W3C

- DRAFT -

SV_MEETING_TITLE

12 Oct 2009

See also: IRC log

Attendees

Present
Regrets
Chair
SV_MEETING_CHAIR
Scribe
matthias_samwald

Contents


 

 

<kei> agena+ introduction [Kei]

west coast outreach for f2f

<kei> scribenick Matthias

<scribe> scribenick: matthias_samwald

Kei: Welcome, Part of our tradition is to invite new people. Today we are joined by Oliver Ruebenacker.

Oliver: I work for the Virtual Cell project (Connecticut Health Center).
... you can simulate how concentrations of entities change etc.
... we have integrated BioPAX, can turn BioPAX into models. We are looking into Bio2RDF.
... using Jena, inference, querying etc.
... I created a bridging ontology (between BioPAX / pathways and modelling)

Gene Expression Atlas

------

<curoli> Virtual Cell: http://vcell.org

Kei: Helen, can you give us an update?

Helen: I don't have a demo right now.
... 30 neuroscience experiments have been annotated.

They have been released to the public

scribe: not Semantic Web accessible right now, but available as triples.
... we have a development instance with a cleaner object model, which is mapped to triples.
... scott marshall and ericP visited EBI and helped with making progress
... we can answer questions such as "whcih gene was observed in which experiment" etc.
... we have a working SPARQL endpoint
... we got JavaDoc for the code
... now we have all the data loaded, we will need to change it to load even more data

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2

kei: i extracted a list of experiments from Helen's e-mail, available on this wiki page

helen: we can also do this on request, the next chunk of data will be immunology-related, and we can do more neuroscience for this group
... right now we don't have concepts like "gene", "variant" etc in the ontology
... we are looking for existing work. For example, Sequence ontology.
... making an ontology design decision will be the next step.
... we are now thinking about what federated queries we want to do.
... we were looking at Neurocommons (get all genes with certain criteria, then get GO ids... etc.)
... but how we model things is still open, will be dependent on data.

kei: you mentioned data will be available as RDF. in which form, where?

helen: it is a virtuoso instance, it should be possible to get an RDF dump
... not deployed yet, if you have a preference, i will pass it along to my colleague

kei: in biordf we are looking into how to expand our query federation use case

<ericP> hello from CIB (Geneva) where mscottm and ericP are geeking with swissprot folks

kei: we could look into using the HCLS KB in this context

helen: we have some money from Pfizer, the idea is to make the entire codebase stand-alone, making it open-source
... regarding federated queries, we have quite rich data, although the current triples are not so rich (only association between gene and experiment)

kei: would you use some of MGED / MageML etc.?

helen: we are not using MageML, it is quite complicated, does not treat datafiles as external, leads to XML bloat
... if we had a MageTAB to RDF transform, that would be nice. Code not written yet.
... we might do that

<kei> Lena Deus

Lena: i might volunteer.

helen: we already have an open source parser for MageTab, making RDF extensions should be simple, it is not entirely bug-free
... we have an opensource Perl library that can interconvert MageTab and MageML

Jane: the problem with "gene" is that there are several meanings, e.g., gene name, things with a sequence... we need to capture all that

helen: we have things like gene knock out, allels etc., how can we represent it generically
... i don't want to use half of the sequence ontology

<kei> EFO -- Experimental Factor Ontology

<jun> they try to link to external identities as much as possible. but they don't maintain the namespace themselves, but as cross-references

helen: http://www.ebi.ac.uk/efo/

james: we are also trying to put relationships between classes of EFO

<kei> EFO -- cross links of classes (e.g., anatomy, cell lines, etc)

Summary of Action Items

[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.135 (CVS log)
$Date: 2009/10/12 15:42:54 $

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Guessing input format: RRSAgent_Text_Format (score 1.00)

Succeeded: s/???/Jane/
Found ScribeNick: matthias_samwald
Inferring Scribes: matthias_samwald

WARNING: Dash separator lines found.  If you intended them to mark
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        <Philippe> Review of Action Items


WARNING: No "Present: ... " found!
Possibly Present: Helen Jan Jane Kei_Cheung Lena LenaDeus Oliver P1 P12 P15 P17 P2 aaaa aabb aacc aadd curoli ericP inserted is james jun kei perhaps rfrost scribenick
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy


WARNING: No meeting title found!
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<dbooth> Meeting: Weekly Baking Club Meeting


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<dbooth> Chair: dbooth

Got date from IRC log name: 12 Oct 2009
Guessing minutes URL: http://www.w3.org/2009/10/12-hcls-minutes.html
People with action items: 

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