HCLSIG/PharmaOntology/Meetings/2009-05-28 Conference Call

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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: 

       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

ChristiDenney:

  • 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

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