22 Sep 2008

See also: IRC log


Kei_Cheung, Olivier_Bodenreider, +1.781.662.aaaa, matthias_samwald_w3c, +1.617.949.aabb, TN, +1.203.737.aacc




roll call and introduction

matthias, are you on the phone?

scott, susie, kei, luis, matthias, olivier, benjamin ...

<matthias_samwald> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-09-22?action=AttachFile


UMLS presentation

olivier: high level presentation of umls
... methathesaurus and semantic network
... terminology integration system (UMLS)
... UMLS has been developed in past 20 years
... license: an agreement needs to be signed with NLM
... IP of UMLS developers needs to be protected.
... umls is mainly organized by concepts
... 17 translations for MeSH
... umls consists of a set of relational db's
... umls realized integration across namespaces
... semantic network is fully curated by NLM
... semantic labels are assigned to relationships in semantic network
... no easy conversion between umls and smenatic web format
... umls as a terminology integration system which is most relevant to semantic web

susie: identifer: which URI's to be used?
... likely NLM will assign global URI to its terms?
... URI-based identifiers are preferred by this IG?

olivier: easy mappings should be provided between different name spaces. Base URI's need to be in place.

susie: anything we can do to help NLM to move towards this global URI scheme?

olivier: RDF version of MESH can serve as a testbed?

scott: URI's (slide 8), Addison disease in multiple vocabularies?

olivier: unresolved problem -- uri assigned by the the 1st vocabulary
... use of a precedence list (for choosing the preferred term)

benjamin: chief software architect of NCBO

<mscottm> missing the powerpoint - was a link put out in irc?

BioPortal presentation

<mscottm> just found - nevermind

benjamin: one stop shop for biomedical ontologies

bejamin: PURL in collaboration with Safari

benjamin: loose definition of ontologies is used
... tracking of history and different formats (e.g. obo, owl) are supported
... navigation view of concepts in ontology (see URL listed at the end of the slide)
... metadata associated with concetps are avaiable
... point-to-point mappings vs bulk mappings
... upload of bulk mappings is also possible
... how to decide which mappings to use? Provenance may help. For example filter by sources.
... equivalent mappings (different kinds of mappings)
... local forum for each ontology (community feedback)
... annotations of clinical trials. gov

<matthias_samwald> (sounds great!)

benjamin: netkernel for NCBO fabric
... rest services are available externally
... uri security gating (how this can be used to address the licensing issue)
... performance issue -- heuristic may be applied to improve performance
... bioportal -- available through rest services
... ncbo purl server (in collaboration with Zepheira -- headed by Eric Miller)

scott: where is the bottleneck?
... purl pointing to UMLS?

kei: overlap of ontologies?

olivier: 5 ontologies: nci thesaurus, fma, gene ontologies, ...

benjamin: licensing issue is not trivial ...

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.133 (CVS log)
$Date: 2008/09/22 16:23:07 $

Scribe.perl diagnostic output

[Delete this section before finalizing the minutes.]
This is scribe.perl Revision: 1.133  of Date: 2008/01/18 18:48:51  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

No ScribeNick specified.  Guessing ScribeNick: kei
Inferring Scribes: kei
Default Present: Kei_Cheung, Olivier_Bodenreider, +1.781.662.aaaa, matthias_samwald_w3c, +1.617.949.aabb, TN, +1.203.737.aacc
Present: Kei_Cheung Olivier_Bodenreider +1.781.662.aaaa matthias_samwald_w3c +1.617.949.aabb TN +1.203.737.aacc

WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting

WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 22 Sep 2008
Guessing minutes URL: http://www.w3.org/2008/09/22-BioRDF-minutes.html
People with action items: 

WARNING: Input appears to use implicit continuation lines.
You may need the "-implicitContinuations" option.

[End of scribe.perl diagnostic output]