|comparative effectiveness; market efficiency more important||CostBenefitAnalysis||maybe; defer to Vipul and Chime||treat as process or as the document resulting from the process?||Cost, Benefit, Analysis||TrishWhetzel||Susie: maybe|
|5; split up if needed|
|merge into study||AnimalStudy||no||Study, HumanStudy||JuliaKozlovsky||A laboratory experiment using animals to study the development and progression of diseases||NCI Dictionary of Cancer Terms: http://www.cancer.gov/Templates/db_alpha.aspx?print=1&cdrid=454774||"Animal Testing" is better defined. In NCI: "The use of animals for testing the safety and efficacy of drugs or treatments." ID = Animal_Testing. Link: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Animal_Testing||Susie: How about AnimalSubject (to mirror HumanSubject)? Subclasses could be tissueSample, RNASample, Species, etc. The animalsubject could then be in an arm of an investigation, and the investigation could relate to a protocol.|
Christi: Maybe use a more generic 'study' entity? or use 'experiment'? Colin: different regulatory authorities are involved.
|Consider changing to generic study with codes indicating the type of study. For example, animal or human.|
|mark up as drug or target as appropriate||Antibody||no||Protein||TrishWhetzel||An antibody is a protein found in the blood and other bodily fluids of vertebrates produced by B cells.||Wikipedia||Susie: small compounds and antibodies are important, however I'm not convinced that we need to differentiate between them.|
Descendant of protein, which is descendant of drug.
|should be descendent of protein; see also in ONTIE|
|use Compound instead||ChemicalSubstance||no||Compound||MichelDumontier||Susie: no. I'd drug, molecule or compound. Chemical excludes large molecules.||"BulkStuff"; 5; needs def or link to other ontology|
|ClinicalGuideline||no||GDC (information artifact, part of a specification)||Dosage|
|consider company, organization as synonyms||Company||no||GDC (institution)||Company; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Company||Institution||ElgarPichler||Any formal business entity for profit, which may be a corporation, a partnership, association or individual proprietorship.http://dictionary.law.com||NCI [NCIt:Company]||Susie: maybe organization|
Christi: organization is good
|maybe Institution instead if needed|
|Effector||no||role played by a molecule||Regulator, Repressor|
|Finding||no||GDC (information artifact)||OBI_0000120||Finding is an assessment of data, observations or evaluations from a clinical study which can be used to form a diagnosis||5; defer to IAO/OBI/SWAN|
|need to be able to get to somewhere||Generic||no||role (status function) played by a material entity||Drug, Compound, ActiveIngredient||A pharmaceutical product equivalent to the brand name drug in dosage, safety, strength, how it is taken, quality, performance, and intended use. The FDA bases evaluations of substitutability, or therapeutic equivalence of a generic drug on scientific evaluation. A generic drug product must contain the identical amounts of the same active ingredient(s) as the brand name product and is expected to have equal effect when substituted for the brand name product.||NCI Thesaurus||in the pharmacists's sense, defer to Elgar's hierarchy|
|Lead||no||role played by a molecule||maybe defer to a cheminformatics ontology|
|3DMolecularStructure||no||GDC (information artifact about a molecule)||3DMolecularStructure||ColinBatchelor||A generically-dependent continuant that is about a molecule and is written in terms of its atoms.||Colin||Need not refer to a molecule that actually exists, nor to a whole molecule.||Colin: important|
Michel: no; replace by Chemical Structure
Christi: Would prefer this to Chemical Structure (and Molecule over Chemical); Susie: no too detailed
|rename to 3dMolecularStructure|
|Molecule||no||material entity||Susie: yes, or drug||look at in context of/merge with Molecule|
|PatientPrognosis||no||GDC (information artifact; a prediction)||Prognosis; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Prognosis||Prognosis||ElgarPichler||The likely outcome or course of a disease; the chance of recovery or recurrence.||NCI [NCIt:Prognosis]||ER: replace by Prognosis?||Elgar: no; replace by Diagnosis|
Michel: no; covered by Prognosis; Susie: use prognosis
|too far downstream for TMO; maybe keep; if so keep as Prognosis|
|Receptor||no||function exercised by a protein molecule||TrishWhetzel||A receptor is a protein located on the cell surface, or in the cytoplasm, that binds to a specific signaling factor, such as a hormone, antigen, or neurotransmitter, causing a conformational and functional change in the receptor molecule. The ligand-bound receptor then alters its interaction with target molecules, which leads to changes in cellular physiology through modification of the activity of one or more signal transduction pathways.||NCIT||Susie: maybe||5; yes if needed|
|Repressor||no||role played by a molecule||Effector, Regulator||MichelDumontier||Susie: no||5; same as regulator, pull in from ChEBI if needed|
|replace by outcome||ResponseBySubjectToDrug||no||process||ImmuneResponse||instead of ImmuneResponse|
|Risk||no||ontologically hard||SubjectRisk||ChristiDenney||The potential future harm that may arise from some present action. It is often combined or confused with the probability of an event which is seen as undesirable.||NCI (NIH)||Susie: maybe||3; subject risk|
|TherapyCostBenefit||no||unclear here whether we're talking about the process or the result||HealthOutcome||TrishWhetzel||A therapy cost benefit analysis is an analysis to compare the costs of different therapies for the same disease compared to the overall benefits of the different therapies.||Suggest to change to CostBenefitAnalysis||Susie: maybe||5; consider HealthOutcome|
|Amount||no||ColinBatchelor||A determinable quality that inheres in a material entity by virtue of the number of grains of that entity.||Colin||Necessary?||Susie: I don't believe we need this.|
Michel: We can refer to OBI/IAO's measurable quantity
|link to Information Ontology; pull definition from there; drop term|
|Competitor||no||http://www.thefreedictionary.com/dict.asp?Word=competitor||ElgarPichler||One that competes with another, as in sports or business; a rival.||TheFreeDictionary||Michel: no; unnecessary; Susie: no|
Joanne: need to consider in terms of the usecase - consider using InstitutionalRelationship
|drop?; revisit use case; redefine Competitor in other terms if necessary|
|Country||no||probably covered by Brand plus Authority. Wouldn't cover different diet, life expectancy, or disease prevalence across different countries|
|Dose||no||ColinBatchelor||same as Dosage (vide supra)||Susie: prefer clinical protocol (see below)||too specific?|
|DrugMetabolizingProtein||no||Metabolism, DrugMetabolism||ColinBatchelor||A protein molecule that exhibits the disposition to metabolize the active ingredient of a drug.||Colin||Doesn't anabolize drugs, as far as I know.|
Michel: DME's can add functional groups (e.g hydroxyl) which make it more soluble and easier to excrete
|Susie: maybe drug metabolism||various types of drug iacts exist; keep; replace by DrugMetabolism|
|DrugNonDrugInteraction||no||DrugInteraction||TrishWhetzel||?||Elgar: no; group under interaction; specify which one|
Michel: see DrugInteraction; Susie: no
|subsumed by DrugInteraction?|
|Excipient||no||InactiveIngredient||MichelDumontier||An ingredient contained in a drug formulation that is not a medicinally active constituent.||required to describe the roles of each component of an approved pharmaceutical product||Susie: no||keep and/or inactive ingredient|
|MarketOpportunity||no||Market Opportunity||MarketOpportunity||JuliaKozlovsky||Newly identified need, want, or demand trend that a firm can exploit because it is not being addressed by the competitors.||BusinessDictionary.com: http://www.businessdictionary.com/definition/market-opportunity.html||Susie: no|
Joanne: double check against use case
|maybe same as market|
|Metabolism||no||DrugMetabolism||ChristiDenney||1. Intermediary Metabolism|
All the reactions in an organism concerned with storing and generating metabolic energy and with the biosynthesis of low-molecular weight compounds, energy-storage compounds, and basic materials needed for important life processes.
2. Energy Metabolism
Any subcellular or molecular event, process, or condition concerned with storing and generating metabolic energy.
|NCI (NIH)||Listed as a 'retired concept' in NCI Thesaurus.||Susie: no, too broad||rename to DrugMetabolism and modify def. and keep an eye on Response|
|PatientDiagnosis||no||OBI_0000075; http://purl.obofoundry.org/obo/OBI_0000075||Diagnosis||ElgarPichler||Diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. [Editor note: The act or process of identifying or determining the nature and cause of a disease or injury through evaluation.]||OBI [obi:Diagnosis]||ER: replace by Diagnosis?||Elgar: no; replace by Diagnosis|
Michel: no; covered by Diagnosis; Susie: no, covered by Diagnosis
|keep as diagnosis|
|PharmaceuticalBrand||no||Brand||ElgarPichler||A set (for marketing purposes) of >=1 products.|
Wikipedia: name or trademark connected with a product or producer
|Elgar: compare also brand product/name and generic product/name||keep as Brand|
|Placebo||no||An inactive substance, treatment, or procedure that is intended to mimic as closely as possible a therapy in a clinical trial.||NCI Thesaurus|
|Population||no||Study_Population||StudyPopulation||JuliaKozlovsky||A target study population with characteristics, including inclusion and exclusion criteria, precisely defined in the study protocol. This is a population to which the study results could be reasonably generalized.||NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Study_Population||do we need this? Can this be a combination of Patient+Phenotype+etc. Meanwhile, replacing "Population" with "Study Population"||Elgar: no; replace by PatientGroup/PatientPopulation; Susie: maybe as it could more easily relate our work to epidemiology ||keep as StudyPopulation|
|StatisticalPower||no||0; covered by Evidence terms|
|TreatmentManagementPlan||no||ClinicalProtocol||ChristiDenney||A document outlining the essential treatment issues which will be addressed. This may include the problem to be addressed, the proposed treatment, the treatment goal, the time frame to meet goals, and an estimate of the costs.||NCI (NIH)||Elgar: no; replace by Treatment; Susie: prefer treatment:|
Joanne: Use Clinical Protocol instead.
|merge into ClinicalProtocol|
|Expert||yes||role played by a human being||. also modify definition||JuliaKozlovsky||A clinically trained and registered medical practitioner involved in the assessment or administration of treatment to a patient or healthy volunteer.||Ontology of Clinical Research (OCRe)Version 0.92||Christi: Could this be covered by a more generic healthcare role? Susie: Do we need to include the roles people play?|
Joanne: I would like to consider this more - in particular if we need, for the purpose of connecting research and practice the three roles, clinician, patient, and researcher
|MolecularStructure||yes||GDC (information artifact)||ColinBatchelor||A generically-dependent continuant that describes atoms in terms of the connections between them.||Colin||Susie: no, too specific|
Michel: suggests chemical structure
|5;have cases with connection but corresponding molecule|
|we should be aware that drugs are increasingly large molecules such as antibodies, which have their own special requirements and safety concerns. maybe have several children of 'drug'||Drug||yes||role (status function)||ActiveIngredient||ColinBatchelor||A status function inhering in a material entity by virtue of it having been approved by a regulatory authority and allowing it to be administered as part of a treatment.|
Elgar: a compound with actual or potential therapeutic use; active pharmaceutical ingredient;
Wikipedia: ...when absorbed into the body of a living organism, alters normal bodily function
|Colin||Bosse: Drug has caused confusion in the LODD work, need clear definition.|
Elgar: is a drug also to include Biologic?
Joanne: keep - but what identifer do we use? generic, commercial trademark name? how do we assure consistency in what's named here as the drug? is there an ID we can use?
|too ambiguous - maybe; definition?: a compound with actual or potential therapeutic use; discuss further; also consider ActiveIngredient;|
|Hypothesis||yes||GDC (information artifact)||Hypothesis is a role played by a proposition describing a reasoned proposal suggesting a possible correlation between multiple phenomena.||OBI_0000074||5; defer to IAO/OBI/SWAN|
|MedicalHistory||yes||GDC (information artifact about a person)||Example: this person has presented six times.||5; keep; distinct from signs and symptoms; maybe too domain-specific|
|MolecularFunction||yes||function exercised by a molecule||ModeOfAction||ColinBatchelor||A function that inheres in a molecule and is realized through the execution or alteration of a biological process.||Colin||Or is this intended to be read quantitatively?||Susie: I'd prefer Mechanism of Action.||rework definition?; consider MOA; may be too broad; different term maybe: e.g., MolecularFunction|
|Subject||ChristiDenney||A person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary.||NCI (NIH)||Susie: maybe, or how about 'HumanSubject' as the person may not be ill.||keep as Subject; if necessary subclassify: animal, human;|
|Prognosis||yes||GDC (information artifact; a prediction)||PatientPrognosis||The likely outcome or course of a disease; the chance of recovery or recurrence.||NCI [NCIt:Prognosis]|
|Safety||yes||ontologically hard||Outcome||Relative freedom from harm. In clinical trials, this refers to an absence of harmful side effects resulting from use of the product and may be assessed by laboratory testing of biological samples, special tests and procedures, psychiatric evaluation, and/or physical examination of subjects.||NCI Thesaurus (originally defined for CDISC)||5---keep on table in order at least to inform other classes such as outcome|
|SubsetOfPopulation||yes||role played within a planned process by a collection of material entities (here people, but maybe macaques, beagles?)||Stratification||population subset||exists NCI term||change to SubsetOfPopulation|
|Study||yes||planned process||AnimalStudy, HumanStudy|
|but bear in mind Chris's beta-lactamase example||ActiveIngredient||yes||role played by a molecule||ColinBatchelor||The molecule in a formulation that is believed to have the pharmacological effect.||Colin||Susie: No, I don't think we need to go into this level of detail. We need a generic name that covers the thing patients take or are given, whether it's a large or small molecule.|
Christi: Would be good to know the role that a particular molecule plays within the drug. (active vs. inactive ingredient)
Michel: A chemical substance bearing pharmacological activity that is part of a drug formulation
|keep in DO|
|AdverseDrugEvent||yes||process participated in by patient||ChristiDenney||Any untoward medical occurrence in a patient or clinical investigation subject administered a pharmaceutical product and which does not necessarily have a causal relationship with this treatment. An adverse event (AE) can therefore be any unintended sign (including an abnormal laboratory finding), symptom,or disease temporally associated with the use of a medicinal (investigational) product, whether or not related to the medicinal (investigational) product.||CDISC glossary||Need to contrast with adverse drug experience and adverse drug reaction from BioOntology|
NOTE: For further information, see the ICH Guideline for Clinical Safety Data Management: Definitions and Standards for Expedited Reporting. "[Modified from ICH E2A]" Synonyms: side effect, adverse experience. See also serious adverse event, serious adverse experience.
Bosse: AdverseEvent could be an observation that occurred un-planned. It has some negative implication and might be related to a drug (i.e. ADR)
Michel: important; Joanne: important
|keep, but rework definition|
|ArmOfClinicalStudy||yes||collection of objects (people)||Joanne Luciano||In a randomized clinical trial, any of the treatment groups. Most randomized trials have two "arms," but some have three "arms," or even more.||http://www.medterms.com/script/main/art.asp?articlekey=8738||For more detail see http://prsinfo.clinicaltrials.gov/definitions.html |
For example: Number of Arms (FDAAA)
Definition: Number of intervention groups (enter 1 for single-arm study). 8. Arms, Groups and Interventions
For interventional studies specify the arms:
Arm Label * (FDAAA) - the short name used to identify the arm.
Arm Type * (FDAAA) - select one
Arm Description (FDAAA) - brief description of the arm. This element may not be necessary if the associated intervention descriptions contain sufficient information to describe the arm.
|keep; but maybe defer to trial ontology|
|Assay||yes||process||OBI_0000070; http://purl.obofoundry.org/obo/OBI_0000070||ElgarPichler||An assay is a process with the objective to create as an output information about a material entity (bearing evaluant role).||OBI [obi:assay]||Susie: maybe||defer to OBI; 10|
|Biologic||yes||material entity; also role played by material entity||OBI_0000267||ChristiDenney||A preparation, such as a drug, a vaccine, or an antitoxin, that is synthesized from living organisms or their products and used as a diagnostic, preventive, or therapeutic agent.||The American Heritage® Stedman's Medical Dictionary||This is obsolete in the OBI.|
DermLex has it under RID13805
|Colin: is this the parent of a drug?|
Christi: I see this as a classification of something higher level than drug. I'm not sure 'therapeutic' is that higher level thing because this also talks about diagnosics?
Michel: no; vague
Susie: no, I think of a biologic being an antibody based drug, so a subclass of drug
|The first definition might be wrong. According to my source (http://www.everythingbio.com/glos/definition.php?word=biomarker does NIH use definition 2. I suggest we do that to. (Bosse) An FDA presentation on Biomarkers: www.cc.nih.gov/researchers/training/.../woodcock_2006-2007.ppt||Biomarker||yes||tricky||ChristiDenney||1. A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker and signature molecule.|
2. A characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.3. A parameter that can be used to identify a toxic effect in an individual organism and can be used in extrapolation between species, or as an indicator signalling an event or condition in a biological system or sample and giving a measure of exposure, effect, or susceptibility. The term 'biomarker' is generally used in scientific publications. In occupational hygiene and health, 'biological monitoring' and 'biological effect monitoring' are used with the meaning 'monitoring biomarkers'.
|1. NCI (NIH)|
2. FDA Guidance for Industry: Pharmacogenomic Data Submissions. 3. IUPAC Gold Book doi:10.1351/goldbook.BT06904.
|Subclass of 'Diagnostic or Prognostic Factor'|
Bosse: Biomarker for me is an observation that can be used to measure response to an intervention, both for safety and efficacy reasons.
|Christi: keep; Susie: keep. I think a biomarker can be used to measure disease progression too, regardless of whether there has been an intervention. There are stratification, toxicity, prognosis, efficacy and screening markers. Joanne: keep.||keep;10|
|BiomedicalMeasure||yes||GDC (information artifact)||michel: have an ontology of various biomedical measures:|
|CellLine||yes||material entity||Tissue||Joanne Luciano||a cell line is a permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space.||http://www.biology-online.org/dictionary/Cell_lines||Susie: maybe||defer to other ontology; 10; keep|
|ClinicalProtocol||yes||GDC (specification for a process)||Joanne Luciano||A Clinical Trial Protocol is a document that describes the objective(s), design, methodology, statistical considerations, and organization of a clinical trial. The protocol contains a study plan on which the clinical trial is based. |
The format and content of clinical trial protocols sponsored by pharmaceutical, biotechnology or medical device companies in the United States, European Union, or Japan has been standardized: they are written to follow the Good clinical practice guidance issued by the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). Regulatory authorities in Canada and Australia also follow the ICH guidance.Clinical trial protocols for other clinical trials do not necessarily follow the standard format.
|http://en.wikipedia.org/wiki/Clinical_protocol||Susie: Keep, this is the treatment regime, it'd include dose, frequency of dose, exercise requirement, dietary restrictions, frequency of checkups, etc.|
|ClinicalTrial||yes||process participated in by patients, physicians and specified by a clinical trial protocol||ClinicalTrial; http://epoch.stanford.edu/ClinicalTrialOntology.owl#ClinicalTrial||ElgarPichler||ClinicalTrial specifies the study id, the title, the protocol and the operational plan of a clinical trial.||Epoch Clinical Trial Ontologies||ClinicalTrial specifies the study id, the title, the protocol and the operational plan of a clinical trial.||Susie: keep|
Michel: Need better def
|need def; 10|
|ComparativeEffectiveness||yes||?||keep and reexamine in the light of outcome|
|Compound||yes||material entity||ChemicalCompound, Molecule||ColinBatchelor||A material entity that is self-connected and has as determinate parts two or more atoms connected by covalent bonds.|
Elgar: one chemical entity
|Colin, based on Colin's FOIS paper and further discussions.||Better: molecule.|
Elgar: could be a mixture of enantiomers
|Michel: suggest Chemical Compound; Molecule has additional restriction of having no charge.|
Susie: I'd like us to use a term that is relevant for both large and small molecules.
Christi: 'Molecule' is what I have typically seen.
Joanne: - needs more discussion - may be simply choose another term.
|keep; work out relationship to / need of Molecule|
|CopyNumberVariation||yes||GDC (sequence)||A variation that increases or decreases the copy number of a given region.||Sequence Ontology|
|Cost||yes||The amount paid, charged, or engaged to be paid, for purchasing goods, services and financial instruments.||NCI Thesaurus||keep to discuss later|
|DiagnosisProcess||yes||process participated in by patient and physician||Diagnosis||JuliaKozlovsky||The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation.||NCI ThesaurusVersion 08.12d: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Diagnosis||Susie: keep|
|as in diagnosis result;|
|DiagnosisResult||yes||GDC (information artifact)||ElgarPichler -- definition and source added by JoanneLuciano||In medicine, diagnosis (plural, diagnoses) is the process of identifying a medical condition or disease by its signs, symptoms, and from the results of various diagnostic procedures. The conclusion reached through this process is called a diagnosis.||en.wikipedia.org/wiki/Diagnosis_(medical)||Bosse: an interpretative process that has as input the clinical picture and as output an assertion that a patient have a disase ...|
Elgar: patient need not necessarily have a disease, right?
|as in diagnosis progress; also different from diagnosis for insurance; ==> 10; rename single diagnoses|
|Disease||yes||disposition in document Bosse mentions||DOID: 4 (Christi)||TrishWhetzel||A disease is a condition or process that impairs physiological processes of the organism.||Bosse: Disease is well defined in the document, Towards an ontological treatment of disease and diagnosis.||Susie: keep - but what about Indication?|
Joanne: keep (xref to Disease Ontology (DO)) -- also wondering if it is restricted to physiological processing - are mental disorders considered diseases? i.e. if the psychological process is impared?
|10; link to specific disease ontology|
|DrugInteraction||yes||process||MichelDumontier||The modification of the action of one drug by the concurrent or prior administration of another substrance.||Michel||Important for explaining adverse events or suboptimal treatments resulting from dietary intake (eg. grapefruit juice) or drug-drug interactions||Susie: maybe |
Joanne: this may be more than value and more complex then one term.
|this process may happen in a patient or out of patient (syringe, IV bag, etc.); keep|
|Efficacy||yes||need examples||ChristiDenney||The ability of a chemical agent or a device to treat a disease.||NCI (NIH)||May also be known as clinical efficacy (per bioontology.org). Colin: this is quantitative, right?||Susie: keep|
Michel: important drug concept
|Environment||yes||really hard---need examples||The totality of surrounding conditions.||NCI Thesaurus||keep (maybe needs to be split up)|
|Evidence||yes||GDC (piece of evidence)||Joanne Luciano||Evidence includes everything that is used to determine or demonstrate the truth of an assertion.||http://en.wikipedia.org/wiki/Evidence&ei=QTOESqmzJIGxlAep54jBBQ&sa=X&oi=define&ct=&cd=1&usg=AFQjCNGxgMjmHMJz7ngtrFy4FH985WoNsw||Joanne: We need to choose which evidence code system to use or state that we will use multiple depending on the term. Two to consider at GO http://www.geneontology.org/GO.evidence.tree.shtml and The Pathway Tools Evidence Ontology http://brg.ai.sri.com/evidence-ontology/|
Michel: consider ontologies of scientific discourse
|10; consider LevelOfEvidence and ItemOfEvidence|
|ExclusionCriterion||yes||GDC (part of a specification)||Joanne Luciano||Exclusion criteria are the standards used to determine whether a person may or may not be allowed to participate in a clinical trial.||en.wikipedia.org/wiki/Exclusion_criteria||keep; but maybe defer to trial ontology|
|Gene||yes||GDC (sequence)||SO:0000704||ChristiDenney||A functional unit of heredity which occupies a specific position (locus) on a particular chromosome, is capable of reproducing itself exactly at each cell division, and directs the formation of a protein or other product.||NCI (NIH)||Inquit SO: "A sequence region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions."||Susie: maybe, prefer target, but still need a way to cover genetic heterogeneity||10|
|Genotype||yes||GDC (sequence)||The genetic constitution of an organism or cell, as distinct from its expressed features or phenotype.||NCI Thesaurus||keep|
|Image||yes||GDC (information artifact)||An image is an information content entity which provides a visual representation of for the result of a measurement.||IAO_0000101||keep; child of item of evidence?|
|InactiveIngredient||yes||role played by a molecule||Excipient||ElgarPichler||NCIt & EP: That which enters into a compound, or is a component part of any combination or mixture; an element and which has no or negligible biological activity; an inactive constituent. [From On-line Medical Dictionary]|
A role played by a molecule in the context of a drug by virtue of its not bearing a pharmacological activity. [Colin]
|further subspecify NCI:Ingredient||Elgar: no; replace by Ingredient with activity specification|
Michel: synonym with Excipient;
|keep (or excipient)|
|InclusionCriterion||yes||GDC (specification)||JoanneLuciano||Inclusion criteria are a set of conditions that must be met in order to participate in a clinical trial.||en.wikipedia.org/wiki/Inclusion_criteria||keep; but maybe defer to trial ontology|
|Intervention||yes||process participated in by at least one patient||Procedure||JuliaKozlovsky||An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects.||NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Procedure||NCI calls it "Intervention or Procedure"|
Bosse: How about Intervention as a subclass of Observation (see comment to Observation)
|Lifestyle||yes||ontologically difficult---probably treat as processes||A manner of living that reflects the person's values and attitudes.||NCI Thesaurus also: wordnetweb.princeton.edu/perl/webwn||Joanne - found that this definition at wordnetweb.princeton.edu/perl/webwn (so am adding this as an additional source)||keep (maybe fits under Environment)|
|Market||yes||markets have a generic dependence on their participants, hence probably a GDC (institution)||MarketOpportunity||TrishWhetzel||Susie: no||keep|
|MechanismOfAction||yes||process participated in by the pharmacologically active material entity and taking place within an organism||The mechanism by which a pharmacologically active substance produces an effect on a living organism or in a biochemical system.||NCI Thesaurus||Susie: yes, we need to know how the drug works in order to be able to segment the patients||keep; is actually distinct from pathway|
|Metabolite||yes||role played by a molecule||Any substance involved in metabolism, either as a product of metabolism or as necessary for metabolism.||NCI Thesaurus||keep; bring in from ChEBI|
|Observation||yes||Hmm. Probably a GDC (piece of evidence) in the sense I understand||TrishWhetzel||An observation is a process of watching the entity of interest for any changes.||Bosse: observation could have sub-classes Event, Finding and Intervention; this could robustly describe observations in clinical trials; is it useful here?||Bosse: important; Susie maybe, seems very broad, relationship to sign, symptom, and/or phenotype?||keep (important bridge)|
|Outcome||yes||ontologically vague||ChristiDenney||The result of an action.||NCI (NIH)||Colin: this seems otiose.|
Christi: Doesn't stand on its own, but some sort of 'patient outcome' information would be useful.
Elgar: no; replace by more specific/precise term as needed; Susie: 'Patient Outcome' is a very common term, so we should consider it.
|keep much more consideration needed---reference HealthOutcome|
|Patent||yes||GDC (information artifact)||birnlex_2364|
|ChristiDenney||A grant made by a government that confers upon the creator of an invention the sole right to make, use, and sell that invention for a set period of time.||The American Heritage® Stedman's Medical Dictionary||Susie: maybe||keep|
|Pathway||yes||ontologically hard||Pathway; htp://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Pathway GRO:Pathway http://www.bootstrep.eu/ontology/GRO#Pathway||ElgarPichler||NCIt: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical, or other reasons. GRO: A series of related biochemical reactions. [http://www.genpromag.com/Glossary.aspx]||NCI [NCIt:Pathway] GRO [GRO:Pathway]||Susie: maybe||keep|
|Payer||yes||complicated, but probably a GDC (institution)||Healthcare_Payer||JuliaKozlovsky||An entity, organization, government, corporation, health plan sponsor, or any other financial agent who pays a healthcare provider for the healthcare service rendered to a patient or reimburses the cost of the healthcare service.||NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Healthcare_Payer||Michel: no; unrelated; Susie: maybe, as a drug won't be used if payors aren't prepared to pay for it.||keep; might necessitate keeping Prognosis|
|PharmaceuticalProduct||yes||role played by a material entity||Formulation||ElgarPichler||a marketed formulation containing >=1 drug(s)||Elgar: a combination product contains >1 drugs||synonym: Formulation; keep|
|Phenotype||yes||quality or collection of qualities (tricky)||Phenotype||JuliaKozlovsky||The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment.||NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Phenotype||Bosse: Phenotype has, in my experience, several different meanings, depending on domain. We need to explain how/why our definition is used in context of others.||Susie: keep|
Joanne: Keep - link to external ontology
|keep, 10; possibly subclassify (GeneExpressionPhenotype); aslo add Genotype?|
|Protein||yes||material entity||Protein||JuliaKozlovsky||A group of complex organic macromolecules composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Proteins are fundamental genetically encoded components of living cells with specific structures and functions dictated by amino acid sequence.||NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Protein||Susie: maybe, ProteinExpression would be better||10; keep|
|RegulatoryAuthority||yes||complicated, but probably a GDC (institution)||JoanneLuciano||regulatory agency: a governmental agency that regulates businesses in the public interest||wordnetweb.princeton.edu/perl/webwn||example: FDA||keep; see comments above|
|SideEffect||yes||process participated in by patient||Side_Effect; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Side_Effect||ElgarPichler||Problems that occur when treatment affects tissues or organs other than the ones meant to be affected by the treatment. Common side effects of cancer treatment are fatigue, pain, nausea, vomiting, decreased blood cell counts, hair loss, and mouth sores.||NCI [NCIt:Side_Effect]||Susie: Is this different to an adverse event?||10|
|Sign||yes||GDC (piece of evidence)||Objective evidence of disease perceptible to the examining physician.||NCI Thesaurus|
|SNP||yes||GDC (sequence)||SO:0000694||ElgarPichler||SNPs are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s), wherein the least frequent allele has an abundance of 1% or greater.||SO [SO:0000694]||Susie: keep; Joanne: keep||keep|
|Symptom||yes||GDC (piece of evidence)||Symptom||JuliaKozlovsky||Subjective evidence of disease perceived by the patient.||NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Symptom||Bosse: subclass of Observation (see comment to Observation)||Susie: keep|
Joanne: Keep - link to external ontology
|keep, also sign|
|Target||yes||role played by a protein. Pathways acting as targets are ontologically HARD||Target; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Target||ElgarPichler||An object fixed as a goal or point of examination; something to point at; a destination. [NCI]|
A status function inhering in a material entity (?or process) by virtue of it having been chosen by a research group and resulting in it participating in a research project. [Colin]
|NCI [NCIt:Target]; Colin||also defined in OCRe||Susie: keep|
|Toxicity||yes||ElgarPichler Deifintion added by Joanne Luciano||The degree to which a substance can harm humans or animals.|
Toxicity can be acute, subchronic, or chronic:
Acute toxicity involves harmful effects in an organism through a single or short-term exposure.
Subchronic toxicity is the ability of a toxic substance to cause effects for more than one year but less than the lifetime of the exposed organism.
Chronic toxicity is the ability of a substance or mixture of substances to cause harmful effects over an extended period, usually upon repeated or continuous exposure, sometimes lasting for the entire life of the exposed organism.
|http://www.medterms.com/script/main/art.asp?articlekey=34093||Susie: keep||keep as complicated; could be qualitative or quantitative|
|Syndrome||yes but be very careful about clarifying what we mean||need to decide: approach for Disease below would imply a collection of dispositions, but is it a collection of phenotypes (= qualities)||Disease||A set of symptoms or conditions that occur together and suggest the presence of a certain disease or an increased chance of developing the disease.||NCI Thesaurus||5; keep but with a close link to disease (possibly synonymous with Disease)|
|Dosage||yes; non-core||treat as GDC (specification for a planned process)?||efo:EFO_0000428||ClinicalGuideline||ChristiDenney||A quantity of an agent (such as substance or energy) administered, taken, or absorbed at one time.||NCI (NIH)||NCI term is 'Dose'.||Colin: this sounds very detailed.|
Christi: This is part of a treatment regimen.
Elgar: no; replace by Dose; Susie: no
Michel: no; replace by Dose; Joanne: no replace by dose.
Joanne: Keep (agree replace by dose)
|keep?; Clinical Guidelines: Frequency, Amount, Delivery System, Dose ...|
|rewrite definition||ActiveIngredientStabilityRegulator||yes; non-core||role played by a molecule||ChristiDenney||Something that controls the rate or manner in which a process progresses or a product is formed.||NCI (NIH)||Colin: surely this is a regulatory authority?|
Christi: possibly. i interpreted this in the biological context.
Elgar: would have thought of a regulatory authority too; but there is a biochemical regulator too; maybe we should specify that more clearly in the class name if we need both terms
|Susie: maybe for RegulatoryAuthority||Chebi uses Effector for biological regulator; 5; use if needed|