HCLSIG/PharmaOntology/Meetings/2009-04-02 Conference Call
Conference Details
- Date of Call: Thursday April 2, 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)
- Duration: ~1h
- Convener: Susie
Agenda
- Review Actions
- Finalize questions - Christi
- F2F plans - Susie
- International Conference on BioMedical Ontology - Susie
- AOB
Attendees: lynn, bosse, elgar, colin, helen, larisa, christi, johnm, susie
Apologies: Sandor
topic: Action Items
susie: david was to add q's (not here)
lynn: i added ontologies to Roles page
susie: trish and sandor had action items too
susie: colin, did you add ontologies?
colin: yes
christi: strategic/portfolio manager - lots of questions/ontologies added, any areas not covered?
johnm: where is web page?
johnm: better to specify the source vocabulary within umls than umls
susie: yes, and should specify semantic network. who added umls?
christi: was it trish?
elgar: are we mentioning commercial ontologies?
elgar: there is Prous
christi: we use iddb3
helen: interested in patient-related ontology?
christi:think we need to tap into patient information to find out about what physicians are saying.
helen: any plans?
susie: huge range of roles from discovery to patient environment
susie: we haven't actually provided a role for 'the patient'. should we?
elgar: useful for my use case too
christi: important that the patient appears in the ontology or patient becomes view
christi: only existing resource is EPOC clinical trial ontology
helen: CDISC also useful
susie: makes sense to incorporate CDISC
susie: makes sense to list things, like HL7, even if we don't end up using them
helen: is it for a semantic model
susie: we want to use these questions to identify the entities for the ontology (template, lightweight) - if another ontology uses them then reuse them
susie: then look at specific use case and build application around that
christi: computer-based patient record ontology
johnm: CPR is available here as an attachemnt: http://esw.w3.org/topic/HCLSIG/PharmaOntology/CPR
helen: chime had a similar idea to this project and came up with lightweight ontology to describe patient
christi: cpr is in our existing resources page
susie: please add ontologies to http://esw.w3.org/topic/HCLSIG/PharmaOntology/Resources if they're not already there
christi: project manager - not a lot there - most of the detail of projects falls within each ontology
susie: we might be interested in the concept of a project or a person in a project - not necesaarily thinking of a lot of v specific project qs
elgar: project manager subsumed by other roles for us
larisa: sk2 is a formalism for projects and their members
christi: lilly has presented an ontology that contains projects and people
christi: immunology - more questions needed?
susie: large molecules more dominant
lynn: ChEBI?
colin: no - ChEBI is small molecules only
lynn: epitope database
christi: yes
lynn: www.immuneepitope.org, run by bjoern peters
lynn: look at what richard scheuermann's doing, but pull bjoern in
christi - cheminformatics
christi - interested in optimising compounds
colin: no ontology of cheminformatics per se but it wouldn't be hard to draw up a few classes
christi: why is there question mark at obi?
colin: not sure whether these assays within scope of OBI
christi: systems physiologist - pathways and proteins and gene splicing - questions comprehensive enough?
elgar: what does "gene landscape" mean?
christi: providing context "tell me where it sits in context"
susie: change "landscape" to "tell me everything you know"
elgar: same vagueness for "What is our research hypothesis? "
elgar: work on refining that question
susie: what was your preferred question?
elgar: there are hundreds of hypotheses you might have
christi: given a specific hypothesis, does the ontology support it?
larisa: include it so we can search for all hypotheses involving a given gene or entity
christi: new q - what hypothese have been made about this gene?
[various ontology links added to the resources page]
christi: gff3?
colin: http://www.sequenceontology.org/gff3.shtml
christi: what kind of format is that?
colin: flat file, also chado xml
lynn: we use that
christi: is the term target confusing?
bosse: i had this discussion: it seems to mean genes, proteins, mechanisms of action and much much more
bosse: in most cases, proteins
christi: we use it here in a broad context; we don't want a lillyism that isn't meaningful to others
lynn: add PATO and human phenotype ontology
christi: what about mechanisms of action
colin: we have pathways and biological processes in go
larisa: do we have the Disease Ontology?
christi: i had it under the cellular and mol. biol. list - the disease qs were meant to be in the next section
lynn: we have tissues so should add FMA
christi: systems physiologist focusses on pathways and proteins
elgar: we add tissue information to our systems physiology information
christi: within a disease state or within a pathway?
elgar: if you can, you make tissue distinctions.
elgar: you look at gene expression within different tissues
christi: let's look at cell. mol. biol.
elgar: should add nci thesaurus, meddra and snomed in some places
lynn: snomed has licensing issues
lynn: you can't distribute stuff on the web with snomed in it - you have to be really careful
elgar: that was why i asked about commercial sources
christi: need to keep track of licensing issues
susie: i'll update the resources page
susie: we're about halfway through the questions but it's 1 pm
susie: i'm encouraging you all to come to the f2f to discuss what entities and use cases should go in
susie: you can dial in as well
susie: it would be good if more people became aware of the pharma ontology work: icbo.buffalo.edu would be a good place for a poster (deadline April 10th)
lynn: paper deadline just went past
susie: christi has been writing something
susie: i'm on organizing committee for bio-ontologies sig too (deadline also April 10th)