scribenick jun

express gene lists in RDF format

Kei: try to have an RDf graph with minimal semantics to see whether we can answer some example queries
... Jun, Satya and me are in the process of creating a new version of RDF structure to describe the microarray gene lists
... we also want to use this use case to link up with the scientific discource+experiemnt+data sub-task force

<LenaDeus> can anyone post here the link to the latest version of the gene list, please :)

Kei: finally we will discuss future query federation demos

http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2

you can find the gene lists in the RDF structure section

Scott: anyone plans to talk to James Mccusker?

Kei: I have invited James to join us in one of the BioRDF calls

<kei> http://esw.w3.org/images/0/08/RDF_genelists.pdf

<mscottm> http://code.google.com/u/mccusker/

<kei> jim mccusker

<mscottm> http://code.google.com/p/magetab2rdf/

Scott: our bioRDF work seems a lot of overlaps with Jim's work

gene lists discussion

Kei: http://esw.w3.org/images/0/08/RDF_genelists.pdf
... in the tables you can see there are gene-specific information and sample-specific information
... I tried to come up with an RDF structure to describe such data
... Lena created an initial draft of RDF and Satya and Jun are refining it
... more example queries have been added to the wiki page http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2

Lena: what is the microarray ** used in the study might also be useful?

Kei: there are such information in the papers publishing these genes, such as algorithms, statistics methods used in the microarray experiemnts

Satya: I created an OWL ontology and Jun should use it to create the RDF graph conforming to the ontology
... next step could be trying to run the queries

<kei> find genelists that involve AD, pyramidal neuron,

<kei> mouse, and

<kei> hippocampus

http://esw.w3.org/images/7/77/Genelists_20100404_jun.pdf

Satya's ontology: http://esw.w3.org/images/b/b3/Biordfmicroarray-satya-0401.owl.pdf

Jun: Satya and I need to align his ontology and my RDF graph

<mscottm> Is this the origin of the above pdf? : http://knoesis.wright.edu/library/ontologies/provenir/provenir.owl

Satya: we need to align with Scientific Discouse's ontology later, thus we define our ontology in a local namespace atm

Scott: it would be nice to harmonize different ontologies, such as NCBO
... I am working on to get their ontologies through SPARQL endpoints

<ssahoo2> an example term from NIFSTD: Entorhinal Cortex: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_1508

<ssahoo2> http://www.deg.byu.edu/papers/PODS.integration.pdf

Kei: next step, Jun and Satya to have another round and keep Scott and Lena in the loop to prepare the query federation task in the future
... I will also invite Jim to join our call in the future to share his work with us

Lena: shall we use Dropbox to share files?

<LenaDeus> https://www.dropbox.com/

the basic/free version is 2GB space

Scott: how do we identify which ontology to use?

Kei: we are aiming at coming up with a first version modelling and then coordinate with the scientific discourse task force

<LenaDeus> http://www4.wiwiss.fu-berlin.de/diseasome/

<LenaDeus> the noise was me, sorry :)

Kei: we should look at related data resources once we have the initial gene list in RDF

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/Malone/Mccusker/
No ScribeNick specified.  Guessing ScribeNick: jun
Inferring Scribes: jun
Default Present: mscottm, jun, Kei_Cheung, +1.832.386.aaaa, +1.937.775.aabb
Present: mscottm jun Kei_Cheung +1.832.386.aaaa +1.937.775.aabb

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: 05 Apr 2010
Guessing minutes URL: http://www.w3.org/2010/04/05-hcls-minutes.html
People with action items: 

WARNING: Input appears to use implicit continuation lines.
You may need the "-implicitContinuations" option.