HCLSIG/Meetings/2010-01-07 Conference Call

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Conference Details

  • Date of Call: Thursday January 7, 2010
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
  • 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: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use mibbit for IRC access.
  • Duration: ~1h
  • Convener: Scott, Susie
  • Scribe: Harold Solbrig

Agenda

Minutes

HCLS General Meeting, 07 Jan 2010

See also: http://www.w3.org/2010/01/07-hcls-irc

Present Possibly Present: AlexPassant Bosse Harold John_Madden Kei_Cheung Scott Susie bbalsa curoli egonw ericP hsolbrig jerven johnM kei matthias_samwald mscottm oliver

Regrets 

   Tim, Joshua

Chair 

   Scott

Scribe 

   Harold Solbrig

Update from Kei - doing microarry use case, working on RDF structure of representing microarry experiments

<scribe> In process of identifying relevent metadata and putting it into RDF structure.

<mscottm> http://wiki.knoesis.org/index.php/Provenir_Ontology

Looking at Provenir as generic ontology to repreresent gene data

<mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2

<mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2010/01-04_Conference_Call

Q: any idea of how to express gene lists?

A: right now, doing it by hand. MAGE-Tab http://magetab-om.sourceforge.net/ can export results of experiment, refs MGED ontology, but need to incorporate other types of ontologies.

Need to combine MAGE-Tab and other upper level ontologies, need meaningful relationships.

<ericP> hsolbrig: you [kei] should track bioportal

<mscottm> Harold: Please take a look at BioPortal, good resource

<ericP> ... they're creating resources to create and embed exactly that sort of map

<mscottm> http://www.ncbi.nlm.nih.gov/pubmed/19208191

Scott: NCBO is submitting renewal right now. Fingers crossed!

Terminology update - John M.

Terminology is back on line, calls moved to Monday at noon. Still on hcls2

Main project was working w/ Scott on putting SNOMED in AIDA

Now easier to specify mapping rules between SKOS representation of SNOMED and other ontologies. Includes an OWL reasoner.

who is speaking?

<mscottm> ericP

<mscottm> Eric Prud'hommeaux

ericP: COI update - putting together proposal to caBIG to work w/ HCLS

mscottm: Joshua Phillips will submit proposal in Feb., could lead to more alignment and take up of HCLS / caBIG. Would appreciate help from others in HCLS. Contains COI security component BTW.

<ericP> hsolbrig: does the caBIG proposal have a document name?

<ericP> mscottm: no name. working on an ARRA grant

<ericP> hsolbrig: are you working with Booz Allen or SAIC?

<ericP> ... i.e. how can i track this?

Susie: LODD update ... looking at licensing issues. Will always contact data providers going forward.. ... get permission to convert into RDF first. Will be extra cautious and will also ask existing sources. ... In terms of LODD Working with translational medicine ontology group, have alzheimers and fake patient data. ... Working CEMBL - chem db from EBI. ... Outreach - Matthias working on paper on traditional Chinese medicine

kei: What is approach to converting different data and formats to RDF? ... bottom up, syntactic?

Susie: so far bottom up, but becoming increasingly interested in semantic mapping using consistent terminology. ... drugs have been a challenge, work done on consistent naming through NIH and RxNORM, but no drug ontology available. ... Translational Medicine Ontology update ... Submitted paper to JBI issue on translational ontologies ... A huge amount of work went into it. Created draft TM ontology but still working ... worked on a physician centric use case, in dx and rx area. ... include insurance, dx, patient, pharmgkb and other data sources. Mapped to RDF, put in triple store. ... Going forward - work on UI. Idea is one integrated body of data and many specific UI's (physician, researcher, etc.) ... TM Ontology - terms already in other domain ontologies.

mscottm: Scientific Discourse ... next task is use cases for structured rhetorical document. ... how do you represent discourse in scientific articles? ... looking at SWAN, SALT and ABCDE (Elsevier)

<scribe> ... ongoing work with MyExperiment. Looking at CITO from David Shotton.

mscottm: CSHALS ... giving tutorial on HCLS at CSHALS conference Feb 24. ... Lee Feigenbaum and Eric will give general intro in morning. Afternoon will be HCLS tutorial ... Ask folks to think about what sort of material they'd like to contribute. Mark calendar as well. ... Mark calendar for April 19 and 20 or 22 and 23 for F2F at BioIT World ... Will be in MIT in Boston ... Fall meeting will be in Europe ... want to create integrative impression at CSHALS, so need material ahead of time to coordinate.

Susie: Tutorials are 2 hours in the afternoon Not a lot of time.

<ericP> ericP: how valuable would trackability be?

<ericP> hsolbrig: Mayo Clinic has a bunch of RFPs for the caBIG community

<ericP> ... if we can reference this caBIG submission, we can reference it in ours

<ericP> hsolbrig: our focus in caBIG is ontology services

<ericP> ... we're submitting allignment tools and wikis

<mscottm> ..LexCVS - controlled vocabulary services from Mayo, working closely with NCBO

<ericP> hsolbrig, can you make it to Tue 11am EDT COI calls?

<hsolbrig> eric, yes.

<mscottm> http://healthit.hhs.gov/portal/server.pt?open=512&objID=1436&mode=2

<mscottm> = SHARP

johnM: submitted to SHARP grants, ARRA grant turn around was short. ... Duke decided that turn around time was too short, so they changed focus from collaboration to existing work.

<mscottm> johnM: DHCI call this morning decided to change focus away from external participation (not enough time for alignment).

johnM: had hoped to include HCLS, but didn't work. Lesson: ARRA has short turn around. Need on-file biosketches and a couple of pages about possible participation, funding, etc. ... suggests a site as a repository of ideas, etc

kei: formats are changing this year.

johnM: just need starter material, not final format. ... need a collection of small (eg $25k range) projects that can be combined into a larger package. ... will help set one up with ericP.

mscottm: Best way to include W3C is to write them in as a full partner vs. just eric. They need visibility.

<bbalsa> Need to leave for the TMO cal, bye.

next call in one month (Feb. 4).

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