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14:57:08 <kei> Zakim, this will be BioRDF
14:57:08 <Zakim> ok, kei; I see SW_HCLS(BioRDF)11:00AM scheduled to start in 3 minutes
14:57:26 <kei> agenda +introduction [Kei]
14:57:45 <kei> agenda+ +paper submission [All]
14:57:54 <kei> take up next agendum
14:59:11 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
14:59:17 <Zakim> + +1.832.386.aaaa
15:00:00 <Zakim> +Kei_Cheung
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15:02:39 <Zakim> + +1.206.484.aabb
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15:03:20 <Zakim> +[IPcaller]
15:03:35 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
15:03:35 <Zakim> +matthias_samwald; got it
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15:05:49 <matthias_samwald> scribenick: matthias_samwald
15:06:09 <matthias_samwald> kei: over the last days i spent time on editing the discussion section
15:06:39 <Zakim> +mscottm
15:06:53 <matthias_samwald> ... smoother, more readable. i did not delete the old text, so others can have a look and possibly add. i highlighted it in yellow.
15:07:57 <matthias_samwald> ... we made a lot of good progress
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15:09:12 <matthias_samwald> ... how far are we with the examples? 
15:09:33 <matthias_samwald> lena: all federated queries are now also on the demo
15:09:34 <Lena> http://ibl.mdanderson.org/~mhdeus/BioRDF/microarray/sparql_endpoint.html
15:09:48 <matthias_samwald> lena: on that page, you can find the six demo queries
15:10:28 <matthias_samwald> kei: is this the full gene list?
15:10:37 <matthias_samwald> lena: this is a small subset
15:11:15 <Lena> http://mibupload.com/u0PSbD.xml 
15:11:38 <Lena> (never mind this link)
15:11:47 <matthias_samwald> kei: the first queries are querying the gene lists themselves
15:12:03 <matthias_samwald> ... what type of brain regions, disease etc.
15:12:23 <matthias_samwald> ... also something about the data themselves (same software package etc.)
15:12:30 <matthias_samwald> ... looks pretty good to me
15:12:50 <matthias_samwald> ... the last queries focus more on query federation
15:13:00 <matthias_samwald> ... these queries also make use of the origins of the datasets
15:13:23 <matthias_samwald> lena: see Q4
15:13:44 <matthias_samwald> ... as scott suggested, i used the VoID vocabulary.
15:14:50 <matthias_samwald> lena: if you click on the query, the SPARQL query is automatically entered.
15:16:29 <matthias_samwald> lena: for the federated queries -- it does not work on some browsers
15:17:39 <matthias_samwald> michael: would it be possible to have a query that returns all the genes in the final gene list?
15:18:21 <matthias_samwald> michael: i.e., the simple final gene list for a certain experiment.
15:18:44 <matthias_samwald> michael: most of these queries do not return much information, it would be nice to know what the basic information available is
15:19:47 <matthias_samwald> lena: for the first gene list there are 162
15:20:01 <matthias_samwald> lena: i can use VoID for that kind of information
15:21:48 <matthias_samwald> egon: the vocabulary predicate you are using on diseasome, what are you doing with that?
15:22:55 <matthias_samwald> lena: what we are doing for all datasets that have been annotated with that vocabulary.
15:23:11 <matthias_samwald> ... gives us certainty that we are finding the things we are looking for
15:23:27 <matthias_samwald> egon: but are you referring to diseasome as a dataset? it is not.
15:24:21 <mscottm> I am talking about this part of a query:    OPTIONAL {      [ rdf:type void:Dataset ;        void:sparqlEndpoint ?srvc2 ;        void:vocabulary <http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/> ;        dct:issued ?issued2 ] . FILTER (?issued2 > ?issued)
15:24:27 <matthias_samwald> kei: is it a language or vocabulary? how do you use VoID so that machine knows that this dataset has to do with this certain set of diseases.
15:25:15 <matthias_samwald> s/egon/scott/
15:25:35 <matthias_samwald> (sorry, audio quality is quite bad, hard to discern people)
15:27:09 <Lena> void guide: http://semanticweb.org/wiki/VoiD
15:29:29 <matthias_samwald> kei: the concern is: when we are using VoID to describe data origins, how is the data provenance actually captured by VoiD?
15:29:54 <matthias_samwald> lena: you can describe subjects (e.g. "gene").
15:31:27 <kei> I can't hear what Lena said
15:32:03 <Zakim> +EricP
15:33:14 <Lena> +351 21 4469852
15:33:58 <Zakim> - +1.832.386.aaaa
15:34:38 <mscottm> Thank you Eric!
15:34:54 <ericP> the part of Lilly Tomlin's "Operator" will be played by ericP today
15:36:04 <matthias_samwald> lena: to find all datasets that have to do with genes, i would have to figure out the URI -- it is easier with the VoiD vocabulary.
15:36:17 <matthias_samwald> scott: diseasome is not a vocabulary, but a dataset
15:36:18 <ericP> Zakim, who is speaking?
15:36:30 <Zakim> ericP, listening for 10 seconds I heard sound from the following: EricP (63%)
15:37:07 <matthias_samwald> lena: you still have to say what is a disease by indicating a full URL
15:37:37 <matthias_samwald> ... we need a dataset of genes AND diseases
15:38:13 <matthias_samwald> scott: VoID just gives you means to talk about a graph
15:39:27 <matthias_samwald> kei: would it be a lot of work to switch to that use of subject?
15:39:42 <matthias_samwald> ... to make the semantics a bit more understandable
15:39:59 <matthias_samwald> lena: okay. this is easy to change.
15:43:11 <ericP> uname -a
15:43:43 <matthias_samwald> (lena and eric talk about issues with 32 vs. 64 bit version of federation software)
15:45:11 <matthias_samwald> eric: but this is not critical for the paper
15:46:10 <matthias_samwald> kei: for the paper the review period is quite sure (in the next 3 weeks)
15:46:53 <matthias_samwald> eric: the second query we are working on, i got too many resoultions from one endpoint, we need to figure out how to solve this.
15:49:07 <matthias_samwald> kei: the query that makes use of PharmGKB is a good example. we do not need to get into biological details for this paper, though.
15:49:54 <matthias_samwald> lena: there would not be enough papers, also the reviewers would not understand.
15:51:40 <matthias_samwald> scott: about the NCBO sparql endpoint: i don't know if there is a way with this microarray scenario. we would need an appropriate vocabulary (e.g. for diseases). but this is a level of provenance that is not fully formalized on the NCBO sparql endpoint. 
15:52:42 <matthias_samwald> ... e.g., a query that finds all datasets about neurodegenerative diseases -- that would be possible
15:54:03 <matthias_samwald> ... another example: if you have a list of neurodegenerative diseases (based on ontology), then you can find data from other neurodegenarative diseases
15:55:53 <matthias_samwald> lena: we could trim the list of disesases in Q4 to only neurodegenerative diseases
15:57:41 <matthias_samwald> kei: in terms of the paper, how do we go about finalizing it?
15:58:16 <matthias_samwald> lena: we have to calculate ~1 page for abstract, 1 page for references
15:59:10 <matthias_samwald> lena: most of the results can be deferred to links to web pages
15:59:36 <matthias_samwald> kei: lena, you are the person to do the first cut
16:00:58 <matthias_samwald> kei: still, it is interesting to talk about the data model in the paper and give some examples
16:01:43 <matthias_samwald> lena: i would say keep the diagram, lose the triples. i will make these changes.
16:02:12 <matthias_samwald> kei: the deadline is friday, at one time we need to convert it to the IEEE format. when do we make that switch?
16:02:57 <matthias_samwald> lena: my suggestion is to switch to IEEE on wedenesday and have everyone read it.
16:03:12 <matthias_samwald> lena: on thursday we can still have a conference call and see if we all agree
16:07:00 <matthias_samwald> scott: i would like to have some slides about this work that i can present at Oxford Global Pharma conference in october
16:07:30 <Zakim> -mscottm
16:08:54 <Zakim> -Kei_Cheung
16:08:54 <mscottm> Uh oh - on hcls2 Zakim, I get "This passcode is not valid."
16:08:54 <Zakim> -matthias_samwald
16:08:57 <Zakim> - +1.206.484.aabb
16:09:04 <matthias_samwald> Meeting: BioRDF
16:09:05 <mscottm> Can you help, Eric?
16:09:16 <michael> michael has left #hcls
16:09:24 <matthias_samwald> Chair: Kei Cheung
16:09:24 <kei> RRSAgent, please draft minutes
16:09:24 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/30-hcls-minutes.html kei
16:09:33 <matthias_samwald> Scribe: Matthias Samwald
16:09:33 <kei> RRSAgent, please make log world-visible
16:09:46 <mscottm> ericP - can you help with hcls2 (Terminology)?
16:10:05 <matthias_samwald> RRSAgent, please draft minutes
16:10:05 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/30-hcls-minutes.html matthias_samwald
16:10:41 <matthias_samwald> now it's there. the "make world visible" has to come before the "draft minutes" command.
16:11:11 <matthias_samwald> (i just figured that out recently...)
16:12:02 <Zakim> -EricP
16:12:03 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:12:05 <Zakim> Attendees were +1.832.386.aaaa, Kei_Cheung, +1.206.484.aabb, matthias_samwald, mscottm, EricP
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17:12:32 <ericP> oops
17:17:27 <ericP>       (triple ?targetID <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/geneName> ?OverExpressedGenLabel)
17:17:30 <ericP>       (triple ?drug <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/target> ?targetID)
17:17:33 <ericP>       (triple ?drug <http://www.w3.org/2000/01/rdf-schema#label> ?drugName)
17:17:35 <ericP>       (triple ?drug <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/mechanismOfAction> ?actionMechanism)
17:17:38 <ericP>       (triple ?drug <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/possibleDiseaseTarget> ?disease)
17:17:41 <ericP>       (triple ?disease <http://www.w3.org/2000/01/rdf-schema#label> ?diseaseTarget)
17:17:48 <ericP> ?drugName = "H6PD"
17:18:08 <ericP> ?OverExpressedGenLabel
17:18:39 <ericP> SELECT+DISTINCT+%3FtargetID+%3FOverExpressedGenLabel+%3Fdrug+%3FdrugName+%3FactionMechanism+%3Fdisease+%3FdiseaseTarget+%0AWHERE%0A%7B%0A++%3FtargetID+%3Chttp%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdrugbank%2Fresource%2Fdrugbank%2FgeneName%3E+%3FOverExpressedGenLabel+.%0A++%3Fdrug+%3Chttp%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdrugbank%2Fresource%2Fdrugbank%2Ftarget%3E+%3FtargetID+.%0A++%3Fdrug+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23label%3E+%3FdrugName+.%0
17:20:17 <ericP> Querying <http://hcls.deri.org/sparql> for
17:20:17 <ericP> query=SELECT+DISTINCT+%3FdiseasomeGene+%3FgeneLabel+%3Fdisease+%3FdiseaseName+%0AWHERE%0A%7B%0A++%3FdiseasomeGene+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23label%3E+%3FgeneLabel+.%0A++%3Fdisease+%3Chttp%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdiseasome%2Fresource%2Fdiseasome%2FassociatedGene%3E+%3FdiseasomeGene+.%0A++%3Fdisease+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23label%3E+%3FdiseaseName+.%0A%7D%0A yielded 9740 results.
17:22:31 <Lena> http://ibl.mdanderson.org/~mhdeus/BioRDF/microarray/diseasome_query_results.htm
17:30:09 <ericP> http://swobjects.svn.sourceforge.net/viewvc/swobjects/branches/sparql11/lib/SWObjects.cpp?revision=1236&view=markup&sortby=date#l1476
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18:38:55 <ericP> hi Lena, no progress. http://www.w3.org/2001/sw/rdb2rdf/directGraph/ coopted my attention
18:42:02 <Lena> lol
18:42:23 <Lena> i have almost a new full dataset for you :-)
18:42:41 <Lena> in the meanwhile, keep crashing my computer trying to parse it
19:02:35 <ericP> that's the 64big machine, right?
19:07:22 <Lena> no, windows
19:07:39 <Lena> ( crashing probability is higher :-) )
19:08:18 <Lena> going home.. will probably be back online in about 1 hour
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