14:16:28 RRSAgent has joined #hcls 14:16:28 logging to http://www.w3.org/2010/04/05-hcls-irc 14:16:36 Zakim, this will be BioRDF 14:16:36 ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 44 minutes 14:19:14 jun has joined #hcls 14:59:36 SW_HCLS(BioRDF)11:00AM has now started 14:59:40 mscottm has joined #hcls 14:59:42 +mscottm 15:01:51 +??P1 15:01:58 agarcia2 has joined #HCLS 15:02:01 zakim, ??P1 is jun 15:02:01 +jun; got it 15:03:36 +Kei_Cheung 15:04:35 + +1.832.386.aaaa 15:05:54 + +1.937.775.aabb 15:06:53 +??P5 15:08:24 scribenick jun 15:08:59 Topic: express gene lists in RDF format 15:10:06 Kei: try to have an RDf graph with minimal semantics to see whether we can answer some example queries 15:10:39 LenaDeus has joined #hcls 15:10:40 Kei: Jun, Satya and me are in the process of creating a new version of RDF structure to describe the microarray gene lists 15:11:12 Kei: we also want to use this use case to link up with the scientific discource+experiemnt+data sub-task force 15:11:20 can anyone post here the link to the latest version of the gene list, please :) 15:12:22 Kei: finally we will discuss future query federation demos 15:12:31 http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2 15:12:47 you can find the gene lists in the RDF structure section 15:13:41 Scott: anyone plans to talk to James Malone? 15:14:08 Kei: I have invited James to join us in one of the BioRDF calls 15:14:40 http://esw.w3.org/images/0/08/RDF_genelists.pdf 15:14:56 http://code.google.com/u/mccusker/ 15:15:04 jim mccusker 15:15:05 s/Malone/Mccusker/ 15:15:09 http://code.google.com/p/magetab2rdf/ 15:16:59 Scott: our bioRDF work seems a lot of overlaps with Jim's work 15:18:03 ssahoo2 has joined #HCLS 15:18:06 Topic: gene lists discussion 15:18:32 Kei: http://esw.w3.org/images/0/08/RDF_genelists.pdf 15:20:21 Kei: in the tables you can see there are gene-specific information and sample-specific information 15:22:01 Kei: I tried to come up with an RDF structure to describe such data 15:23:36 Kei: Lena created an initial draft of RDF and Satya and Jun are refining it 15:24:41 Kei: more example queries have been added to the wiki page http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2 15:25:42 Lena: what is the microarray ** used in the study might also be useful? 15:26:16 Kei: there are such information in the papers publishing these genes, such as algorithms, statistics methods used in the microarray experiemnts 15:28:53 Satya: I created an OWL ontology and Jun should use it to create the RDF graph conforming to the ontology 15:29:29 Satya: next step could be trying to run the queries 15:29:49 find genelists that involve AD, pyramidal neuron, 15:29:49 mouse, and 15:29:58 hippocampus 15:30:30 http://esw.w3.org/images/7/77/Genelists_20100404_jun.pdf 15:37:51 Satya's ontology: http://esw.w3.org/images/b/b3/Biordfmicroarray-satya-0401.owl.pdf 15:38:08 Jun: Satya and I need to align his ontology and my RDF graph 15:38:09 Is this the origin of the above pdf? : http://knoesis.wright.edu/library/ontologies/provenir/provenir.owl 15:38:32 Satya: we need to align with Scientific Discouse's ontology later, thus we define our ontology in a local namespace atm 15:38:56 Scott: it would be nice to harmonize different ontologies, such as NCBO 15:39:18 Scott: I am working on to get their ontologies through SPARQL endpoints 15:42:20 -??P5 15:45:13 an example term from NIFSTD: Entorhinal Cortex: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_1508 15:48:36 http://www.deg.byu.edu/papers/PODS.integration.pdf 15:51:48 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 15:52:10 Kei: I will also invite Jim to join our call in the future to share his work with us 15:52:36 Lena: shall we use Dropbox to share files? 15:53:27 https://www.dropbox.com/ 15:55:16 the basic/free version is 2GB space 15:55:42 Scott: how do we identify which ontology to use? 15:57:28 Kei: we are aiming at coming up with a first version modelling and then coordinate with the scientific discourse task force 15:57:47 http://www4.wiwiss.fu-berlin.de/diseasome/ 15:58:08 Zakim, who is making noise? 15:58:23 mscottm, listening for 13 seconds I heard sound from the following: mscottm (43%), Kei_Cheung (50%), +1.832.386.aaaa (46%) 15:58:36 the noise was me, sorry :) 15:58:49 Kei: we should look at related data resources once we have the initial gene list in RDF 16:01:22 - +1.937.775.aabb 16:01:24 - +1.832.386.aaaa 16:01:26 -jun 16:06:34 -mscottm 16:06:35 -Kei_Cheung 16:06:35 SW_HCLS(BioRDF)11:00AM has ended 16:06:37 Attendees were mscottm, jun, Kei_Cheung, +1.832.386.aaaa, +1.937.775.aabb 16:31:02 egonw has joined #hcls 16:33:08 rrsagent, set log public 16:33:20 rrsagent, draft minutes 16:33:20 I have made the request to generate http://www.w3.org/2010/04/05-hcls-minutes.html jun 16:43:33 RRSAgent, please draft minutes 16:43:33 I have made the request to generate http://www.w3.org/2010/04/05-hcls-minutes.html kei 16:43:44 RRSAgent, please make log world-visible 16:43:48 RRSAgent, please make log world-visible 19:37:20 egonw has joined #hcls 20:13:16 Zakim has left #hcls 20:15:28 egonw has joined #hcls 22:14:32 mscottm has joined #hcls