W3C

- DRAFT -

SV_MEETING_TITLE

13 Aug 2007

See also: IRC log

Attendees

Present
susie, [IPcaller], Kei_Cheung, Alan, Scott_Marshall, Eric_Neumann, EricP, Jonathan_Reese
Regrets
Chair
SV_MEETING_CHAIR
Scribe
Susie

Contents


 

 

<eneumann> Matthias, when was the HCLSIG meeting?

Matthias - property restrictions in OWL are very verbose in demo

<alanr> http://code.google.com/p/owl1-1/wiki/MacrosAndSyntax

Matthias - Alan Rector thought this problem should be fixed going forward in OWL

<ericP> Scribe: Susie

Review of BioOntology SIG / ISMB [Matthias]

Matthias: Much general interest in poster.

EricN: The demo was well attended at ISMB proper
... Lots of questions about how to access the demo, and contributing in a federated way
... Asked questions about URIs and stability

<ericP> EricN: request for pre-built queries

EricN: Needs to be a way to prebuild queries more easily

<alanr> note that URIs are currently advertised as being *unstable*.

EricN: Should put some effort into the front end.

<alanr> Would become stable after URI recommendation is finished and we adjust them to conform

Progress report on extending the demo [Alan]

<alanr> test

<alanr> 1) Redid Allen Brain Atlas load in order to get rid of spurios NILs as ids, and to merge in MGI orthology to give many more entries entrez gene ids. New graph is http://sw.neurocommons.org/aba-20070807

<alanr> 2) MGI expression database should be target for demo. http://www.informatics.jax.org/menus/expression_menu.shtml Might be worth JAR summarizing out JAX visit

<alanr> 3) Visited AIBS. Note that scraping is (mostly no longer necessary) because they have an XML mirror of their site. http://www.brain-map.org/mouse/gene/browserXml.html They have indicated that they will augment that with some missing information (image locations). They are also willing to release image transformation data (to their 3D atlas). We will follow up.

<alanr> 4) All of OBO as of May 28 is loaded into triple store, and transitive subclass is computed. Results are in graph http://purl.org/hcls/potluck

<alanr> 5) We should update virtuoso used in demo to latest version

<alanr> 6) Satya Sahoo has offered to help set up Knoesis Mirror. Waiting to hear back when he has installed virtuoso.

<alanr> 7) Waiting to hear back from Don about status of his mirror. Last left it as him starting to load pubmesh.

Scott: BioLink and BioOntologies are 2 SIGs at ISMB.
... In text mining, people use concept identifiers, e.g. when a set of synonyms for a concept.
... Concerns of both workshops are combined in URI discussion

<alanr> re text mining: Am currently working on some geneways results. Matthias is working with whatizit.

Scott: No mention of HCLS URI work in the SIGS
... Text mining folks many have interesting input.

Alan: We're the stakeholders, and text mining people don't use good identifiers
... For example, they don't distinguish between genes and proteins, or species.

Scott: Some systems are better than that.

<eneumann> Need to bring Olivier into this conversation: he is planning to convert all MESH and UMLS CUI's as URIs soon....

<alanr> do wordnet senses have distinct uris?

<matthiassamwald> Current snapshot of a result from my RDFa-based Whatizit text mining web application: http://neuroscientific.net/res/soc/example_gene_ontology_1.htm

EricN: Olivier would be happy for others to use their public form of identifiers for MESH
... Should check that their URIs are working well.

AlanR: Olivier should be speaking with Jonathan

Matthias: Has posted RDFa recommendations for using URIs for text mining

EricN: Many text mining companies are using a tagging model from IBM

EricP: Is it way to justify answers, or summarizing knowledge

EricN: It's a standard intermediary processed form.

AlanR: RDF wouldn't be a natural output for text mining

<scribe> ACTION: EricN to get Olivier and Jonathan talking about identifiers [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action01]

<eneumann> UIMA: http://www.research.ibm.com/journal/sj/433/mack.html

UIMA is the text mining framework that many vendors are using from IBM

Alan: RDFa is made for presentation.

<mscottm> http://incubator.apache.org/uima/

Kei: Many input documents to text mining, RDFa could be used if input document is in HTML

<eneumann> ACTION: Have Olivier talk to Jonathan regarding URIs [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action02]

<mscottm> RDFa could also be seen as a way to embed RDF in HTML, non?

Susie: Reeach out to text people for input or outreach?

AlanR: Already reaching out to many text mining group, evaluating results, and influencing direction.
... Got feedback from GeneWave. Matthias is working with other vendors.

Scott: Is very interested in this, and is coordinating a group of people focused on information extraction.
... Huntington's is a focus of his work, as well as Alan's.

<mscottm> To avoid misunderstanding: I have never worked directly on the HD project that I refer to but have contact with those on the project.

EricN: Larry Hunter encouraging people to output results as an RDF graph

Alan: Nice to see samples of Larry's work

<alanr> http://www.w3.org/2007/06/HCLSForm

<ericP> HCLS Charter Questionnaire

Alan: Provide feedback on text mining in the charter document

Scott: Want to couple text mining data to the demo

<scribe> ACTION: Scott provide survey on text mining on August 27 [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action03]

Alan: Redid Allen Brain Atlas load in order to get rid of spurios NILs
... MGI expression database should be target for demo.

<matthiassamwald> (The ISMB2007 Bio-Ontology SIG poster: http://neuroscientific.net/res/ismb2007/poster.svg )

Alan: http://www.informatics.jax.org/menus/expression_menu.shtml

<matthiassamwald> (or alternatively: http://neuroscientific.net/res/ismb2007/poster.png )

Alan: Visited AIBS. Note that scraping is mostly no longer necessary.
... AIBS will augment that with some missing information (image locations).
... All of OBO as of May 28 is loaded into triple store
... Results are in graph http://purl.org/hcls/potluck
... there are about 20 million triples. It has FMA, etc.
... We should update virtuoso used in demo to latest version.
... Satya Sahoo has offered to help set up Knoesis Mirror at Wright State.
... Science Conmmons is looking to hire someone to help with the mirror.
... Waiting to hear back from Don about status of his mirror.
... DERI are having hardware issues with their machine.

Scott: May also be able to be a mirror site. Interested in guidance for downloading triples.

Alan: Don is working on documentation for installing Virtuoso.
... Focus on backend, and other people can work on the UI.
... Could have a question focused UI.

EricP: Been talking to MC about the UI.

EricN: Been playing with UI for 5 questions.
... Can concatenate text.
... Make a small set of forms, where SPARQL queries are guaranteed to work.
... Will work on this locally, and then make it available to Science Commons.

<mscottm> ranked SPARQL queries from keywords: http://spark.apexlab.org/

<mscottm> Sorry - demo site is down at the moment.

EricN: Has there been a discussion about the demo been federated?
... BBI are interested in federation.
... Any interested in DrugBank?

<ericP> [meeting extended for 10 minutes]

Update on progress of URI note [Jonathan]

EricN: Will have DrugBank available in RDF in a month.

JAR: Mainly on vacation from the URI task this month.

<Zakim> eneumann, you wanted to DrugBank data still needed?

JAR: Looking for next victim for talking about URIs.
... Has already spoken with AlanR, Hal Abelson, EricP, John Wilbanks
... Would like to speak with David Booth.
... DanC would be another possibility.

EricP: Would be happy to help set up the call.

AlanR: Sandro would be a good person to speak with

<mscottm> gotta run - bye.

EricP: Would like JAR to read his comments on good URI doc.
... Would be interested in speaking with JAR about URIs.

JAR: Anything I create will have Creative Commons attribution.
... W3C can then do anything they like.

EricP: Tricky for documents in PR space to have a Creative Commons and W3C attribution.
... If it's not a PR doc then attribution isn't a problem.
... A W3C note would be under TR.

AlanR: Would be good to have a call with W3C lawyer.

JAR: The outcome wouldn't affect his work.

<ericP> W3C document license

<ericP> http://www.w3.org/Consortium/Legal/2002/copyright-documents-20021231

<scribe> ACTION: JAR and Alan to review document license by September 24 [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action04]

<eneumann> action- 2

Administrivia

<ericP> Susie: EricN and ericP have sent mail regarding face to face scheduling

<ericP> Susie: note also the HCLS Charter Questionnaire

That'd work

Could you call me in a couple of minutes?

Summary of Action Items

[NEW] ACTION: EricN to get Olivier and Jonathan talking about identifiers [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action01]
[NEW] ACTION: Have Olivier talk to Jonathan regarding URIs [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action02]
[NEW] ACTION: JAR and Alan to review document license by September 24 [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action04]
[NEW] ACTION: Scott provide survey on text mining on August 27 [recorded in http://www.w3.org/2007/08/13-BioRDF-minutes.html#action03]
 
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Default Present: susie, [IPcaller], Kei_Cheung, Alan, Scott_Marshall, Eric_Neumann, EricP, Jonathan_Reese
Present: susie [IPcaller] Kei_Cheung Alan Scott_Marshall Eric_Neumann EricP Jonathan_Reese

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Got date from IRC log name: 13 Aug 2007
Guessing minutes URL: http://www.w3.org/2007/08/13-BioRDF-minutes.html
People with action items: alan ericn have jar olivier scott talk

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