16:00:50 <RRSAgent> RRSAgent has joined #HCLS
16:00:50 <RRSAgent> logging to http://www.w3.org/2012/01/16-HCLS-irc
16:01:24 <michel> michel has joined #hcls
16:03:59 <michael> michael has joined #hcls
16:04:17 <michael> will call in soon
16:10:33 <mscottm2> Michel: Bio2RDF (not BioRDF) is looking at github to share esp. RDF conversion source code
16:12:30 <mscottm2> Scott: Sounds like an important move to provide provenance for RDF and repeatability.
16:12:54 <mscottm2> Scott: Do you have an approach to versioning of scripts yet?
16:13:05 <mscottm2> Michel: Not yet, but that's in the cards.
16:13:45 <michel> https://github.com/bio2rdf/bio2rdf-scripts
16:18:58 <michel> scott: note - results of expression studies (microarray/NGS) from arrayexpress/GEO - give them examples to follow; reassurance of a good RDF representation
16:21:23 <michel>  ... last paper talks about multiple representations; 
16:21:26 <michel>  ... objective 2 - how to make use of the representation; jason etchelman (sp?) python script mageml to rdf; jim mccusker r-script tool to generate rdf with provenance
16:21:56 <egombocz> Jason Eshleman will porvide script code
16:23:52 <michel>  ... note is not quite ready; eric suggests we put it out as a draft over the next 2 months; time to work comments into the document
16:24:46 <michel> michael: generate a todo list; 
16:29:10 <michel> scott: semantic gap - be nice to have a nice OWL representation, beyond the RDF representation
16:30:09 <egombocz> I think he also was suggestiing this to be able to merge nicely with NCBO's ontologies (or parts thereof)
16:31:40 <egombocz> Maybe he could put a short note about what he said in the chat box here
16:32:03 <michel> scott: for linked data - basic information retrieval with sparql - differentially expressed genes with pathways, drug compounds, snps, diseases, etc
16:32:13 <michel> scott: how do we fit an OWL representation into this?
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16:32:51 <michel> scott: with stronger semantics in OWL, we can make very clear the semantics from MAGE-OM
16:33:08 <michel> michael: MAGE-tab to MAGE-RDF would be complete (?)
16:34:59 <michel> scott: add item to to-do list
16:35:12 <mscottm2> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&hl=en_US&authkey=CK-y8Y8C
16:41:36 <ericP> Zakim, who is here?
16:41:36 <Zakim> sorry, ericP, I don't know what conference this is
16:41:37 <Zakim> On IRC I see zelda, michael, michel, RRSAgent, Zakim, mscottm2, egombocz, ericP
16:41:42 <ericP> Zakim, this is hcls
16:41:42 <Zakim> ok, ericP; that matches SW_HCLS(BioRDF)11:00AM
16:41:44 <ericP> Zakim, who is here?
16:41:44 <Zakim> On the phone I see Scott_Marshall, [IPcaller], +1.415.740.aabb, +1.206.605.aacc, Eric
16:41:47 <Zakim> On IRC I see zelda, michael, michel, RRSAgent, Zakim, mscottm2, egombocz, ericP
16:41:59 <michel> Zakim, [IPcaller] is michel
16:41:59 <Zakim> +michel; got it
16:42:18 <egombocz> 415-740-9416 is egombocz
16:42:44 <michael> sorry about the communication gap, i'm traveling.  scott got my points across well.
16:44:20 <Zakim> + +1.832.386.aadd
16:44:32 <Lena> Lena has joined #hcls
16:44:48 <Lena> per eric's request
16:48:33 <ericP> http://www.ebi.ac.uk/~tomasz/pub/rdf_graph.png
16:48:34 <mscottm2> Scott: Ideally, IO Informatics would be able to use our W3C note to produce the 'consensus version' of RDF that it suggests
16:49:15 <michael> eric, what's the link?
16:49:18 <ericP> http://www.ebi.ac.uk/~tomasz/pub/rdf_graph.png
16:49:24 <mscottm2> Erich: I will talk about this with Jason tomorrow.
16:50:37 <ericP> www.ebi.ac.uk/~tomasz/pub/rdf_graph.png
16:50:45 <mscottm2> Eric: Maybe just a small group could talk about this in a teleconference. Jason and perhaps someone who understands the HCLS ontologies better than I do.
16:56:10 <Lena> https://www.dropbox.com/home/bioRDF%40HCLS?select=JBI-11-222R1.pdf
16:56:50 <Lena> https://dl-web.dropbox.com/get/bioRDF%40HCLS/JBI-11-222R1.pdf?w=5833e759&dl=1
16:59:18 <ericP> Lena: in table 1, we prefer GXA terms over blood genomics terms
17:00:07 <Lena> in table 1 also, when there are no GXA terms (empty cells), we use blood genomics terms
17:00:13 <mscottm2> Because today is MLK day in the U.S.: A petition to save his old church from foreclosure: http://act.rebuildthedream.com/sign/is-nothing-sacred?source=FBS
17:00:19 <Zakim> -michel
17:00:51 <mscottm2> MLK's famous Vietnam speech: http://www.youtube.com/watch?v=b80Bsw0UG-U
17:03:13 <egombocz> egombocz@io-informatics.com
17:03:55 <Zakim> -Eric
17:04:20 <michael> by all!
17:04:36 <michael> michael has left #hcls
17:04:37 <Zakim> - +1.206.605.aacc
17:05:20 <Zakim> -Scott_Marshall
17:05:21 <Zakim> - +1.832.386.aadd
17:05:21 <Zakim> - +1.415.740.aabb
17:05:22 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:05:24 <Zakim> Attendees were +1.415.740.aaaa, Scott_Marshall, +1.415.740.aabb, +1.206.605.aacc, Eric, michel, +1.832.386.aadd
17:33:38 <michel> rrsagent, draft minutes
17:33:38 <RRSAgent> I have made the request to generate http://www.w3.org/2012/01/16-HCLS-minutes.html michel
17:33:46 <michel> rrsagent, make log world-visible
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