HCLSIG/PharmaOntology/Meetings/2009-04-02 Conference Call

From W3C Wiki

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

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)