HCLSIG/PharmaOntology/Meetings/2009-05-28 Conference Call
Conference Details
- Date of Call: Thursday May 28, 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 Classes - All
- Material for poster at International Conference on BioMedical Ontology - Colin and Holger
- Abstract submissions - Christi
- Review dates - Susie
- New name for the ontology? Translational Research Ontology? - Susie
- AOB
Attendees
- Bosse Andersson
- Colin Batchelor
- Christi Denney
- Michel Dumontier
- Julia Kozlovsky
- Elgar Pichler
- Matthias Samwald
- Holger Stenzhorn
- Susie Stephens
- Trish Whetzel
Minutes
[...]
Review of Classes
SusieStephens: at F2F initial set of classes were discussed
ElgarPichler: classes published on Wiki:
- ~25 classes from F2F attached to 05/14 meeting agenda (picture and OWL file);
- added flat list of classes to Proposed Classes page, http://esw.w3.org/topic/HCLSIG/PharmaOntology/Ontology, on Wiki; this flat list represents a union of all classes from the F2F and all concepts from the Roles Wiki page, http://esw.w3.org/topic/HCLSIG/PharmaOntology/Roles;
the Classes page had already a shorter list of classes there; don't know who put up that shorter list
ColinBatchelor: put original classes listing up;
the flat list contains ~80 classes
TrishWhetzel: what are top use case to use?
what are roles that were discussed at F2F?
ElgarPichler & SusieStephens: in vivo/vitro biologist & clinician;
started with biologist
ColinBatchelor: can the F2F classes be marked
ElgarPichler: will do
ColinBatchelor: spend next weeks on definitions of classes
SusieStephens: are we using other people's defs?
ElgarPichler: suggest dividing up work - any volunteers?
have the following volunters:
will assign ~20 to each person;
do people agree with getting defs first from OBO if available, and then from Wikipedia if necessary
ALL: OK
TrishWhetzel: how about collecting classes and properties for now in spreadsheet on Google,
later read from table into OWL? editor
ElgarPichler: second spreadsheet on Google idea;
volunteer setting up Google spreadsheet
TrishWhetzel: could offer other properties terms and other fields in spreadsheet;
should include author/source of def in spreadsheet
ElgarPichler: will add my e-mail address to minutes so that others can contact me (elgar.pichler@gmail.com)
MatthiasSamwald: instead of google doc, how about using semantic wiki, media wiki, ontowiki?
would be good for taxonomy editing;
somebody would have to host it;
looked at that recently, could try to reuse what was learned in that exercise
HolgerStenzhorn: Matthias and I would have a server for that @ DERI
SusieStephens: what would be benefit of semantic wiki?
MatthiasSamwald: could edit RDF and OWL directly;
don't have to move Google doc later
ColinBatchelor: all have experience with spreadsheets;
have created ontologies with several 100 terms using spreadsheets;
afraid folks are not familiar with OntoWiki;
not sure going this way would be a win
MatthiasSamwald: thought it would be interesting to try, but ...
SusieStephens: am fan of light weight approach
TrishWhetzel: not much experience with semantic wikis;
but for work needed for conference spreadsheet should be fine;
later explore media wiki option
SusieStephens: assumed later all would be in OWL
ColinBatchelor: and later can convert between OWL and OBO
ALL: Google spreadsheet for now
Use Cases
SusieStephens: should build out ~3 use cases
then choose 1 of them;
have been thinking about informaticsy use case;
one that involves bridging data silos;
others should think about that
ColinBatchelor: could think about chemistry related use case?
are use cases different from roles?
ChristiDenney: we have one use case on Alzheimer's
SusieStephens: should revisit this use case and see if it would serve this purpose
ColinBatchelor: could extend Alzheimer's use case from chemistry perspective
SusieStephens: how about bridging chemistry to genomics data - chemogenomics
ElgarPichler & ColinBatchelor: good idea, second that
SusieStephens: use cases:
- everybody to think about use case in general;
- chemogenomics use case (for Colin);
- integrative genomics (bridging discovery to clinical) (for Susie)
- Alzheimer's UC (for Susie)
- something bridging imaging & gene expression, imaging to genomics
- how about animal models (for Christie)
ICBO poster
SusieStephens: submitted final version of abstract
anybody had any further discussions on actual poster?
ColinBatchelor: emailed Susie sketches of/for posters that he and Holger made:
- diagram on mapping of classes to OBO
- other diagram pharmaontology mapping to drug development pipeline (modeled on Susie's slide of drug development pipeline)
idea: demonstrate how pharmaontology would be mapped onto drug dev pipeline general structure of poster:
- intro
- pharmaontology
- formal ontology part
- 2 diagrams
SusieStephens: will look at diagrams when she has access to email;
who is taking lead?
HolgerStenzhorn: Colin takes lead (on contents);
Holger lead on formal ontology & produces actual poster
ColinBatchelor: both on wrong side of Atlantic
HolgerStenzhorn: am currently in Brazil
TrishWhetzel: will be going to ICBO;
could print out poster and bring it
SusieStephens: to summarize: Holger does layout and ontology part
ColinBatchelor: poster content:
there are / should be panels on
- problem setting
- methodology
- formal ontology (textual description to describe "social ontology")
- diagram of mapping to formal ontology
- projection of pharmaontology to drug dev pipeline
- conclusion and acknowldegements
ColinBatchelor: which poster style to use? W3C, HCLSIG, ...?
SusieStephens: will look into it
TrishWhetzel: how to transition to new name?
like "Translational Medicine Ontology"
ColinBatchelor: second that
ALL: name change to "Translational Medicine Ontology" is OK
SusieStephens: try to update Wiki and name on posters for conferences
ChristiDenney: have received acknowledgment of receipt of poster, but so far not more
SusieStephens: need to send an email to program committee requesting name change on submissions