14:57:00 <RRSAgent> RRSAgent has joined #hcls
14:57:00 <RRSAgent> logging to http://www.w3.org/2009/10/12-hcls-irc
14:57:08 <kei> Zakim, this will be BioRDF
14:57:08 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 3 minutes
14:57:24 <kei> agena+ introduction [Kei]
14:57:32 <kei> agenda+ introduction [Kei]
14:57:46 <kei> agenda+ HCLS KB update [Matthias, Adrian]
14:58:01 <kei> agenda+ Gene Expression Atlas [Helen]
14:58:09 <kei> agenda+ Discussion [All]
14:58:19 <kei> Zakim, take up next agendum
14:58:19 <Zakim> agendum 1. "west coast outreach for f2f" taken up [from ericP]
14:58:24 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
14:58:31 <Zakim> + +1.617.588.aaaa - is perhaps Jan
14:58:59 <matthias_samwald> matthias_samwald has joined #hcls
14:59:08 <Zakim> +Kei_Cheung
14:59:40 <curoli> curoli has joined #hcls
15:00:58 <Zakim> +??P15
15:01:11 <Zakim> -Jan
15:01:23 <Zakim> + +1.617.588.aabb - is perhaps Jan
15:03:28 <LenaDeus> LenaDeus has joined #hcls
15:04:23 <kei> scribenick Matthias
15:04:29 <Zakim> + +1.617.588.aacc - is perhaps Jan
15:04:50 <jun> jun has joined #hcls
15:05:02 <Zakim> +??P12
15:05:27 <Zakim> +??P17
15:05:44 <jun> zakim, +??P17 is jun
15:05:44 <Zakim> sorry, jun, I do not recognize a party named '+??P17'
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15:06:04 <jun> zakim, ??P17 is jun
15:06:04 <Zakim> +jun; got it
15:06:56 <matthias_samwald> scribenick: matthias_samwald
15:07:01 <Zakim> +??P2
15:07:05 <matthias_samwald> Zakim, who is talking
15:07:05 <Zakim> I don't understand 'who is talking', matthias_samwald
15:08:19 <matthias_samwald> Kei: Welcome, Part of our tradition is to invite new people. Today we are joined by Oliver Ruebenacker.
15:08:38 <matthias_samwald> Oliver: I work for the Virtual Cell project (Connecticut Health Center).
15:08:59 <matthias_samwald> ... you can simulate how concentrations of entities change etc.
15:09:35 <matthias_samwald> ... we have integrated BioPAX, can turn BioPAX into models. We are looking into Bio2RDF.
15:09:43 <matthias_samwald> ... using Jena, inference, querying etc.
15:10:14 <matthias_samwald> ... I created a bridging ontology (between BioPAX / pathways and modelling)
15:11:32 <matthias_samwald> TOPIC: Gene Expression Atlas
15:11:37 <matthias_samwald> ------
15:11:43 <curoli> Virtual Cell: http://vcell.org
15:12:10 <matthias_samwald> Kei: Helen, can you give us an update?
15:12:29 <matthias_samwald> Helen: I don't have a demo right now. 
15:12:40 <matthias_samwald> Helen: 30 neuroscience experiments have been annotated.
15:12:52 <matthias_samwald> They have been released to the public
15:13:10 <jun> jun has joined #hcls
15:13:17 <matthias_samwald> ... not Semantic Web accessible right now, but available as triples.
15:13:34 <matthias_samwald> ... we have a development instance with a cleaner object model, which is mapped to triples.
15:13:49 <matthias_samwald> ... scott marshall and ericP visited EBI and helped with making progress
15:14:11 <matthias_samwald> ... we can answer questions such as "whcih gene was observed in which experiment" etc.
15:14:27 <matthias_samwald> .. we have a working SPARQL endpoint
15:14:48 <matthias_samwald> ... we got JavaDoc for the code
15:15:10 <matthias_samwald> ... now we have all the data loaded, we will need to change it to load even more data
15:15:43 <kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2
15:16:05 <Zakim> -??P2
15:16:28 <matthias_samwald> kei: i extracted a list of experiments from Helen's e-mail, available on this wiki page
15:16:51 <matthias_samwald> 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
15:17:09 <Zakim> + +1.617.818.aadd
15:17:10 <matthias_samwald> ... right now we don't have concepts like "gene", "variant" etc in the ontology
15:17:22 <matthias_samwald> ... we are looking for existing work. For example, Sequence ontology.
15:17:34 <matthias_samwald> ... making an ontology design decision will be the next step.
15:17:43 <jun> jun has joined #hcls
15:18:09 <matthias_samwald> ... we are now thinking about what federated queries we want to do.
15:18:40 <matthias_samwald> ... we were looking at Neurocommons (get all genes with certain criteria, then get GO ids... etc.)
15:19:06 <matthias_samwald> ... but how we model things is still open, will be dependent on data.
15:19:53 <matthias_samwald> kei: you mentioned data will be available as RDF. in which form, where?
15:20:07 <matthias_samwald> helen: it is a virtuoso instance, it should be possible to get an RDF dump
15:20:31 <matthias_samwald> ... not deployed yet, if you have a preference, i will pass it along to my colleague
15:21:17 <matthias_samwald> kei: in biordf we are looking into how to expand our query federation use case
15:21:39 <ericP> hello from CIB (Geneva) where mscottm and ericP are geeking with swissprot folks
15:22:12 <matthias_samwald> ... we could look into using the HCLS KB in this context
15:24:23 <matthias_samwald> helen: we have some money from Pfizer, the idea is to make the entire codebase stand-alone, making it open-source
15:25:13 <matthias_samwald> ... regarding federated queries, we have quite rich data, although the current triples are not so rich (only association between gene and experiment)
15:26:14 <matthias_samwald> kei: would you use some of MGED / MageML etc.?
15:26:37 <matthias_samwald> helen: we are not using MageML, it is quite complicated, does not treat datafiles as external, leads to XML bloat
15:26:57 <matthias_samwald> ... if we had a MageTAB to RDF transform, that would be nice. Code not written yet.
15:27:09 <matthias_samwald> ... we might do that
15:28:10 <kei> Lena Deus
15:28:17 <matthias_samwald> Lena: i might volunteer.
15:29:07 <matthias_samwald> helen: we already have an open source parser for MageTab, making RDF extensions should be simple, it is not entirely bug-free
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15:29:59 <matthias_samwald> helen: we have an opensource Perl library that can interconvert MageTab and MageML
15:30:32 <Zakim> +??P1
15:30:39 <Zakim> - +1.617.818.aadd
15:31:15 <Zakim> + +0122330aaee
15:33:05 <matthias_samwald> ???: the problem with "gene" is that there are several meanings, e.g., gene name, things with a sequence... we need to capture all that
15:33:59 <matthias_samwald> helen: we have things like gene knock out,  allels etc., how can we represent it generically
15:34:30 <matthias_samwald> helen: i don't want to use half of the sequence ontology
15:35:47 <matthias_samwald> s/???/Jane
15:38:40 <kei> EFO -- Experimental Factor Ontology
15:38:42 <jun> they try to link to external identities as much as possible. but they don't maintain the namespace themselves, but as cross-references
15:39:33 <matthias_samwald> helen: http://www.ebi.ac.uk/efo/
15:40:18 <matthias_samwald> james: we are also trying to put relationships between classes of EFO
15:40:24 <kei> EFO -- cross links of classes (e.g., anatomy, cell lines, etc)
15:42:49 <matthias_samwald> RRSAgent, draft minutes
15:42:49 <RRSAgent> I have made the request to generate http://www.w3.org/2009/10/12-hcls-minutes.html matthias_samwald
15:42:56 <Zakim> -Jan
15:42:57 <Zakim> -Jan
15:42:57 <Zakim> - +0122330aaee
15:42:59 <Zakim> -jun
15:43:03 <Zakim> -Kei_Cheung
15:43:05 <Zakim> -??P1
15:43:05 <Zakim> -??P12
15:43:06 <matthias_samwald> RRSAgent, make minutes world-readable
15:43:06 <RRSAgent> I'm logging. I don't understand 'make minutes world-readable', matthias_samwald.  Try /msg RRSAgent help
15:44:35 <matthias_samwald> rrsagent, please make logs world-visible
15:45:18 <matthias_samwald> rrsagent, please minutes logs world-visible
15:45:18 <RRSAgent> I'm logging. I don't understand 'please minutes logs world-visible', matthias_samwald.  Try /msg RRSAgent help
15:45:23 <matthias_samwald> rrsagent, please make minutes world-visible
15:45:23 <RRSAgent> I'm logging. I don't understand 'please make minutes world-visible', matthias_samwald.  Try /msg RRSAgent help
15:48:50 <Zakim> -??P15
15:48:51 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
15:48:52 <Zakim> Attendees were +1.617.588.aaaa, Kei_Cheung, +1.617.588.aabb, +1.617.588.aacc, jun, +1.617.818.aadd, +0122330aaee
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