<mscottm> From Satya: I got the following error:

<mscottm> OWLXMLParser: "(Current element Prefix"

<mscottm> RDFXMLParse: [line=18:column=61] Expecting rdf:RDF element.

<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?

<mscottm> Are you saving as OWLXML or RDFXML?

<mscottm> [Discussing parse problem reading in the biordfmicroarray owl file that Lena sent to us]

<satya> <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>

<satya> I agree

mscottm: there is overlap between rdf genelistst
... ongoing dicussions between rdf for gene expression atlas and what james malone produced within R package
... define where the middle ground is
... alignemtn with arrayExpress very important
... give people from arrayExpress, and others, an aim for producing data
... choice of ontologies has been ad-hoc
... w3c note should suggesgt ontologies

satya: collected all terms from bioportal

http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/QueryFederation2

http://www.w3.org/wiki/images/b/b3/Biordfmicroarray-satya-0401.owl.pdf

<satya> http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext

<mscottm> http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/QueryFederation2_old

<mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext

mscottm: differentially expressed gene class
... e.g. if gene has p-value < 0.001 (and fold change > 1.5??), it would belong to that class
... sparql for gene list would be asking for everything in that clas

michael: class would have some identifier in a sequence db and value of how differentially expressed it was
... fold change is specific to a set of experimental factor on a particular microarray
... stop at differentially expressed gene (no need to go into upregulated or downregulated)

(hey, eric)

<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

@michael, we are on the same page, then :)

mscottm: nanopublication represeting differentialy expressed genes
... publish data before writting an article about it

<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#

mscottm: goal of w3c note: create consensus out of publication of RDF

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

Mission Statement

mmiller: query based document writting

(correction: mscottm instead of mmiller)

<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

<mscottm> take a look at this for the overview diagram: http://biordfmicroarray.googlecode.com/hg/sparql_endpoint.html

<mmiller> eric, that's already been done: http://scientificdatasharing.com/general/interview-with-susanna-assunta-sansone/

<ericP> nice!

<ericP> i'm ok with meeting monday, but i'm also not contributing much to this conversation so far

<ericP> what was the decision re: monday?

<mscottm> Monday = yes

<mscottm> Can you talk for a minute?

<ericP> almost done

<ericP> done

<ericP> callable?

<mscottm> yes

<mscottm> James will join BioRDF next week - was off sick today.

This is scribe.perl Revision: 1.136  of Date: 2011/05/12 12:01:43  
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Got date from IRC log name: 23 May 2011
Guessing minutes URL: http://www.w3.org/2011/05/23-hcls-minutes.html
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