release version 2017-11-01
Minimum PDDI (Potential Drug-Drug Interaction) Information Ontology
Maria Herrero-Zazo
Mathias Brochhausen
Richard D. Boyce
Definition
Synonym
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example of usage
has curation status
definition
definition
definition
textual definition
textual definition
editor note
editor note
definition editor
definition editor
definition editor
term editor
term editor
alternative term
alternative term
definition source
definition source
definition source
curator note
imported from
elucidation
MPIO user-centered definition
temporal interpretation
Unique Apollo Label
Source
Source
label
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
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://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
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
http://purl.obolibrary.org/obo/iao.owl
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
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
http://purl.obolibrary.org/obo/obi.owl
has_specified_input
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
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
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
bearer_of
is bearer of
http://purl.obolibrary.org/obo/obib.owl
bearer of
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
http://purl.obolibrary.org/obo/obi.owl
participates in
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
has member
has member is a mereological relation between a collection and an item.
SIO
http://purl.obolibrary.org/obo/obib.owl
has member
http://semanticscience.org/ontology/sio.owl
SIO_000095
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.
Mathias Brochhausen
http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl
A measurement datum that is the output of counting.
count
count
The planned process of finding the number of elements in a finite set of objects.
Mathias Brochhausen
http://en.wikipedia.org/wiki/Counting
http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl
The planned process of finding the number of elements in a finite set of objects.
counting
A biological process that results in a clinically meaningful change to the response of at least one co-administrated drug.
DDI
http://purl.obolibrary.org/obo/dideo.owl
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
An entity that is the result of a drug-drug interaction.
http://purl.obolibrary.org/obo/dideo.owl
obsolete_drug-drug interaction effect
true
A biological process that is the result of a drug-drug interaction.
Mathias Brochhausen
http://purl.obolibrary.org/obo/dideo.owl
drug-drug interaction effect
The process or processes by which one drug B alters the disposition and/or effect of another drug A.
http://purl.obolibrary.org/obo/DINTO.owl
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
http://purl.obolibrary.org/obo/DINTO.owl
clinically relevant DDI effect
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/dideo.owl
biological_process
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
OBI_0000305
group:OBI
http://purl.obolibrary.org/obo/iao.owl
measurement datum
“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
https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZGlrcmFuZGlyfGd4OjUzNzBkOGYzN2NkYWQ3OWY
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.
https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZGlrcmFuZGlyfGd4OjdhOGVkMzY5MzgxNzkw
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.
https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZGlrcmFuZGlyfGd4OjdhOGVkMzY5MzgxNzkw
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.
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
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.
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 information
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.
Bjoern Peters
branch derived
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)
http://purl.obolibrary.org/obo/obi.owl
planned process
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
OBI
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
http://purl.obolibrary.org/obo/obi.owl
participant under investigation role
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
biological replicate
OBI
http://purl.obolibrary.org/obo/obi.owl
biological replicate role
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
reference participant
OBI
http://purl.obolibrary.org/obo/obi.owl
reference subject role
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.
Jennifer Fostel
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.
http://purl.obolibrary.org/obo/obi.owl
cohort role
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
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.
group of organism
organism collection
http://purl.obolibrary.org/obo/obib.owl
collection of organisms
http://purl.obolibrary.org/obo/dideo.owl
Obsolete Class