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14:56:04 <kei> Zakim, this will be BioRDF
14:56:04 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 4 minutes
14:56:18 <kei> agenda+ introduction [Kei]
14:56:48 <kei> agenda+ rdf representation of genelists [lena, jun, satya, michael, scott]
14:57:05 <kei> agenda+ paper [All]
14:57:16 <kei> Zakim, take up next agendum
14:57:16 <Zakim> agendum 2. "RDF genelist representation" taken up [from Jun, Lena, Satya, Scott, Michael]
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15:01:27 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
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15:01:34 <Zakim> +Kei_Cheung
15:02:16 <Zakim> + +1.510.527.aaaa
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15:03:08 <Zakim> +[IPcaller]
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15:03:25 <jun> zakim, [IPcaller] is jun
15:03:25 <Zakim> +jun; got it
15:03:27 <Zakim> +??P6
15:03:40 <Zakim> +mscottm
15:03:49 <matthias_samwald> zakim, ??P6 is matthias_samwald
15:03:49 <Zakim> +matthias_samwald; got it
15:04:19 <jun> I can scribe
15:05:13 <kei> scribenick lena
15:05:23 <Zakim> - +1.832.386.aabb
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15:08:11 <kei> io-informatics.com
15:08:46 <Zakim> + +1.832.386.aacc
15:09:14 <Lena> Lena has joined #hcls
15:09:25 <Lena> sorry... my internet connection was lost
15:09:57 <Lena> IO informatics is moving towards  integration of biomedical data;
15:10:14 <Lena> mscottm: data sharing in bioinformatics 
15:10:37 <Lena> (sorry... who is talking?)
15:12:31 <mscottm> That was Chuck Raffi (sp?) from IO Informatics
15:12:35 <Lena> kei: been working on data integration using rdf/owl to standardize in machine understandable way
15:13:22 <Lena> kei: provennace, data used to describe experiments; how to link to existing ontologies
15:13:30 <matthias_samwald> lena, you are causing noise while typing.
15:13:50 <Lena> (thaks, just mutted myself :-) )
15:14:29 <Lena> kei: could recommend best practices to facilitate data integration 
15:14:46 <Lena> kei:  could be applied to microaray data but to other datasets as well
15:15:27 <Lena> kei: capture the relationships to support semantic queries
15:16:31 <Lena> kei: finalizing the genelist as soon as possible due to deadline submission approaching
15:17:09 <jun> I think I should talk about Lena
15:17:38 <jun> s/about/after/
15:19:03 <Lena> kei: introduction almost complete
15:20:35 <Lena> kei: possible link to other ontologies (provenir?) that our structure could be related to
15:22:13 <Lena> jun: provenance information is quite rich
15:22:28 <Lena> jun: looking at what used to generate the samples
15:23:21 <Lena> kei: capture the version of software
15:23:42 <Lena> satya: have not modified the ontology
15:25:26 <Lena> jun: doap ( ?) has been used to describe software
15:26:16 <Lena> jun: makes sense to start with the queries and decide how the rdf representation of the data looks like and then represent in the ontology
15:26:54 <jun> http://usefulinc.com/ns/doap#
15:27:02 <Lena> kei: our work should be in line with other existing efforts
15:27:13 <Lena> kei: examples are array express or mged group
15:27:54 <Lena> ssahoo2 (breaking up): ncbo and obi ontologies
15:28:06 <Lena> ssahoo2: making sure we are not re-inventing the wheel
15:28:32 <Lena> ssahoo2: nci thesaurus and other ontologies, need to be careful to avoid re-creating the ontologies
15:29:08 <Lena> mscottm: in contact with EBI who have said that they have not done this yet
15:29:43 <Lena> mscottm: software ontologies have been used
15:30:27 <Lena> kei: look at the rdf structure and see how well the queries can be answered
15:31:05 <Lena> kei: decide what are the unique things that we have contributed and how can we link to other groups work
15:31:07 <mscottm> http://bioportal.bioontology.org/ontologies/42036
15:31:18 <mscottm> http://www.ebi.ac.uk/efo/swo
15:32:30 <Lena> kei: other potential datasets that we can integrate with (pathway/protein/diseasome)
15:33:47 <Lena> kei: scott mentions uniprot dataset
15:34:01 <Lena> mscottm: uniprot has its own rdf representation - not in hcls kb because it is very large
15:34:23 <Lena> mscottm: we can integrate relevant parts of the uniprot datasets
15:34:35 <Lena> kei: interesting to integrate genomics and proteomics
15:35:10 <Lena> mscottm: uniprot datasets behind a sparql endpoint has been done (but used their own flavor of rdf structure)
15:36:00 <Lena> mscottm: sticky point is coordination with others in the community
15:36:10 <Lena> mscottm: is there a way to coordinate with bio2rdf?
15:36:31 <Lena> mscottm: while we are at it, why not integrate shared vocabularies?
15:37:05 <Lena> mscottm: use some of the information in the protein records
15:37:14 <mscottm> http://www.stanford.edu/~coulet/material/ontology/phare.owl
15:37:31 <Lena> mscottm: another source of rdf it's a pharma ontology about genes, drugs and diseases
15:37:52 <Lena> mscottm: put together at ncbo by Adrian Cullet (?)
15:38:02 <Lena> mscottm: the source of information is nlp techniques
15:38:11 <mscottm> http://sparql.bioontology.org/webui
15:38:16 <Lena> mscottm: (not a text miner)
15:38:18 <mscottm> http://www.stanford.edu/~coulet/material/sparql_queries
15:38:44 <Lena> mscottm: already behind a sparql endpoint
15:39:43 <Lena> scott agreed to coordinate with other sparql endpoints
15:40:35 <Lena> matthias_samwald: annotating some of the text associated with the microarray studies
15:40:45 <Lena> matthias_samwald: need to know which kinds of studies did we chose
15:42:15 <Lena> mscottm: use void
15:42:37 <Lena> mscottm: void statement can be inserted into the graph itself
15:42:52 <Lena> mscottm: can also put the statement in the second graph
15:43:19 <Lena> mscottm: use void to refer to who created a particular statement
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15:46:05 <ssahoo2> to follow up on Scott's idea - should we treat Lena's RDF file and Jun's RDF file as two separate sources?
15:46:28 <Lena> satya - they are not separate representations, they are follow ups
15:46:56 <Lena> the name at the end of the files is not its owner but the latest person who made the modifications
15:47:15 <Lena> mscottm: idea is coming up with interesting provenance information
15:47:53 <ssahoo2> right - we add distinct named graph ids with each of the ttl files and issue a federated SPARQL query directed to each named graph
15:48:09 <mscottm> yes
15:48:23 <ssahoo2> ok
15:48:58 <Lena> http://ibl.mdanderson.org/~mhdeus/sparql_federation/endpoint2.php
15:52:05 <jun> yes, sure
15:52:13 <ssahoo2> yes
15:53:35 <Lena> matthias_samwald: if we focus on some example it is easier to connect to other sources
15:54:06 <Lena> kei: think about some example queries that will give broader integration with other types of data
15:54:58 <Lena> mscottm: will look into how niff is doing relatively to its work with microarrays
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15:56:27 <Lena> mscottm: problem is our focus queries are too directed to the neurosciences, but not so much towards provenance
15:56:46 <Lena> kei: jun is adding the provenance dimension to the paper
15:58:16 <Lena> mscottm: if we know where the genelist came from and the microarray experiment, we can come up with the experiments as results from previous provenance queries
15:58:35 <Lena> mscottm: we can build a query that preceeds the selection of the 3 datasets
15:58:48 <Lena> kei: all the examples are affy platforms, but different statistical approachas
16:02:49 <Lena> kei: main tasks - get the examples working!
16:03:29 <Zakim> -matthias_samwald
16:03:41 <Zakim> -jun
16:03:48 <mscottm> mscottmarshall@gmail.com 
16:03:53 <Zakim> -??P3
16:04:07 <Zakim> - +1.832.386.aacc
16:04:11 <Zakim> -mscottm
16:04:14 <kei>  RRSAgent, please draft minutes
16:04:14 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/09-hcls-minutes.html kei
16:04:15 <Zakim> - +1.510.527.aaaa
16:04:23 <kei> RRSAgent, please make log world-visible
16:09:14 <Zakim> disconnecting the lone participant, Kei_Cheung, in SW_HCLS(BioRDF)11:00AM
16:09:18 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:09:20 <Zakim> Attendees were Kei_Cheung, +1.510.527.aaaa, +1.832.386.aabb, jun, mscottm, matthias_samwald, +1.832.386.aacc
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