HCLSIG BioRDF Subgroup/Meetings/2009-05-11 Conference Call
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 #: +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)
- Duration: ~1 hour
- Frequency: bi-weekly
- Convener: Kei Cheung
- Scribe: Rob Frost
Attendees
- Rob Frost, Kei Cheung, Jun Zhao, Eric Prud'hommeaux, Helena Deus, Satya Sahoo
Regrets
- Scott Marshall, Adrian Paschke
Agenda
- Introduction and Roll Call (Kei)
- HCLS F2F meeting BioRDF overview and follow-up (All)
- Finalize revisions of the BMC Bioinformatics paper (All)
Minutes
<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@152.78.189.84) 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@64.62.228.82) Quit (Client exited^o)
- rfrost (47ebbc1f@64.62.228.82) Quit (Client exited^o)
- rfrost (47ebbc1f@64.62.228.82) has joined #hcls
<@ericP> http://lists.w3.org/Archives/Public/public-semweb-lifesci/2007May/0067.html
HelenaDeus (8f6f161c@64.62.228.82) 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