: A risk classification that suggests specific management criteria for a specific patient context.

planned process
type: Class
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: http://purl.obolibrary.org/obo/obi.owl

participant under investigation role
type: Class
editor preferred label: participant under investigation role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: IAO_0000122
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: http://purl.obolibrary.org/obo/obi.owl

biological replicate role
type: Class
subclass of: reference subject role
editor preferred label: biological replicate role
example of usage: A member of a dose-time group; a patient in a given arm of a trial
has curation status: IAO_0000120
definition: a reference participant role realized by equivalent treatment of participants
definition editor: Person:Jennifer Fostel
alternative term: biological replicate
definition source: OBI
imported from: http://purl.obolibrary.org/obo/obi.owl

reference subject role
type: Class
subclass of: participant under investigation role
editor preferred label: reference subject role
example of usage: Saline treated rat; one of three identically-treated subjects
has curation status: IAO_0000120
definition: a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
definition editor: Jennifer Fostel
alternative term: reference participant
definition source: OBI
imported from: http://purl.obolibrary.org/obo/obi.owl

cohort role
type: Class
subclass of: biological replicate role
editor preferred label: cohort role
example of usage: In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
has curation status: IAO_0000123
definition: a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
definition editor: Jennifer Fostel
definition source: WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
definition source: WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
definition source: WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
imported from: http://purl.obolibrary.org/obo/obi.owl

organism
type: Class
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: IAO_0000122
definition: 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.
editor note: 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')
editor note: 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.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: http://purl.obolibrary.org/obo/obi.owl

clinical finding
type: Class
subclass of: IAO_0000027
definition: A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:02Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

clinical history
type: Class
subclass of: clinical finding
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:59Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

collection of organisms
type: Class
example of usage: Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative term: group of organism
alternative term: organism collection
imported from: http://purl.obolibrary.org/obo/obib.owl

Obsolete Class
type: Class
imported from: http://purl.obolibrary.org/obo/dideo.owl