IRC log of hcls on 2011-05-23
Timestamps are in UTC.
- 15:01:36 [RRSAgent]
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- 15:01:36 [RRSAgent]
- logging to http://www.w3.org/2011/05/23-hcls-irc
- 15:01:48 [jodi]
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- 15:02:39 [michael]
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- 15:06:08 [KeesVBochove]
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- 15:07:44 [satya]
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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
- 15:47:13 [mmiller]
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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.
- 16:25:28 [jodi]
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- 16:34:37 [egonw]
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- 16:48:33 [jodi]
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- 17:24:39 [mscottm]
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- 18:11:06 [mscottm]
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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
- 18:30:09 [Zakim]
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