HCLSIG/PharmaOntology/Meetings/2009-08-13b Conference Call

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Conference Details

  • Date of Call: Thursday August 13 2009
  • Time of Call: 12:00pm Eastern Daylight Time (EDT), 17:00 British Summer Time (BST)
  • 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: ~1h
  • Convener: Susie

Agenda

  • Review Actions
  • Review of ontology call - TBD
  • Chemogenomics use case - Colin
  • Integrative Informatics Use Case - Susie
  • AOB

Minutes

Attendees: Colin, Michel, Elgar, Matthias, Bosse, Joanne, Christi, Trish, EricP, Julia

<Susie> Agenda: Discussing Terms for the Ontology

<Susie> Susie: Added some extra terms at the end of the spreadsheet

<Susie> Elgar: Added some terms within th e main document

<Susie> Elgar: Described the color code scheme

<Susie> Elgar: Asked to add drug definitions

<Susie> Elgar: Thought it'd clarify some terms

<Susie> Elgar: Added definitions for Product, Brand, Drug, Compound

<Susie> Colin: Use classification of 'keep', 'not keep', or further 'definition'

<Susie> GoogleDoc is at http://spreadsheets.google.com/ccc?key=0AnMubpgEiFW6cmF4TlA1SjdGNmVleXBNM25RTjVwMEE&hl=en

<Susie> Elgar: + = keep

<Susie> Elgar: - = remove

<Susie> Elgar x = more work

<ericP> matthias_samwald, i'm not active here, but i'd be happy to peer over your shoulder if you add eric+google@w3.org

<Susie> Currently no drug ontology, so would need to capture this information

<Susie> Joanne: Need definitions that scientists can understand, rather than the ontologist

<Susie> Discussion as to increasing definition of 'Activator'

<Susie> Susie: Ontologies are becoming smaller and more modular

<Susie> Susie: TMO is meant to be lightweight

<Susie> Susie: Therefore should we put the drug specific information into a Drug Ontology

<Susie> Should indicate if term is for TMO or Drug Ontology

<Susie> Elgar: Compound is the chemical entity

<jluciano> Term are either local or in another ontology, not both

<Susie> Elgar: The drug is compound with therapeutic use, and includes the active ingredient

<Susie> Elgar: Brand bunches together one or more product

<Susie> Elgar: Touches what we are discussing now

<Susie> Colin: Should capture that the FDA says you can treat a patient with it

<jluciano> Since this is would be characterized as an "application ontology" we are reference rather than authoring most (if not all) terms (if we choose a different term - they we still referene the other ontology)

<Susie> Bosse: Substance and Compound are quite often synonyms

<Susie> Bosse: What is a combination

<Susie> Elgar: A drug has a potential or actual therapeutic use

<Susie> Susie: Need to include biologics too

<Susie> Elgar: There are synonyms for many terms, but I think drug and compound are different

<Susie> Elgar: We administer a product, not a drug

<Susie> Elgar: Would call combination drugs, combination products

<Susie> Bosse: We have a compound that is used for different therapeutic purposes

<Susie> Bosse: We should make this clear

<Susie> Elgar: I would this a brand, and within a brand you can have the same drug in different formulations, and used for different formulations

<Susie> Bosse: I think your definitions are good

<Susie> Bosse: Need to make sure we capture the differences in the defintions

<Susie> Elgar: Are we happy that ActiveIngredient may be a synonym for drug

<Susie> Colin: Defines 'ActiveIngredient' wihout using the word 'drug'. Text goes in column D of spreadsheet

<Susie> Colin: The molecule in a formulation that is believed to have the pharmacological effect

<Susie> Colin: Keep 'ActiveIngredient' in DO

<matthias_samwald> Could someone please add Google-Doc permissions to 'samwald@gmx.at' ?

<Susie> Will do

<Susie> Colin: Biological Function and Mechanims of Action is close

<Susie> Michel: Activity is more of a description of the whole process

<Susie> Joanne: can we use a definition for activity from another ontology

<Susie> Colin: current definition from my head based on BFO

<Susie> Michel: The problem is with the term name, rather than the definition

<Susie> Maybe molecular function would be better

<Susie> Michel: Activator likely to be included in ChEBI

<Susie> Colin: Could be included as child of effector in ChEBI

<Susie> Colin: Conclusion is to defer to ChEBI

<Susie> Elgar: Move to Adverse Event

<Susie> Trish: Think there is an AdverseEvent ontology

<matthias_samwald> ... but costart is proprietary.

<Susie> Colin: costart has been replaced by Medra

<Susie> Bosse: AdverseDrugEvent is an adverse event when a drug is taken

<Susie> Bosse: An AdverseEvent could be breaking a leg

<Susie> Bosse: AdverseDrugEvent is when there is a link between a drug and an adverse event

<Susie> Elgar: Agreement that we keep 'AdverseDrugEvent' and work on the defintion

<Susie> Elgar: Move onto 'Amount'

<Susie> Michel: Need to think if the term should be included in the DO or the TMO

<Susie> Michel: Even if term is in other ontologies we should make sure the term is being used in a domain appropriate way

<Susie> Michel: Need to decide if terms are relevant or irrelevant

<Susie> Michel: Should we have a column that states that a term is interesting, even if we aren't going to be including it ourselves, but making reference to it

<Susie> Elgar: We would use terms from other ontologies

<Susie> Agreement that amount is too broad to include

<Susie> Susie: 9-12 on August 27 for next extended session

<Susie> Elgar: Rank terms 0-10

<Susie> Elgar: 0 = no importance; 10 is very important

<Susie> Elgar: Animal Study

<Christi> Any idea why the first class now just says the name is 'C'?

<Susie> Susie: Maybe we should have 'Animal' and 'Study'

<Susie> Christi: Agree may need re-classification

<Susie> Elgar: Antibody is next

<Susie> Susie: Antibody is important, but maybe should be under drug

<Susie> Elgar: Assay

<Susie> Colin: Defer to OBI

<Susie> Trish: Defer to ONTIE

<Susie> ONTIE is an option for antibody

<Susie> Elgar: BioAssay

<Susie> Colin to me all assays are biological, so no difference between assay and bioassay

<Susie> Trish: History of bioassay?

<Susie> Elgar: uncertain as to origin

<Susie> Elgar: Bioinformatics

<Susie> Scratch

<Susie> Elgar: Biologic

<Susie> Susie: Ambiguous meaning - either drug or biological process

<Susie> Elgar: Should keep and consider where it fits in drug/pharmaceutical product tree

<Susie> Colin: It's a drug that is manufactured using living organisms

<Susie> Trish: Flu vaccines have to go through different manufacture compared to small molecules

<Susie> Joanne: Why do we need this in the ontology?

<Susie> Elgar: Need to talk about biologic effects

<Susie> Elgar: What's not clear from the definition is exactly what it is

<Susie> Colin: Keep for moment and discuss more later

<Susie> Elgar: Biomarkers

<Susie> Susie: Keep

<Susie> Elgar: BioProcess

<Susie> Elgar: Not in favor of keeping

<Susie> Colin: If it's needed it's in GO

<Susie> Joanne: Does this mean what pathway something in

<Susie> Elgar: Michel pointed out it's too vague

<Susie> Elgar: We do have pathway further down

<Susie> Elgar: And so are other processes

<Susie> Elgar: Would prefer process over bioprocess if it is needed

<Susie> Trish: Processing of haemophillia products

<Susie> Elgar: Cell Line

<Susie> Michel: Often 2nd line of experimental procedure for drug molecules

<Susie> Michel: Important aspect of the translation

<Susie> Christi: Need to know which cell lines were used for oncology

<Susie> Michel: Sure can refer to other ontologies

<Susie> Elgar: Also think it's very important. Need to be aware of cell line and tissue classifications

<Susie> Elgar: Need more of a definition for cell line

<Susie> Elgar: Chemical

<Susie> Colin: Chemical is vague, so needs to go

<Susie> Colin: Prefer: Compound, mix, etc.

<Susie> Michel: Was thinking of a chemical based substance

<Susie> Colin: A bulk substance that's inactive

<Susie> Trish: Like inert material

<Susie> Elgar: this is broader than bulk stuff, because pharmaceutical product would be subclass of bulk stuff

<Susie> Colin: Would be handled by ChEBI

<Susie> Elgar: Need definition or link to other ontology

<Susie> Elgar: chemicalProperty

<Susie> Elgar: ChemicalStructure

<Susie> Christi: Would call it molecular structure

<Susie> Joanne: Would want to point to the structures

<Susie> Colin: Most probabably belongs in a chemisty ontology, which doesn't exist yet

<Susie> Elgar: Would expect this would be subclasses of ChEBI with time

<Susie> Elgar: Therefore don't need chemical structure and chemical property

<Susie> Susie: Seems rather detailed for a TMO

<Susie> Christi: Kill it

<Susie> Elgar: Cheminformatics

<Susie> Everyone: kill

<Susie> Elgar: Chemical Similarity

<Susie> Colin: Delete, as it doesn't belong here.

<Susie> Elgar: Clinical Trial

<Susie> Susie: Keep

<Susie> Colin: Needs definition

<Susie> Elgar: Clinician

<Susie> Some discussion as need to include

<Susie> Susie: Seems like the odd one out as no other roles (other than patient)

<Susie> Joanne: Maybe need more roles

<Susie> Elgar: Comapnies

<Susie> Elgar: Keep Institution

<Susie> Elgar: Competition

<Susie> Kill

<Susie> Elgar: Complex forumlation

<Susie> Kill

<Susie> Elgar: Compound

<Susie> Keep

<Susie> Susie: Sometimes collaborators and competitors

<Susie> Susie: Prefer to keep institution, and then define collaborators and competitors as relationships

<Susie> Trish: Discussed RA example

<Susie> Trish: Are we still planning to meet F2F

<Susie> Susie: Trish to explore flight prices to Philly

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