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<jun> what conference is this?
<jun> trackbot, prepare telcon
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<jun> trackbot, prepare telcon
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<jun> http://prezi.com/pr7qkiw_5yk2/
on the agenda: Jim McCusker talk
<jun> scribenick, LenaDeus
Jim: programmer at Yale
... rdfizing mage tab documents
<Donald_Doherty> http://prezi.com/pr7qkiw_5yk2/rdf-izing-mage-tab-magetab2magerdf/
mccuskej: tool is
magetab2rdf
... jim's piece is called magetab2magerdf
<mscottm> http://prezi.com/pr7qkiw_5yk2/
mccuskej: usage: downoad the
script, provide url, run
... Jena is used to handle the RDF
... reusing most of the classes from mged ontology; introducing
a few more classes
re-used: person; protocol package; biomaterial package
mccuskej: biospeciment
characteristics - describes diagnosis, age, etc
... tried to reconstruct the uri of biospeciment
characteristic
mmiller: arrayexpress can be
usde
... arrayexpress can be used
... cannot always rely on arrayexpress (institution may not be
submitting to arrayexpress)
mccuskej: cannot always rely on
arrayexpress (institution may not be submitting to
arrayexpress)
... how best to create the uri?
... no specific field saying that this is an arrayexpress
experiment
... need an easy to read arrayexpress
jun: any plans to publish the rdf graph on the web?
mccuskej: yes, that is the goal
of using accession numbers in URI
... autogenerated uri, if possible, to link between
experiments~
... accession nr can be used to create a uri (by
inverseFunctionalProperty)
kei: depending on the context, treat the accession nr as URI or literal value
ssahoo2: does it conform to mged schema?
mccuskej: where it can, it does
mmiller: magetab started informally; internally accession nr could be transformed into key; therefore in some cases accession nrs are literals, today, if submitted to arrayexpress, they are already converted to URI
ssahoo2: some accession nrs are
not resolvable today, they can be treated differentelly at the
schema level
... the current state can be reflected in terms of solvable or
non-solvable accession nrs, it does not affect the quality of
the RDF
mccuskej: if there is a deferencenceable uri for a protocol, that is the one used;
mmiller: for example, investigationTitle is often the array accession, but programatically there is no way to know that
mccuskej: SDRF portion
biosource
mccuskej: disease state as a type of tumor cell line
kei: the disease state can be revisited for the microarray use case
mmiller: along with the data, this is the most important part of sdrf
mccuskej: last slide:
hybridization, set of experimental values;
... factor values are used in the same way as parameters
<mscottm> Thanks Jim!
<jun> Kei: the future with MAGE and OBI
<jun> Jim: I would prefer to use OBI
jun: satya to give update on the microarray use case
ssahoo2: created schema with set of concepts; created a placeholder schema that jun is using to generate proper RDF
Affy ID for gene1 in genelist2: http://bio2rdf.org/page/affymetrix:1556743_at
<mscottm> http://SharedName.org is about to provide URI's to ncbi genes.
<mccuskej> At Yale I am using the bio2rdf gene and trancript URIs.
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) Succeeded: s/McKuster/McCusker/ No ScribeNick specified. Guessing ScribeNick: LenaDeus Inferring Scribes: LenaDeus WARNING: No "Topic:" lines found. Default Present: jun, +1.832.386.aaaa, +1.860.673.aabb, +1.832.386.aacc, mscottm, Kei_Cheung, Don_Doherty, +1.937.775.aadd, +1.206.605.aaee, +1.832.386.aaff Present: jun +1.832.386.aaaa +1.860.673.aabb +1.832.386.aacc mscottm Kei_Cheung Don_Doherty +1.937.775.aadd +1.206.605.aaee +1.832.386.aaff 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: 19 Apr 2010 Guessing minutes URL: http://www.w3.org/2010/04/19-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]