See also: IRC log
<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 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) No ScribeNick specified. Guessing ScribeNick: Lena Inferring Scribes: Lena WARNING: No "Topic:" lines found. Default Present: mscottm, Lena, michael, SatyaSahoo, ericP Present: mscottm Lena michael SatyaSahoo ericP WARNING: No meeting title found! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth Got date from IRC log name: 23 May 2011 Guessing minutes URL: http://www.w3.org/2011/05/23-hcls-minutes.html People with action items: WARNING: Input appears to use implicit continuation lines. You may need the "-implicitContinuations" option. WARNING: No "Topic: ..." lines found! Resulting HTML may have an empty (invalid) <ol>...</ol>. Explanation: "Topic: ..." lines are used to indicate the start of new discussion topics or agenda items, such as: <dbooth> Topic: Review of Amy's report[End of scribe.perl diagnostic output]