HCLSIG BioRDF Subgroup/Meetings/2009-05-11 Conference Call

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Conference Details

  • Date of Call: Monday May 11, 2009
  • Time of Call: 11:00 am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (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)
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Rob Frost


  • Rob Frost, Kei Cheung, Jun Zhao, Eric Prud'hommeaux, Helena Deus, Satya Sahoo


  • Scott Marshall, Adrian Paschke


  • Introduction and Roll Call (Kei)
  • HCLS F2F meeting BioRDF overview and follow-up (All)
  • Finalize revisions of the BMC Bioinformatics paper (All)


<kei> introduction

<kei> Helena: working on integration of clinical data and other data (e.g., molecular) using rdf

<rfrost> Helena is working on her PhD at UofT, focusing on issues of data privacy/security/access

<rfrost> Eric: going to begin focusing on the security aspect of query federation soon

<rfrost> first agenda item: HCLS F2F

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup

<rfrost> First day: all task forces gave updates during morning; task force breakouts for biordf, lodd, scientific discourse

<rfrost> reviewing slides for biordf breakout: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup?action=AttachFile&do=get&target=biordf_f2f_breakout_2009.pdf

<rfrost> two presentations: AIDA, Bio2RDF

<rfrost> AIDA presentation: discussed possibility to connect AIDA with FeDeRate

<rfrost> Scott and Eric worked on this over the next week: main challenge was how to build FeDeRate

<rfrost> Scott is planning on setting up server at his university to on which he will deploy the FeDeRate server that can be integrated with AIDA

<rfrost> Helen Chen gave nice demo of FeDeRate/SWTransformer for COI

<rfrost> Helen proposed possibility of linking COI demo system with BioRDF query federation system: integrate COI patient data with BioRDF HCLS KB data

<rfrost> NIF (neuroscience information framework): presentation by Maryanne Martone

<rfrost> discussed idea of federating various NIF resources

<rfrost> NIF standard ontologies (can potentially be accessed via a SOAP API)

<rfrost> discussed idea of SPARQL Protocol API

<rfrost> Bio2RDF presentation:

<rfrost> there is a lack of a high-level metadata description of the various datasets contained in bio2rdf

<rfrost> discussed the potential to use void to encode this metadata

<Zakim> + +1.937.775.aaaa

<rfrost> f2f coincided with shared name meeting; discussed issues of identifier synonyms

<rfrost> kei: can biordf apply lessons of shared names group?

<rfrost> eric: how to align sets of identifiers (e.g. protiens) defined by different groups?

<rfrost> eric: the idea of shared names is a social convention that can be used by groups (e.g. ncbi, ebi) to ensure that they use common names rather than create new name spaces and resort to mappings (e.g. owl:sameAs)

<rfrost> eric: need a set of metrics that can be used to decide if something should be a shared name

<rfrost> eric: pathway identifier may be a good area for initial exploration of shared names (define the shared names, then define the mappings to specific org names)

<rfrost> kei: KEGG vs reactome

<rfrost> rob: asked about alignment between shared names initiative and UMLS

<rfrost> eric is going to look further into leveraging shared names; Helena has some experience with pathways and can provide help on a specific usecase

<HelenaDeus> mhdeus@mdanderson.org

<rfrost> kei: people often execute the same query multiple times (with different permutations)

david_newman (drn05r@ has joined #HCLS

<rfrost> kei: discussed benefits of combining workflow technology with query execution

<rfrost> kei: image data: discussed possibility to incorporate neuro imaging data

<rfrost> rob: asked about what was done in prior biordf effort with Allen Brain Altas - will investigate status of that data and status of current brain atlas repository/APIs

  • HelenaDeus (8f6f161c@ Quit (Client exited^o)
  • rfrost (47ebbc1f@ Quit (Client exited^o)
  • rfrost (47ebbc1f@ has joined #hcls

<@ericP> http://lists.w3.org/Archives/Public/public-semweb-lifesci/2007May/0067.html

HelenaDeus (8f6f161c@ has joined #hcls

<rfrost> helen: knows about various gene expression image repositories

<rfrost> helen: once we have a specific use case, can identify something more specific/appropriate

<rfrost> kei: need for establishing image provenance and supporting image annotation

<rfrost> kei: several tools were supported

<rfrost> kei: open provenance model; open standard for establishing provenance

@ericP Zakim, who is here?

Zakim sees on the phone: Kei_Cheung, ??P12, ??P15, ??P14, EricP, +1.937.775.aaaa

Zakim sees on irc: HelenaDeus, rfrost, david_newman, jun, RRSAgent, Zakim, kei, Cloud, ericP

<@ericP> satya sahoo

@ericP that was to make the scribe's life easier

<rfrost> satya sahoo: described an OWL-based provenance tool/approach

<rfrost> will send more detailed information to the group

jun is now known as junzhao

<@ericP> -> http://twiki.ipaw.info/bin/view/Challenge/OPM Open Provenance Model

<rfrost> discussing biordf query federation paper

<rfrost> now making final edits on version in svn

<Zakim> - +1.937.775.aaaa

<junzhao> eric+gmail@w3c.org

<HelenaDeus> 700 British pounds = 1 057.21 U.S. dollars

<@ericP> junzhao, sorry, eric+google@w3.org

<junzhao> yes, got it.

<@ericP> tx