HCLSIG/PharmaOntology/Meetings/2009-08-13b Conference Call
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
- ** ElgarPichler [9c46de1c@64.62.228.82] has joined #hcls2
<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