<mib_hv7s1y> EBI

http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/11-08_Conference_Call

<ericP> hey all, i'm still on another call. i'll show up in a few

ok, see ya soon

<scribe> scribenick: mscottm

Dietrich: Interested in how to make use of content from publishers - content that you don't own
... Important to provide the information that allows consumers of the data to draw the appropriate conclusions.
... Semantic Web provides the means to do this.

Slide 1 (pdf page 2): Pistoia Background

Dietrich: Pistoia formed to enable Pharma companies to share pre-competitive IT resources

Now on page 4, slide 3

scribe: Semantic Web sets up the first 'layer' of interoperability for Pistoia. We are now in the test phase.

page 5, slide 4

scribe: Brokering service uses vocabularies and rules

page 6, slide 5

Dietrich: Do you care about licenses?

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.

page 8 (SESL user interface mock up)

Tim: How did you get a 'co-occurrence'?

Dietrich: algorithmically

page 9: (Mockup) Diabetes genes in SESL prototype

page 10: (Mockup) Diabetes genes in SESL prototype II

Dietrich: Used UniprotDB for part of it (gene/protein)

page 12: Full triple store schema

page 13: Access to document / sentence content

Tim: Are you using URI's?

Dietrich: Yes but not everywhere. LexEBI doesn't use them internally - we map to URI's.

Michael: Do you use UIMA or 'roll your own'?

Dietrich: We don't use UIMA but are collaborating with colleagues who do.
... [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.
... The particular corpus is limited to the last several years. Literature doubles every 8 years or so.
... We have reached a starting point and would like to work with others to build on this experience.
... Questions?

Scott: Are there resources from this project that we can access such as SPARQL endpoint, Lexicon, etc.?

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.

<ericP> am i late?

<ericP> apologies for being so late. hoping to catch the next steps

Scott: We would be interested in a sample access sooner to start the conversation about formats for sharing.

<KeesVanBochove> @ericP the meeting started about an hour ago

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.

Tim: I see some definite overlap such as the Annotation Ontology (AO).

Dietrich: We would be interested in how to harmonize annotations on a document.
... Interested in combining manual and automatic annotations?

Tim: Yes.

ack

Satya: How do you create queries? GUI?

Dietrich: Queries are built into the web services at the moment. A query builder interface would be nice.

Satya: Where are your schemas stored? How are they used?

Dietrich: We use a number of different namespaces, such as for dates, etc.

Satya: More specifically, AO for authorship of a particular annotation, Uniprot for proteins/genes, etc.

Dietrich: Haven't gotten to that level of detail yet on, for example, annotations but am interested.

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.

<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!

Dietrich: You would be interested in the CALBC SSC corpus III (ready by next summer), we currently have immunological resources. Working hard on normalization.
... We can always use UIMA because we work with web services but I want annotations in the *stream* of the data between services.

[answering followup question from Michael]

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.

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Got date from IRC log name: 08 Nov 2010
Guessing minutes URL: http://www.w3.org/2010/11/08-hcls-minutes.html
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