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16:00:07 <mscottm> Zakim, who is here?
16:00:07 <Zakim> sorry, mscottm, I don't know what conference this is
16:00:08 <Zakim> On IRC I see RRSAgent, rfrost, Zakim, matthias_samwald, mscottm, ericP
16:00:15 <mscottm> Zakim, this is Biordf
16:00:15 <Zakim> ok, mscottm; that matches SW_HCLS(BioRDF)11:00AM
16:00:17 <mscottm> Zakim, who is here?
16:00:17 <Zakim> On the phone I see no one
16:00:20 <Zakim> On IRC I see RRSAgent, rfrost, Zakim, matthias_samwald, mscottm, ericP
16:00:39 <phil> phil has joined #hcls
16:00:55 <mscottm> Zakim, why don't you see me on the phone?
16:00:55 <Zakim> I don't understand your question, mscottm.
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16:04:02 <KeesVanBochove> KeesVanBochove has joined #hcls
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16:05:09 <mib_hv7s1y> EBI
16:06:41 <mroos> mroos has joined #hcls
16:07:38 <mscottm> Zakim, who is here?
16:07:38 <Zakim> On the phone I see no one
16:07:39 <Zakim> On IRC I see mroos, mib_hv7s1y, KeesVanBochove, mdmiller, phil, RRSAgent, rfrost, Zakim, matthias_samwald, mscottm, ericP
16:09:48 <Tim> Tim has joined #hcls
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16:13:53 <mscottm> http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/11-08_Conference_Call
16:15:23 <ericP> hey all, i'm still on another call. i'll show up in a few
16:16:27 <mscottm> ok, see ya soon
16:16:33 <mscottm> scribenick: mscottm
16:17:11 <mscottm> Dietrich: Interested in how to make use of content from publishers - content that you don't own
16:17:44 <mscottm> ..Important to provide the information that allows consumers of the data to draw the appropriate conclusions.
16:17:59 <mscottm> ..Semantic Web provides the means to do this.
16:19:03 <mscottm> Slide 1 (pdf page 2): Pistoia Background
16:20:14 <mscottm> Dietrich: Pistoia formed to enable Pharma companies to share pre-competitive IT resources
16:20:31 <mscottm> Now on page 4, slide 3
16:21:49 <mscottm> ..Semantic Web sets up the first 'layer' of interoperability for Pistoia. We are now in the test phase.
16:22:56 <mscottm> page 5, slide 4
16:23:15 <mscottm> ..Brokering service uses vocabularies and rules
16:23:24 <mscottm> page 6, slide 5
16:26:56 <mscottm> Dietrich: Do you care about licenses?
16:27:44 <mscottm> Scott: Yes, we have discussed ways to deal with access control and security, as well as describe that an RDF graph has a certain license attached to it.
16:29:52 <mscottm> page 8 (SESL user interface mock up)
16:30:09 <mscottm> Tim: How did you get a 'co-occurrence'?
16:30:24 <mscottm> Dietrich: algorithmically
16:31:09 <mscottm> page 9: (Mockup) Diabetes genes in SESL prototype
16:32:26 <mscottm> page 10: (Mockup) Diabetes genes in SESL prototype II
16:33:42 <mscottm> Dietrich: Used UniprotDB for part of it (gene/protein)
16:35:23 <mscottm> page 12: Full triple store schema
16:39:01 <mscottm> page 13: Access to document / sentence content
16:40:47 <mscottm> Tim: Are you using URI's?
16:41:55 <mscottm> Dietrich: Yes but not everywhere. LexEBI doesn't use them internally - we map to URI's.
16:42:38 <mscottm> Michael: Do you use UIMA or 'roll your own'?
16:43:27 <mscottm> Dietrich: We don't use UIMA but are collaborating with colleagues who do.
16:45:02 <mscottm> ..[continuing] because we use a uniform format, we can query across many different types of data. The only drawback is that query performance begins to slow.
16:46:59 <mscottm> Dietrich: The particular corpus is limited to the last several years. Literature doubles every 8 years or so.
16:49:48 <mscottm> ..We have reached a starting point and would like to work with others to build on this experience.
16:50:58 <ssahoo2> q+
16:51:05 <mroos> q+
16:52:29 <mscottm> Dietrich: Questions?
16:53:09 <mscottm> Scott: Are there resources from this project that we can access such as SPARQL endpoint, Lexicon, etc.?
16:57:03 <mscottm> Dietrich: Lexicon and other resources such as SPARQL will be public. I would prefer to do this starting January after checking with administrative people. I could give a sample sooner.
16:57:04 <ericP> am i late?
16:57:43 <ericP> apologies for being so late. hoping to catch the next steps
16:57:47 <mscottm> Scott: We would be interested in a sample access sooner to start the conversation about formats for sharing.
16:57:50 <KeesVanBochove> @ericP the meeting started about an hour ago
16:59:36 <mscottm> Scott: I think that we could form a 'block' of consumers and eventually form consensus on best practices and RDF that could motivate RDF services from ArrayExpress.
16:59:56 <mscottm> Tim: I see some definite overlap such as the Annotation Ontology (AO).
17:00:52 <mscottm> Dietrich: We would be interested in how to harmonize annotations on a document.
17:01:19 <mscottm> Dietrich: Interested in combining manual and automatic annotations?
17:01:22 <mscottm> Tim: Yes.
17:02:13 <mscottm> ack
17:02:18 <mscottm> q-
17:02:34 <mscottm> Zakim, ack ssahoo
17:02:34 <Zakim> I see mroos on the speaker queue
17:03:02 <mdmiller> q+
17:03:23 <mscottm> Satya: How do you create queries? GUI?
17:04:10 <mscottm> Dietrich: Queries are built into the web services at the moment. A query builder interface would be nice.
17:04:32 <mscottm> Satya: Where are your schemas stored? How are they used?
17:05:18 <mscottm> Dietrich: We use a number of different namespaces, such as for dates, etc.
17:06:32 <mscottm> Satya: More specifically, AO for authorship of a particular annotation, Uniprot for proteins/genes, etc.
17:07:34 <mscottm> Dietrich: Haven't gotten to that level of detail yet on, for example, annotations but am interested.
17:08:41 <mscottm> Marco: These types of resources would be interesting for use in a Biobanking project, which is getting a next round of funding in the Netherlands.
17:11:33 <KeesVanBochove> My connection dropped and the conference system doesn't allow me to enter again. I will follow up with Scott and Marco next Wednesday. Thanks for inviting me and see you next time!
17:11:37 <mscottm> Dietrich: You would be interested in the CALBC SSC corpus III (ready by next summer), we currently have immunological resources. Working hard on normalization.
17:12:45 <mscottm> Dietrich: We can always use UIMA because we work with web services but I want annotations in the *stream* of the data between services.
17:13:24 <mscottm> [answering followup question from Michael]
17:14:02 <mdmiller> mdmiller has left #hcls
17:16:12 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:16:14 <Zakim> Attendees were 
17:18:27 <mscottm> Scott: Thanks Dietrich and group at EBI. I hope that we can continue to explore this convergence of efforts around the themes of federated triplestores, microarray RDF, and RDF representations of assertions mined from text. Probably the best way to get started is to attempt to share data located in our respective SPARQL endpoints. Thanks to all for coming. Bye. 
17:18:59 <mscottm>   RRSAgent, please draft minutes
17:18:59 <RRSAgent> I have made the request to generate http://www.w3.org/2010/11/08-hcls-minutes.html mscottm
17:19:06 <mscottm>   RRSAgent, please make log world-visible
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