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comment_review_2classkeep_statusclass_typeexternal_reference_IDsame_as/compare_tocurator_originaldefinitiondefinition_sourcecomment_originalcomment_keepcomment_review_1

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comparative effectiveness; market efficiency more importantCostBenefitAnalysismaybe; defer to Vipul and Chimetreat as process or as the document resulting from the process?Cost, Benefit, AnalysisTrishWhetzelSusie: maybe
Michel: no
5; split up if needed

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merge into studyAnimalStudynoStudy, HumanStudyJuliaKozlovskyA laboratory experiment using animals to study the development and progression of diseasesNCI 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_TestingSusie: 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.

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mark up as drug or target as appropriateAntibodynoProteinTrishWhetzelAn antibody is a protein found in the blood and other bodily fluids of vertebrates produced by B cells.WikipediaSusie: 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

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use Compound insteadChemicalSubstancenoCompoundMichelDumontierSusie: no. I'd drug, molecule or compound. Chemical excludes large molecules."BulkStuff"; 5; needs def or link to other ontology

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ClinicalGuidelinenoGDC (information artifact, part of a specification)Dosage

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consider company, organization as synonymsCompanynoGDC (institution)Company; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#CompanyInstitutionElgarPichlerAny formal business entity for profit, which may be a corporation, a partnership, association or individual proprietorship.http://dictionary.law.comNCI [NCIt:Company]Susie: maybe organization
Christi: organization is good
maybe Institution instead if needed

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Effectornorole played by a moleculeRegulator, Repressor

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FindingnoGDC (information artifact)OBI_0000120Finding is an assessment of data, observations or evaluations from a clinical study which can be used to form a diagnosis5; defer to IAO/OBI/SWAN

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need to be able to get to somewhereGenericnorole (status function) played by a material entityDrug, Compound, ActiveIngredientA 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 Thesaurusin the pharmacists's sense, defer to Elgar's hierarchy

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HealthOutcomenoontologically hardTherapyCostBenefit

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Leadnorole played by a moleculemaybe defer to a cheminformatics ontology

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3DMolecularStructurenoGDC (information artifact about a molecule)3DMolecularStructureColinBatchelorA generically-dependent continuant that is about a molecule and is written in terms of its atoms.ColinNeed 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

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Moleculenomaterial entitySusie: yes, or druglook at in context of/merge with Molecule

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PatientPrognosisnoGDC (information artifact; a prediction)Prognosis; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#PrognosisPrognosisElgarPichlerThe 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
Joanne: agree.
too far downstream for TMO; maybe keep; if so keep as Prognosis

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Receptornofunction exercised by a protein moleculeTrishWhetzelA 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.NCITSusie: maybe5; yes if needed

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Repressornorole played by a moleculeEffector, RegulatorMichelDumontierSusie: no5; same as regulator, pull in from ChEBI if needed

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replace by outcomeResponseBySubjectToDrugnoprocessImmuneResponseinstead of ImmuneResponse

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Risknoontologically hardSubjectRiskChristiDenneyThe 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: maybe3; subject risk

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TherapyCostBenefitnounclear here whether we're talking about the process or the resultHealthOutcomeTrishWhetzelA 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 CostBenefitAnalysisSusie: maybe5; consider HealthOutcome

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AmountnoColinBatchelorA determinable quality that inheres in a material entity by virtue of the number of grains of that entity.ColinNecessary?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

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Competitornohttp://www.thefreedictionary.com/dict.asp?Word=competitorElgarPichlerOne that competes with another, as in sports or business; a rival.TheFreeDictionaryMichel: 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

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Countrynoprobably covered by Brand plus Authority. Wouldn't cover different diet, life expectancy, or disease prevalence across different countries

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DosenoColinBatchelorsame as Dosage (vide supra)Susie: prefer clinical protocol (see below)too specific?

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DrugMetabolizingProteinnoMetabolism, DrugMetabolismColinBatchelorA protein molecule that exhibits the disposition to metabolize the active ingredient of a drug.ColinDoesn'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 metabolismvarious types of drug iacts exist; keep; replace by DrugMetabolism

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DrugNonDrugInteractionnoDrugInteractionTrishWhetzel?Elgar: no; group under interaction; specify which one
Michel: see DrugInteraction; Susie: no
subsumed by DrugInteraction?

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ExcipientnoInactiveIngredientMichelDumontierAn 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 productSusie: nokeep and/or inactive ingredient

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MarketOpportunitynoMarket OpportunityMarketOpportunityJuliaKozlovskyNewly 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.htmlSusie: no
Joanne: double check against use case
maybe same as market

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MedicalProblemno

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MetabolismnoDrugMetabolismChristiDenney1. 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 broadrename to DrugMetabolism and modify def. and keep an eye on Response

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PatientDiagnosisnoOBI_0000075; http://purl.obofoundry.org/obo/OBI_0000075DiagnosisElgarPichlerDiagnosis 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
Joanne: agree
keep as diagnosis

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PharmaceuticalBrandnoBrandElgarPichlerA 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/namekeep as Brand

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PlacebonoAn inactive substance, treatment, or procedure that is intended to mimic as closely as possible a therapy in a clinical trial.NCI Thesaurus

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PopulationnoStudy_PopulationStudyPopulationJuliaKozlovskyA 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_Populationdo 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

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SampleRestrictionnonot clear

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StatisticalPowerno0; covered by Evidence terms

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Timeno

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TreatmentManagementPlannoClinicalProtocolChristiDenneyA 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

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Expertyesrole played by a human being. also modify definitionJuliaKozlovskyA 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 0.92Christi: 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
5

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MolecularStructureyesGDC (information artifact)ColinBatchelorA generically-dependent continuant that describes atoms in terms of the connections between them.ColinSusie: no, too specific
Michel: suggests chemical structure
5;have cases with connection but corresponding molecule

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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'Drugyesrole (status function)ActiveIngredientColinBatchelorA 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
ColinBosse: Drug has caused confusion in the LODD work, need clear definition.
Elgar: is a drug also to include Biologic?
Susie: keep
Christi: keep
Bosse: important
Elgar: keep
Michel: yes
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;

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HypothesisyesGDC (information artifact)Hypothesis is a role played by a proposition describing a reasoned proposal suggesting a possible correlation between multiple phenomena.OBI_00000745; defer to IAO/OBI/SWAN

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InstitutionyesGDC (institution)Company

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MedicalHistoryyesGDC (information artifact about a person)Example: this person has presented six times.5; keep; distinct from signs and symptoms; maybe too domain-specific

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MolecularFunctionyesfunction exercised by a moleculeModeOfActionColinBatchelorA function that inheres in a molecule and is realized through the execution or alteration of a biological process.ColinOr 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

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Patientyescpr:patient
SOPHARM_51000
OBI_144
acgt:Patient
SubjectChristiDenneyA 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;

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Subjectyes

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PrognosisyesGDC (information artifact; a prediction)PatientPrognosisThe likely outcome or course of a disease; the chance of recovery or recurrence.NCI [NCIt:Prognosis]

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Safetyyesontologically hardOutcomeRelative 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

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SubsetOfPopulationyesrole played within a planned process by a collection of material entities (here people, but maybe macaques, beagles?)Stratificationpopulation subsetexists NCI termchange to SubsetOfPopulation

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Studyyesplanned processAnimalStudy, HumanStudy

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but bear in mind Chris's beta-lactamase exampleActiveIngredientyesrole played by a moleculeColinBatchelorThe molecule in a formulation that is believed to have the pharmacological effect.ColinSusie: 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

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AdverseDrugEventyesprocess participated in by patientChristiDenneyAny 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 glossaryNeed 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)
Colin: important
Christi: agreed;
Susie: important;
Bosse: important;
Michel: important; Joanne: important
keep, but rework definition

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ArmOfClinicalStudyyescollection of objects (people)Joanne LucianoIn 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=8738For 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.
Examples:

Metformin
Lifestyle counseling
Sugar pill
Arm Type * (FDAAA) - select one

Experimental
Active Comparator
Placebo Comparator
Sham Comparator
No intervention
Other
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

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AssayyesprocessOBI_0000070; http://purl.obofoundry.org/obo/OBI_0000070ElgarPichlerAn assay is a process with the objective to create as an output information about a material entity (bearing evaluant role).OBI [obi:assay]Susie: maybedefer to OBI; 10

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Biologicyesmaterial entity; also role played by material entityOBI_0000267ChristiDenneyA 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 DictionaryThis 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
keep: 10

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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 BiomarkeryestrickyChristiDenney1. 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

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BiomedicalMeasureyesGDC (information artifact)michel: have an ontology of various biomedical measures:
http://ontology.dumontierlab.com/biomedical-measure-primitive
keep

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CellLineyesmaterial entityTissueJoanne 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_linesSusie: maybedefer to other ontology; 10; keep

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ClinicalProtocolyesGDC (specification for a process)Joanne LucianoA 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_protocolSusie: Keep, this is the treatment regime, it'd include dose, frequency of dose, exercise requirement, dietary restrictions, frequency of checkups, etc.

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ClinicalTrialyesprocess participated in by patients, physicians and specified by a clinical trial protocolClinicalTrial; http://epoch.stanford.edu/ClinicalTrialOntology.owl#ClinicalTrialElgarPichlerClinicalTrial specifies the study id, the title, the protocol and the operational plan of a clinical trial.Epoch Clinical Trial OntologiesClinicalTrial specifies the study id, the title, the protocol and the operational plan of a clinical trial.Susie: keep
Christi: important
Michel: Need better def
Joanne: keep.
need def; 10

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ComparativeEffectivenessyes?keep and reexamine in the light of outcome

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Compoundyesmaterial entityChemicalCompound, MoleculeColinBatchelorA 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

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CopyNumberVariationyesGDC (sequence)A variation that increases or decreases the copy number of a given region.Sequence Ontology

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CostyesThe amount paid, charged, or engaged to be paid, for purchasing goods, services and financial instruments.NCI Thesauruskeep to discuss later

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DiagnosisProcessyesprocess participated in by patient and physicianDiagnosisJuliaKozlovskyThe 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#DiagnosisSusie: keep
Christi: keep
as in diagnosis result;

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DiagnosisResultyesGDC (information artifact)ElgarPichler -- definition and source added by JoanneLucianoIn 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

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Diseaseyesdisposition in document Bosse mentionsDOID: 4 (Christi)TrishWhetzelA 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?
Christi: important
Bosse: important
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

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DrugInteractionyesprocessMichelDumontierThe modification of the action of one drug by the concurrent or prior administration of another substrance.MichelImportant for explaining adverse events or suboptimal treatments resulting from dietary intake (eg. grapefruit juice) or drug-drug interactionsSusie: 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

.

Efficacyyesneed examplesChristiDenneyThe 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
important; 10

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Environmentyesreally hard---need examplesThe totality of surrounding conditions.NCI Thesauruskeep (maybe needs to be split up)

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EvidenceyesGDC (piece of evidence)Joanne LucianoEvidence 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=AFQjCNGxgMjmHMJz7ngtrFy4FH985WoNswJoanne: 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

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ExclusionCriterionyesGDC (part of a specification)Joanne LucianoExclusion 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_criteriakeep; but maybe defer to trial ontology

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GeneyesGDC (sequence)SO:0000704
ChristiDenneyA 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 heterogeneity10

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GenotypeyesGDC (sequence)The genetic constitution of an organism or cell, as distinct from its expressed features or phenotype.NCI Thesauruskeep

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ImageyesGDC (information artifact)An image is an information content entity which provides a visual representation of for the result of a measurement.IAO_0000101keep; child of item of evidence?

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InactiveIngredientyesrole played by a moleculeExcipientElgarPichlerNCIt & 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:IngredientElgar: no; replace by Ingredient with activity specification
Michel: synonym with Excipient;
Susie: no.
keep (or excipient)

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InclusionCriterionyesGDC (specification)JoanneLucianoInclusion criteria are a set of conditions that must be met in order to participate in a clinical trial.en.wikipedia.org/wiki/Inclusion_criteriakeep; but maybe defer to trial ontology

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Interventionyesprocess participated in by at least one patientProcedureJuliaKozlovskyAn 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#ProcedureNCI calls it "Intervention or Procedure"
Bosse: How about Intervention as a subclass of Observation (see comment to Observation)
Susie: maybekeep

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Lifestyleyesontologically difficult---probably treat as processesA 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)

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Marketyesmarkets have a generic dependence on their participants, hence probably a GDC (institution)MarketOpportunityTrishWhetzelSusie: nokeep

.

MechanismOfActionyesprocess participated in by the pharmacologically active material entity and taking place within an organismThe mechanism by which a pharmacologically active substance produces an effect on a living organism or in a biochemical system.NCI ThesaurusSusie: yes, we need to know how the drug works in order to be able to segment the patientskeep; is actually distinct from pathway

.

Metaboliteyesrole played by a moleculeAny substance involved in metabolism, either as a product of metabolism or as necessary for metabolism.NCI Thesauruskeep; bring in from ChEBI

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ObservationyesHmm. Probably a GDC (piece of evidence) in the sense I understandTrishWhetzelAn 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)

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Outcomeyesontologically vagueChristiDenneyThe 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

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PatentyesGDC (information artifact)birnlex_2364
FBcv:0000213
RID5895
ChristiDenneyA 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 DictionarySusie: maybekeep

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Pathwayyesontologically hardPathway; htp://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Pathway GRO:Pathway http://www.bootstrep.eu/ontology/GRO#PathwayElgarPichlerNCIt: 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: maybekeep

.

Payeryescomplicated, but probably a GDC (institution)Healthcare_PayerJuliaKozlovskyAn 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_PayerMichel: 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

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PharmaceuticalProductyesrole played by a material entityFormulationElgarPichlera marketed formulation containing >=1 drug(s)Elgar: a combination product contains >1 drugssynonym: Formulation; keep

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Phenotypeyesquality or collection of qualities (tricky)PhenotypeJuliaKozlovskyThe 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#PhenotypeBosse: 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?

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Proteinyesmaterial entityProteinJuliaKozlovskyA 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#ProteinSusie: maybe, ProteinExpression would be better10; keep

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RegulatoryAuthorityyescomplicated, but probably a GDC (institution)JoanneLucianoregulatory agency: a governmental agency that regulates businesses in the public interest wordnetweb.princeton.edu/perl/webwnexample: FDAkeep; see comments above

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SideEffectyesprocess participated in by patientSide_Effect; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Side_EffectElgarPichlerProblems 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

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SignyesGDC (piece of evidence)Objective evidence of disease perceptible to the examining physician.NCI Thesaurus

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SNPyesGDC (sequence)SO:0000694ElgarPichlerSNPs 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: keepkeep

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SymptomyesGDC (piece of evidence)SymptomJuliaKozlovskySubjective evidence of disease perceived by the patient.NCI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#SymptomBosse: subclass of Observation (see comment to Observation)Susie: keep
Christi: keep
Joanne: Keep - link to external ontology
keep, also sign

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Targetyesrole played by a protein. Pathways acting as targets are ontologically HARDTarget; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#TargetElgarPichlerAn 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]; Colinalso defined in OCReSusie: keep
Joanne: Keep
10

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ToxicityyesElgarPichler Deifintion added by Joanne LucianoThe 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=34093Susie: keepkeep as complicated; could be qualitative or quantitative

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Syndromeyes but be very careful about clarifying what we meanneed to decide: approach for Disease below would imply a collection of dispositions, but is it a collection of phenotypes (= qualities)DiseaseA 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 Thesaurus5; keep but with a close link to disease (possibly synonymous with Disease)

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Dosageyes; non-coretreat as GDC (specification for a planned process)?efo:EFO_0000428ClinicalGuidelineChristiDenneyA 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 ...

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rewrite definitionActiveIngredientStabilityRegulatoryes; non-corerole played by a moleculeChristiDenneySomething 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 RegulatoryAuthorityChebi uses Effector for biological regulator; 5; use if needed