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15:10:24 <eneumann> Matthias, when was the HCLSIG meeting?
15:11:34 <Susie> Matthias - property restrictions in OWL are very verbose in demo
15:12:04 <alanr> http://code.google.com/p/owl1-1/wiki/MacrosAndSyntax
15:12:18 <Susie> Matthias - Alan Rector thought this problem should be fixed going forward in OWL
15:13:00 <ericP> Scribe: Susie
15:13:27 <ericP> topic: Review of BioOntology SIG / ISMB [Matthias]
15:13:39 <Susie> Matthias: Much general interest in poster. 
15:16:41 <Susie> EricN: The demo was well attended at ISMB proper
15:17:04 <Susie> EricN: Lots of questions about how to access the demo, and contributing in a federated way
15:17:16 <Susie> EricN: Asked questions about URIs and stability
15:17:33 <ericP> EricN: request for pre-built queries
15:17:37 <Susie> EricN: Needs to be a way to prebuild queries more easily
15:17:41 <alanr> note that URIs are currently advertised as being *unstable*. 
15:18:00 <Susie> EricN: Should put some effort into the front end.
15:18:36 <alanr> Would become stable after URI recommendation is finished and we adjust them to conform
15:18:37 <ericP> Topic: Progress report on extending the demo [Alan]
15:19:55 <alanr> test
15:20:05 <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
15:20:07 <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
15:20:08 <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.
15:20:10 <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
15:20:11 <alanr> 5) We should update virtuoso used in demo to latest version
15:20:13 <alanr> 6) Satya Sahoo has offered to help set up Knoesis Mirror. Waiting to hear back when he has installed virtuoso.
15:20:14 <alanr> 7) Waiting to hear back from Don about status of his mirror. Last left it as him starting to load pubmesh.
15:20:23 <Susie> Scott: BioLink and BioOntologies are 2 SIGs at ISMB.
15:20:51 <Susie> Scott: In text mining, people use concept identifiers, e.g. when a set of synonyms for a concept.
15:21:09 <Susie> Scott: Concerns of both workshops are combined in URI discussion
15:21:22 <alanr> re text mining: Am currently working on some geneways results. Matthias is working with whatizit. 
15:21:26 <Susie> Scott: No mention of HCLS URI work in the SIGS
15:21:49 <Susie> Scott: Text mining folks many have interesting input.
15:22:12 <Susie> Alan: We're the stakeholders, and text mining people don't use good identifiers
15:22:42 <Susie> Alan: For example, they don't distinguish between genes and proteins, or species.
15:23:54 <Susie> Scott: Some systems are better than that.
15:24:03 <eneumann> Need to bring Olivier into this conversation: he is planning to convert all MESH and UMLS CUI's as URIs soon....
15:24:20 <eneumann> q+
15:24:20 <alanr> do wordnet senses have distinct uris?
15:24:26 <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
15:25:20 <Susie> EricN: Olivier would be happy for others to use their public form of identifiers for MESH
15:26:22 <Susie> EricN: Should check that their URIs are working well.
15:27:01 <Susie> AlanR: Olivier should be speaking with Jonathan
15:27:02 <matthiassamwald> q+
15:28:16 <Susie> Matthias: Has posted RDFa recommendations for using URIs for text mining
15:28:54 <Susie> EricN: Many text mining companies are using a tagging model from IBM
15:29:16 <Susie> EricP: Is it way to justify answers, or summarizing knowledge
15:29:47 <Susie> EricN: It's a standard intermediary processed form.
15:30:11 <Susie> AlanR: RDF wouldn't be a natural output for text mining
15:31:10 <Susie> Action: EricN to get Olivier and Jonathan talking about identifiers
15:31:25 <eneumann> UIMA:  http://www.research.ibm.com/journal/sj/433/mack.html
15:31:45 <Susie> UIMA is the text mining framework that many vendors are using from IBM
15:32:15 <Susie> Alan: RDFa is made for presentation.
15:32:33 <mscottm> http://incubator.apache.org/uima/
15:32:37 <Susie> Kei: Many input documents to text mining, RDFa could be used if input document is in HTML
15:33:39 <eneumann> action: Have Olivier talk to Jonathan regarding URIs
15:33:45 <mscottm> RDFa could also be seen as a way to embed RDF in HTML, non?
15:34:31 <Susie> Susie: Reeach out to text people for input or outreach?
15:34:58 <Susie> AlanR: Already reaching out to many text mining group, evaluating results, and influencing direction.
15:35:23 <Susie> AlanR: Got feedback from GeneWave. Matthias is working with other vendors.
15:35:57 <Susie> Scott: Is very interested in this, and is coordinating a group of people focused on information extraction.
15:36:17 <Susie> Scott: Huntington's is a focus of his work, as well as Alan's.
15:37:55 <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.
15:38:01 <Susie> EricN: Larry Hunter encouraging people to output results as an RDF graph
15:38:27 <Susie> Alan: Nice to see samples of Larry's work
15:38:30 <alanr> http://www.w3.org/2007/06/HCLSForm
15:39:12 <ericP> -> http://www.w3.org/2007/06/HCLSForm HCLS Charter Questionnaire
15:39:17 <Susie> Alan: Provide feedback on text mining in the charter document
15:39:33 <Zakim> + +1.617.538.aaaa
15:40:06 <Susie> Scott: Want to couple text mining data to the demo
15:40:27 <alanr> zakim, 538.aaaa is Jonathan_Reess
15:40:27 <Zakim> sorry, alanr, I do not recognize a party named '538.aaaa'
15:41:00 <ericP> Zakim, +1.617.538.aaaa is Jonathan_Reese
15:41:00 <Zakim> +Jonathan_Reese; got it
15:42:01 <Susie> Action: Scott provide survey on text mining on August 27
15:42:22 <Susie> Alan: Redid Allen Brain Atlas load in order to get rid of spurios NILs  
15:42:43 <Susie> Alan: MGI expression database should be target for demo. 
15:43:14 <matthiassamwald> (The ISMB2007 Bio-Ontology SIG poster: http://neuroscientific.net/res/ismb2007/poster.svg )
15:43:14 <Susie> Alan: http://www.informatics.jax.org/menus/expression_menu.shtml
15:43:26 <matthiassamwald> (or alternatively: http://neuroscientific.net/res/ismb2007/poster.png )
15:43:36 <Susie> Alan: Visited AIBS. Note that scraping is mostly no longer necessary.
15:44:00 <Susie> Alan: AIBS will augment that with some missing information (image locations).
15:44:21 <Susie> Alan: All of OBO as of May 28 is loaded into triple store
15:44:41 <Susie> Alan: Results are in graph http://purl.org/hcls/potluck 
15:45:03 <Susie> Alan: there are about 20 million triples. It has FMA, etc.
15:45:17 <Susie> Alan:  We should update virtuoso used in demo to latest version.
15:45:45 <Susie> Alan: Satya Sahoo has offered to help set up Knoesis Mirror at Wright State.
15:46:03 <Susie> Alan: Science Conmmons is looking to hire someone to help with the mirror.
15:46:12 <Susie> Alan: Waiting to hear back from Don about status of his mirror.
15:46:30 <Susie> Alan: DERI are having hardware issues with their machine.
15:48:15 <Susie> Scott: May also be able to be a mirror site. Interested in guidance for downloading triples.
15:48:37 <eneumann> q+
15:48:44 <Susie> Alan: Don is working on documentation for installing Virtuoso.
15:50:51 <Susie> Alan: Focus on backend, and other people can work on the UI.
15:51:06 <Susie> Alan: Could have a question focused UI.
15:51:39 <eneumann> q+: DrugBank data still needed?
15:52:37 <eneumann> q+, DrugBank data still needed?
15:53:12 <eneumann> q+ to DrugBank data still needed?
15:53:15 <Susie> EricP: Been talking to MC about the UI. 
15:54:35 <Susie> EricN: Been playing with UI for 5 questions.
15:54:47 <Susie> EricN: Can concatenate text.
15:55:08 <Susie> EricN: Make a small set of forms, where SPARQL queries are guaranteed to work.
15:55:43 <Susie> EricN: Will work on this locally, and then make it available to Science Commons.
15:55:51 <mscottm> ranked SPARQL queries from keywords: http://spark.apexlab.org/
15:56:54 <mscottm> Sorry - demo site is down at the moment.
15:57:28 <Susie> EricN: Has there been a discussion about the demo been federated?
15:57:52 <Susie> EricN: BBI are interested in federation.
15:57:56 <Susie> q?
15:58:59 <matthiassamwald> zakim, ack matthiassamwald
15:59:00 <Zakim> I see eneumann on the speaker queue
15:59:01 <Susie> EricN: Any interested in DrugBank?
15:59:54 <ericP> [meeting extended for 10 minutes]
15:59:56 <ericP> topic: Update on progress of URI note [Jonathan]
16:00:11 <Susie> EricN: Will have DrugBank available in RDF in a month.
16:00:13 <ericP> q+ to mention licensing issues
16:00:41 <Susie> JAR: Mainly on vacation from the URI task this month.
16:00:44 <eneumann> ack eneumann
16:00:44 <Zakim> eneumann, you wanted to DrugBank data still needed?
16:00:55 <Susie> JAR: Looking for next victim for talking about URIs.
16:01:24 <Susie> JAR: Has already spoken with AlanR, Hal Abelson, EricP, John Wilbanks
16:01:38 <Susie> JAR: Would like to speak with David Booth.
16:02:21 <Susie> JAR: DanC would be another possibility.
16:02:42 <Susie> EricP: Would be happy to help set up the call.
16:03:56 <Susie> AlanR: Sandro would be a good person to speak with
16:05:53 <mscottm> gotta run - bye.
16:05:56 <Zakim> -Scott_Marshall
16:06:09 <Susie> EricP: Would like JAR to read his comments on good URI doc.
16:06:34 <Susie> EricP: Would be interested in speaking with JAR about URIs.
16:07:26 <Susie> JAR: Anything I create will have Creative Commons attribution.
16:07:45 <Susie> JAR: W3C can then do anything they like.
16:08:23 <Susie> EricP: Tricky for documents in PR space to have a Creative Commons and W3C attribution.
16:08:50 <Susie> EricP: If it's not a PR doc then attribution isn't a problem.
16:09:56 <Susie> EricP: A W3C note would be under TR.
16:10:22 <Susie> AlanR: Would be good to have a call with W3C lawyer.
16:11:10 <Susie> JAR: The outcome wouldn't affect his work.
16:11:40 <ericP> -> http://www.w3.org/Project/copyright W3C document license
16:12:10 <ericP> http://www.w3.org/Consortium/Legal/2002/copyright-documents-20021231
16:13:34 <Susie> Action: JAR and Alan to review document license by September 24
16:14:12 <eneumann> action- 2
16:15:00 <ericP> Topic: Administrivia
16:15:43 <Zakim> -Kei_Cheung
16:15:44 <Zakim> -Eric_Neumann
16:15:45 <Zakim> -Jonathan_Reese
16:15:46 <Zakim> -Alan
16:15:47 <Zakim> -susie
16:15:49 <ericP> Susie: EricN and ericP have sent mail regarding face to face scheduling
16:15:56 <Zakim> -EricP
16:16:02 <alanr> alanr has left #biordf
16:16:04 <Zakim> -[IPcaller]
16:16:05 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:16:06 <Zakim> Attendees were susie, [IPcaller], Kei_Cheung, Alan, Scott_Marshall, Eric_Neumann, EricP, Jonathan_Reese
16:16:22 <ericP> Susie: note also the HCLS Charter Questionnaire
16:18:17 <Susie> That'd work
16:18:27 <Susie> Could you call me in a couple of minutes?
16:18:43 <ericP> RRSAgent, please draft minutes
16:18:43 <RRSAgent> I have made the request to generate http://www.w3.org/2007/08/13-BioRDF-minutes.html ericP
16:18:54 <Susie> You want me leave my lovely house?
16:19:02 <Susie> I could easily meet up tomorrow?
16:19:34 <ericP> actually, a quick phone call would be fine
16:19:45 <ericP> +1.617.258.5741
16:20:01 <ericP> oops, perhaps 30 mins from now?
16:20:06 <ericP> then i can eat lunch
16:20:15 <Susie> Make you're mind up!
16:20:30 <Susie> I'll call you at 1pm. :-)
16:21:12 <ericP> RRSAgent, please make log world-visible
16:21:35 <ericP> tty in 40 mins
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17:56:28 <Susie> hello
17:58:42 <Susie> http://cgi.w3.org/member-bin/irc/irc.cgi
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18:02:44 <ericP> RRSAgent, please make logs world-visible
18:02:53 <ericP> http://www.w3.org/2007/08/13-BioRDF-minutes
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