Minimum PDDI (Potential Drug-Drug Interaction) Information Ontology
Sarah Bost
Richard D. Boyce
Maria Herrero-Zazo
Mathias Brochhausen
Definition
Synonym
BFO OWL specification label
BFO CLIF specification label
editor preferred label
editor preferred term
editor preferred term~editor preferred label
example of usage
has curation status
definition
editor note
definition editor
term editor
alternative term
definition source
curator note
imported from
elucidation
has associated axiom(nl)
has associated axiom(fol)
has axiom label
MPIO user-centered definition
temporal interpretation
Unique Apollo Label
Source
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
preceded by
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
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
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
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
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
has member
has member is a mereological relation between a collection and an item.
is member of is a mereological relation between a item and a collection.
is member of
A measurement datum that is the output of counting.
count
The planned process of finding the number of elements in a finite set of objects.
counting
An identifier that denotes a drug product.
drug identifier
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
A potential drug-drug interaction (PDDI) is an information content entity that specifies the possibility of a drug-drug interaction based on either reasonable extrapolation about drug-drug interaction mechanisms or a data item created by clinical studies, clinical observation or physiological experiment.
potential drug-drug interaction
A biological process that results in a clinically meaningful change to the response of at least one co-administrated drug.
DDI
A clinically meaningful alteration in the exposure and/or response to a drug (object drug) that has occurred as a result of the co-administration of another drug (precipitant drug)Oates JA. Chapter 5. Goodman and Gilman 11th ed (2006):117–36; Hines. Response can refer to either precipitating an adverse event or altering the therapeutic effect of the object drug. Although some DDIs may be used for therapeutic benefit, this paper focuses on those with adverse clinical consequences. (based on the 2013 DDI conference series) / has participant some mechanism.
drug-drug interaction
A planned process of administering more than one drug to the same individual over a specific time interval.
This class currently does not have a restriction. One candidate restriction is a necessary condition: 'has participant at some time' min 2 'drug product'. I was not able to find an OWL reasoner for Protege 5 that supports cardinality restrictions.
An instance of this occurs when at least two or more drugs are taken in a specific time interval and the individual time interval for each drug administration overlaps with the other drug's or drugs' time interval(s). (SG1)
drug co-administration
An entity that is the result of a drug-drug interaction.
obsolete_drug-drug interaction effect
An information content entity that is used to support or refute an assertion.
"Addressing PDDI Evidence Gaps" Standards Development Group
evidence information content entity
A biological process that is the result of a drug-drug interaction.
drug-drug interaction effect
An identifier that denotes a set of drug identifiers.
Term and definition provided by Richard D. Boyce.
drug concept set identifier
The process or processes by which one drug B alters the disposition and/or effect of another drug A.
DDI mechanism
A clinically relevant DDI effect is a DDI Effect that has clinical relevance for the patient clinical status or therapeutic outcome.
significant DDI effect
clinically relevant DDI effect
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
clinical drug role
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.
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
PERSON: Bjoern Peters
directive information entity
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
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
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
“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.)”
“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.)”
An information content entity that is about factors known to affect the pharmacodynamics or pharmacokinetics of a drug.
contextual information/modifying factors
modifying factors information
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.
medical context information
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.
Changes in patient health status from baseline that can be observed or measured by a clinician or reported by a patient.
clinical consequences information
An acute hypertensive reaction may be a clinical consequence of epinephrine given in the presence of beta-blockade.
An acute upper gastrointestinal bleed or other bleeding event may be a clinical consequence of NSAIDs taken in conjunction with warfarin.
Boosting of the antiretroviral effect of darunavir is a clinical consequence of co-administration with cobicistat.
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.
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.
information about clinical consequences suspected to be the result of a drug-drug interaction
"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."
“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”
“Colestyramine and colestipol do not appear to have any clinically important effects on the absorption of aspirin.”
An information content entity that provides support for or refutation of a drug-drug interaction statement.
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.
suspected drug-drug interaction evidence
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 is about the process or processes by which a drug-drug interaction clinical consequence occurs
An assertion about the process or the processes by which a drug-drug interaction clinical consequence occurs.
mechanism of interaction information
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%.
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.
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 harm information
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%.
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.
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.
frequency of exposure information
"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."
"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)
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.
recommended action
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 for potential drug-drug interaction
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.
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).
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.
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.
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.
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.
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)
seriousness information
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.
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).
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.
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.
An information content entity about the intensity of a clinical consequence of a drug-drug interaction.
The intensity of a drug-drug interaction clinical consequence.
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.
severity information
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
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).
A risk classification that suggests specific management criteria for a specific patient context.
operational classification statement
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
participant under investigation role
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.
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.
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.
GROUP: Role Branch
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
biological replicate role
A member of a dose-time group; a patient in a given arm of a trial
a reference participant role realized by equivalent treatment of participants
Person:Jennifer Fostel
OBI
reference subject role
Saline treated rat; one of three identically-treated subjects
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
Jennifer Fostel
cohort role
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
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.
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.
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).
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.
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms