<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  
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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

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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: 

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<dbooth> Topic: Review of Amy's report