introduction

<kei> scribenick jun

RDF gene expression representation and the provenance paper

Kei: let's start with the RDF structure of the gene list
... last time, we agreed to let Lena to try some queries with the current structure

<kei> http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2

Lena: I tried the queries shared in the google doc
... Which gene is overexpressed in the brain region "Entorhinal cortex"?
... we can't do the first query, Find experiments involving the same disease/phenotype, brain region, and species

Kei: we do have experiments sharing the same condition or experimental context, such as brain regions
... it's true that it's hard to find genes that are commonly expressed in different brain regions

Scott: will try to find some queries along the line of provenance information

michael: the different array design 1, 2 would lead to different probe ids

michale: agree with Lena that by the time they get to the gene list, the different versions of probe design wouldn't matter any more

Kei: they may only need to go back to the raw datasets when they want to repeat the experiments themselves

michael: people have done analysis over the process of experiment and realised that the process was not good

<michael> not so much the process as the actual oligos used for the probe set not matching the target gene

Scott: it could be easy to use provenance to demonstrate how we can choose which dataset is more recent than another.

Jun: we have published this use case in ipaw 2010

Lena: I have played with the javascript library for query federation
... how can we publish a voiD description for the gene lists?
... I have added the example queries in the google doc

<ericP> SPARQL -npq \

<ericP> -M '<r12> CONSTRUCT { ?s <p1> ?o1 ; <p2> ?o2 } WHERE { SERVICE <S12> { ?s <p1> ?o1 ; <p2> ?o2 } }' \

<ericP> -M '<r23> CONSTRUCT { ?s <p2> ?o2 ; <p3> ?o3 } WHERE { SERVICE <S23> { ?s <p2> ?o2 ; <p3> ?o3 } }' \

<ericP> -e 'SELECT * WHERE { ?x1 <p1> ?n1 ; <p2> ?n2 ; <p3> ?n3 }'

Kei: can voiD help with decomposing the query

Eric: I am only using my rules in my implementation

Kei: could Lena incorporate the query federation and voiD part for the paper demo?

Lena: Lena will work on this with Eric offline

Kei: summarize the paper status: 1) we should add new authors if appropriate; 2) I completed the introduction section and need to polish it;
... 3) we should continue to work on the google doc in parallel, including the method and implementation sections, and finalize the demo examples;
... 4) we can schedule additional calls for this week

Eric: maybe Lena and I could spend some time together and let the rest of the group know about our findings

<mscottm> I have to go to the Terminology call - bye!

<michael> what is the URL for the go0ogle doc? thanks

we will have an intermediate call this Friday, 12:00 EST, using the hcls line

<ericP> eric+google@w3.org

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Got date from IRC log name: 16 Aug 2010
Guessing minutes URL: http://www.w3.org/2010/08/16-hcls-minutes.html
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