See also: IRC log
<kei> agena+ introduction [Kei]
<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)
------
<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)
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ 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 the start of a new topic, you need the -dashTopics option. For example: <Philippe> --- <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! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <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:[End of scribe.perl diagnostic output]