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15:07:52 <mscottm> From Satya: I got the following error:
15:07:52 <mscottm> OWLXMLParser: "(Current element Prefix"
15:07:52 <mscottm> RDFXMLParse: [line=18:column=61] Expecting rdf:RDF element.
15:07:52 <mscottm> I am not sure why the <Prefix> elements are used - sice the rdfs, rdf, and xsd namespaces are being defined before in the <Ontology> element?
15:07:52 <mscottm> Are you saving as OWLXML or RDFXML?
15:08:26 <mscottm> [Discussing parse problem reading in the biordfmicroarray owl file that Lena sent to us]
15:09:52 <satya> <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>
15:14:24 <satya> I agree
15:16:27 <Lena> mscottm: there is overlap between rdf genelistst
15:16:54 <Lena> mscottm: ongoing dicussions between rdf for gene expression atlas and what james malone produced within R package
15:17:10 <Lena> mscottm: define where the middle ground is
15:17:25 <Lena> mscottm: alignemtn with arrayExpress very important
15:17:51 <Lena> mscottm: give people from arrayExpress, and others, an aim for producing data
15:18:43 <Lena> mscottm: choice of ontologies has been ad-hoc
15:18:57 <Lena> mscottm: w3c note should suggesgt ontologies
15:19:33 <Lena> satya: collected all terms from bioportal
15:20:28 <Lena> http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/QueryFederation2
15:21:27 <Lena> http://www.w3.org/wiki/images/b/b3/Biordfmicroarray-satya-0401.owl.pdf
15:21:30 <satya> http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
15:21:41 <mscottm> http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/QueryFederation2_old
15:22:12 <mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext
15:24:51 <Lena> mscottm: differentially expressed gene class
15:25:22 <Lena> mscottm: e.g. if gene has p-value < 0.001 (and fold change > 1.5??), it would belong to that class
15:25:39 <Lena> mscottm: sparql for gene list would be asking for everything in that clas
15:26:10 <Lena> michael: class would have some identifier in a sequence db and value of how differentially expressed it was
15:26:35 <Lena> michael: fold change is specific to a set of experimental factor on a particular microarray
15:30:45 <Lena> michael: stop at differentially expressed gene (no need to go into upregulated or downregulated)
15:32:30 <ericP> Zakim, who is here?
15:32:30 <Zakim> sorry, ericP, I don't know what conference this is
15:32:31 <Zakim> On IRC I see satya, KeesVBochove, michael, RRSAgent, Zakim, Lena, egonw, mscottm, ericP
15:32:33 <ericP> Zakim, this is hcls
15:32:33 <Zakim> ok, ericP; that matches SW_HCLS(BioRDF)11:00AM
15:32:36 <ericP> Zakim, who is here?
15:32:36 <Zakim> On the phone I see mscottm, Lena, michael, ??P5, SatyaSahoo, ericP
15:32:42 <Zakim> On IRC I see satya, KeesVBochove, michael, RRSAgent, Zakim, Lena, egonw, mscottm, ericP
15:32:46 <Lena> (hey, eric)
15:33:37 <michael> actually, lena you are right if one is talking about control vs disease, then over expressed or under expressed genes makes sense.  my context would be multiple condotions beyond control
15:34:15 <Lena> @michael, we are on the same page, then :)
15:34:40 <Lena> mscottm: nanopublication represeting differentialy expressed genes
15:35:12 <Lena> mscottm: publish data before writting an article about it
15:36:17 <mscottm> Here is the current W3C note: https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&hl=en_US#
15:39:07 <Lena> mscottm: goal of w3c note: create consensus out of publication of RDF 
15:40:33 <Lena> Lena: produce a document, using what we already know (the biordf microarray use case), then show them to the other groups that are creating RDF for genelists and ask them to add their own comments/alteartions
15:43:20 <Lena> Mission Statement
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15:52:22 <Lena> mmiller: query based document writting
15:52:36 <Lena> (correction: mscottm instead of mmiller)
15:53:18 <KeesVBochove> Sorry to interject a practical message here: If you haven't done so please fill in enquete about face 2 face meeting! About 12 responses now, most indicate ISMB meeting as option. https://spreadsheets.google.com/a/thehyve.nl/viewform?hl=en&formkey=dGZBbDFIV2hQTWFMbklHYmVacXc5UlE6MQ#gid=0
15:55:46 <mscottm> take a look at this for the overview diagram: http://biordfmicroarray.googlecode.com/hg/sparql_endpoint.html
15:56:03 <mmiller> eric, that's already been done: http://scientificdatasharing.com/general/interview-with-susanna-assunta-sansone/
15:57:13 <ericP> nice!
16:04:52 <Zakim> -ericP
16:05:15 <ericP> i'm ok with meeting monday, but i'm also not contributing much to this conversation so far
16:05:32 <Zakim> -SatyaSahoo
16:05:33 <Zakim> -michael
16:05:33 <Zakim> -Lena
16:05:35 <Zakim> -??P5
16:05:47 <Zakim> -mscottm
16:05:48 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:05:50 <Zakim> Attendees were mscottm, Lena, michael, SatyaSahoo, ericP
16:06:04 <ericP> what was the decision re: monday?
16:06:16 <mscottm> Monday = yes
16:06:25 <mscottm> Can you talk for a minute?
16:10:07 <ericP> almost done
16:11:02 <ericP> done
16:11:04 <ericP> callable?
16:11:14 <mscottm> yes
16:11:28 <mscottm> James will join BioRDF next week - was off sick today.
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18:11:36 <mscottm>   RRSAgent, please draft minutes
18:11:36 <RRSAgent> I have made the request to generate http://www.w3.org/2011/05/23-hcls-minutes.html mscottm
18:11:41 <mscottm>   RRSAgent, please make log world-visible
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