HCLSIG/PharmaOntology/Meetings/2009-08-27 Conference call

Conference Details

• Date of Call: Thursday August 27 2009
• Time of Call: 9:00am - 1pm ET
• Dial-In #: +1.617.761.6200 (Cambridge, MA)
• Dial-In #: +33.4.89.06.34.99 (Nice, France)
• Dial-In #: +44.117.370.6152 (Bristol, UK)
• Participant Access Code: 42572 ("HCLS2").
• IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC)
• Mibbit instructions: go to http://www.mibbit.com/chat and click the server link. Enter irc.w3.org:6665 into that box, enter a nickname, and enter #HCLS2 for the channel
• Duration: 4h
• Convener: Susie

Agenda

• Review of Classes and Class Definitions

Minutes

Translational Medicine Ontology
August 27, 2009
Attendees: Susie, Colin, Christi, Elgar, Chris, Michel, Anja, Julia, Trish

Efficacy
Colin: too low level Colin: this will probably do. It’s a collection of outcomes Susie: this has an element of how active the drug is… relationships between efficacy and outcome Colin: depends on patient Decision: keep Efficacy

Excipient
Susie: this goes back to discussion on terms to describe drug (inactive, active, etc.) Elgar: compound, drug, pharma product, brand were term from last time. In discussion from drug, have not concluded that drug=active ingredient Elgar: do we need inactive/active? Yes. Need drug or active ingredient. Need to know which are synonyms. Elgar: this and active ingredient seem to be synonyms Colin: agree that we need inactive ingredient Susie: it does need to be captured

Experiment
Colin: experiment is collection of assays Susie: would be good to hear from Bosse Elgar: considering study, experiment, investigation... how relate Colin: study and investigation the same? Colin: experiment may be collection of assays? Susie: want to expose the conclusions Colin: defer to OBI? Michel: OBI has something like assay, but not clinical trial. could potentially be added. ElgarPichler    concepts in this space: study investigation experiment assays test trial Elgar: investigation as main term Michel: OBI has investigation w/ hypothesis generating investigation and hypoth driven investigation Michel: should be able to add what we need to OBI

Experimental Output
Colin: same as experiment Experimental Result Colin: same as experiment

Fragment
Colin: should drop, too specific Susie: might want something to reflect that it's part of a chemical series Colin: punt to Chebi Elgar: substructure search for related compounds Elgar: would be use for this

Gene
See spreadsheet

Gene Expression
Colin: why have this here? Elgar: Gene Expression Profile collected by Elgar; all suggestions Elgar: important is that certain phenotype has genetic profile Elgar: these are common ways of classifying patient Colin: phenotypes that don’t arise from gene expression? Susie: yes Colin: is tennis elbow phenotypic? Susie: phenotype is what it looks like, rather than why it got there Susie: likes gene expression for classifying patients Colin: genotypic handled by things like SNP Susie: gene expression on it’s own isn’t quite what we want Elgar: do we need phenotype and genotype? Elgar: if we need phenotype and genotype, then we should go down to what type and what things we are actually looking at for phenotype and genotype Elgar: revisit how gene expression fits in? Gene Expression Phenotype Colin: prefer phenotype

Gene Expression Profile

Gene Expression Profiling

Genomic Sequence
Colin: pull from SO

Immune Response
Susie: there are many ways a human would respond to a drug Colin: there are many responses. This is too specific. Colin: patient response? Susie: don’t think we captured drug metabolism? Colin: yes , in 38 Colin: add response instead of immune response Susie: product response? Susie: similar to outcome, but could include toxicology Elgar: could be effect on cell line Christi: subject could include that

Inactive Ingredient
Michel: prefer excipient Michel: not aware of term for active ingredient

Information
Colin: vague

Intervention
Colin: rename to perturbation? Elgar: has positive intent, perturbation is just what’s going in/out and what’s measurable Elgar: intervention is better known in the field Colin: keep intervention

Market
Susie: important, but would choose market opportunity instead Colin: market opportunity is a gap in the market Susie: would unmet need be more appropriate?

Market Opportunity
Colin: may be same as market

Material Entity
Colin: in BFO, we don’t need

Measure
Susie: loose Colin: vague

Metabolic Pathway
Michel: suggests some pathway Michel: pathway is important to explain the mechanism, how something occurs Susie: replace with biological pathway? Colin: use pathway

Metabolism
Susie: drug metabolism is the focus Michel: and how the drug affects a normal metabolism Susie: drug effect covered by response? Elgar: drug metabolizing enzyme would be covered by drug metabolism Elgar: need metabolite to further specify phenotype? Colin: yes

Molecular Structure
Susie: need something about structure to have concept of chemical families Colin: Chebi doesn’t deal with non-existent molecules Colin: say 3D molecular structure instead

Observation
Susie: connects into C-DISC, may be in HL7

Organ
Elgar: refer to FMA

Outcome
Susie: patient outcome would be preferred, depends on whether we want to cover experiments too Susie: patient outcome is a common phrase in pharma Elgar: finding observation outcome results…. Same category Elgar: concept group: (subject, patient) outcome, observation, diagnosis, ... Elgar: diagnosis too when look at outcome? Colin: complicated, need to think about more Susie: reference health outcome

Patent
Susie: market opportunity depends on existing patents Elgar: agree

Pathway

Patient
Group: Prefer subject, if needed, can sub-classify Michel: this is clinical setting

Patient Diagnosis
Elgar: not sure why need the ‘patient’ on there

Patient Prognosis

Payer
Susie: need to include the organization that pays for the drug Christi: includes patient Elgar: how far down does the ontology stretch? Elgar: need to look at prognosis too

Person

Pharmaceutical Brand

Pharmaceutical Product

Pharmacological Activity
Elgar: describe by active/inactive and interactions between protein and compound Christi: like the mechanism of action? (the how) Michel: this is functional-type

Pharmacophore
Michel: important with respect to drug design and development, a mathematical model Susie: seems detailed for this ontology Michel: important for the drug description

Phenotype

Polypharmacology
Elgar: could interact with different sites, true for most of the compounds Elgar: too specific? Michel: don’t need a set concept, can refer to activity

Population
Susie: how tie into epidemiology and longitudinal studies? Do we have a term to represent this set of people? Elgar: collection of subjects in the study? Elgar: get to study population by grouping on various qualities? Susie: study population is good

Project

Protein

Protein Sequence
Elgar: make attribute of protein, gene

Receptor
Susie: we would say it binds to protein, but not specific receptor Michel: may need for signaling pathways in drug targeting

Referral
Michel: too much in the health care domain

Regulator
Michel: Chebi has ‘effector’ for the biological context Christi: prefer to call the approval body for drugs a Regulatory Authority

Regulatory Authority (new)

Repressor
Elgar: maybe Chebi (activator or inhibitor)

Resource

Risk
Colin: needs to be taken into account or something that has happened before Susie: risk of developing a drug Colin: subject risk and financial risk Elgar: don’t need core financial risk Colin: this will be subject risk

Role
Colin: pull from elsewhere? Christi: not as valuable in a generic sense

Sample
Michel: OBI has a term ‘sample population’

Scaffold
Colin: too specific

Sequence
Michel: use the sequence ontology (SO)

Side Effect
Susie: Need either side effect or adverse event Michel: not all side effects are adverse events All: keep

Signaling
Colin: Too specific

Signaling Pathway
Michel: use pathway

SNP
Colin: adding copy number variation

Solution
All: delete

Symptom
Susie: need sign as well Elgar: need sign, symptom, observation defined Chris: from clinical – symptoms are patient, signs are visible finding on clinical examination Observation -> recording signs

Synthesis
Colin: too domain specific

Target

Test
Elgar: replace Susie: study, assay, or investigation preferred

Therapy
Chris: Treatment and therapy may be used somewhat interchangeably Elgar: like Bosse’s comment about using intervention

Therapy Cost Benefit

Tissue
Susie: similar to organ Michel: organs in FMA

Toxicity
Michel: quantifiable measures or likelihood Michel: predictive outcome

Toxicology
Colin: out (field of study)

Treatment

Treatment Management Plan
Michel: a specification to undertake treatment Colin: we have clinical protocol Michel: need to understand what the clinical protocol is meant to specify Colin: merge into clinical protocol

Unit

Clinical Protocol (new)

Safety

Evidence
Susie: ties into tailored therapeutics Chris: UK evidence database, quantifiable Pharmacogenetics Susie: still need to capture concepts around tailoring of drugs

Lead
Colin: role played by a molecule, defer to Cheminformatics ontology

Pathology
Susie: covered by disease

PK/PD
Colin: sounds ‘field-y’ Chris: refers to metabolism or drug interaction Susie: may still want to consider pharmacodynamics

Syndrome
Elgar: collection of signs, synonymous to disease?

Cost
Susie: any ontologies with this? Trish found a few

Physiology

Molecule

Mechanism of Action

Heredity
Chris: interested in the generations and how they metabolize drug Michel: not sure these are necessary for what we are trying to do

Event

Finding
Susie: vague Michel: part of scientific discourse, outcomes of experiments can be used for evidence Trish: in OBI

Comparative Effectiveness
Chris: initially placebo, then to other drugs in the class Susie: keep and look at in the context of outcomes

Sign (new)

Stratification
Susie: patient grouping

Prognosis

Inclusion/Exclusion Criterion
Christi: defer to trial ontology?

Arm
- Changed to arm of clinical study - Defer to trial ontology

Experiment Design

Image
Christi: seems like evidence, e.g. image of slide of cells Susie: not the final term we would want to include Colin: could be evidence Class (of compound) Colin: defer to Chebi

ADME
Susie: covered by drug metabolism Chris: that would give us better control over the information, classify by transdermal, sublingual, etc. Colin: defer to domain ontology Elgar: this is like PK/PD – a bundling

Baseline

Locus

Polymorphism

Genotype

Gene List/ Gene Signature
Susie: for gene expression analysis Susie: don’t think we need it

Validation
Susie: don’t think we need

Evidence

Hypothesis

Medical History

Cognition
Susie: may be able to cover with disease - Replaced with Biomedical Measure

Geography
- Replaced by country

Environment
Elgar: includes geographical factors Susie: include lifestyle factors? Trish: keep separate Chris: may include upbringing Elgar: Subject defined by phenotype Environment influences phenotype

Lifestyle
Susie: important

Sample Restriction
Unclear

Statistical Power
Chris: measure of credibility in claiming you have accepted your HO or HA, your hypothesis; power in the study Colin: covered by evidence?

Response by Subject to Drug

Metabolite

Generic
Susie: for comparative analysis and cost/benefit analysis Susie: generic drug name should be covered Trish: a synonym

Copy Number Variation (new)

Next steps:

Look at clean version of spreadsheet, categorize by keep/remove Add definitions for new terms

Action Items:

Elgar will restructure spreadsheet and do conceptual grouping Susie will go into BioPortal and look for definitions