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15:05:39 <RRSAgent> logging to http://www.w3.org/2010/08/23-hcls-irc
15:05:44 <matthias_samwald> zakim, this is hcls
15:05:44 <Zakim> ok, matthias_samwald; that matches SW_HCLS(BioRDF)11:00AM
15:05:55 <jun> zakim, this is biordf
15:05:55 <Zakim> jun, this was already SW_HCLS(BioRDF)11:00AM
15:05:57 <Zakim> ok, jun; that matches SW_HCLS(BioRDF)11:00AM
15:06:33 <matthias_samwald> scribenick: matthias_samwald
15:07:08 <Zakim> +[IPcaller]
15:08:16 <kei> kei has joined #HCLS
15:10:37 <matthias_samwald> kei: deadline for paper is 27., last week we had an extra meeting, over the weekend i revised introduction and abstract of the article, also added more references.
15:10:47 <matthias_samwald> kei: i also added acknowledgements.
15:11:08 <matthias_samwald> ... jun, maybe you can give us an update?
15:11:40 <matthias_samwald> jun: i had a look at the paper this morning, i did not manage to do work over weekend
15:12:01 <matthias_samwald> ... lena said she managed to give example for level 2 and level 3 provenance data
15:12:17 <matthias_samwald> ... i looked into MIAME protocols
15:12:24 <jun> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5281
15:12:27 <matthias_samwald> ... i found one for the second paper
15:14:08 <matthias_samwald> ... we can use tool by (?) from EBI which can transform XML into RDF
15:14:39 <matthias_samwald> s/EBI/RPI/
15:15:18 <mscottm> mscottm has joined #hcls
15:15:22 <matthias_samwald> kei: our focus has been the processed, relevant gene list
15:15:26 <jun> James McCuster
15:16:38 <matthias_samwald> michael: this is based on MAGE-ML, not MAGE-TAB
15:16:56 <Zakim> +mscottm
15:17:16 <mscottm> sorry - technical difficulties
15:17:25 <matthias_samwald> kei: anyways, these data are not containing gene lists in that sense.
15:17:28 <mscottm> joined now
15:18:08 <matthias_samwald> jun: i hope to finish this work by tomorrow and describe it in the google doc.
15:19:00 <matthias_samwald> kei: it is a bit confusing that there are so many ontologies describing diseases
15:19:14 <matthias_samwald> kei: scott managed the disease ontology, which seems to be quite comprehensive
15:20:38 <matthias_samwald> scott: diesease ontology is indeed comprehensive. if we know which ontology is used to described diseases, that helps us to do automated federation
15:21:22 <matthias_samwald> scott: if you have a purl ID, then you can add statements about the graph to the graph itself.
15:21:52 <matthias_samwald> ... lena told us that that she needs help with that approach
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15:22:20 <matthias_samwald> ... this could also be an example of using provenance for federation
15:22:39 <matthias_samwald> s/managed/mentioned/
15:23:36 <matthias_samwald> kei: eric and lena worked together on query federation.
15:24:05 <matthias_samwald> kei: about the VOID data... jun, can you help lena use the VOID vocabulary?
15:25:29 <matthias_samwald> kei: lena's e-mail said she will be away, i don't know what her availability is during that time.
15:25:51 <matthias_samwald> ... we should still aim to submit the paper on 27.
15:27:22 <matthias_samwald> scott: will be moving back to netherlands soon, that might limit my ability to work on the paper.
15:29:32 <matthias_samwald> kei: we need to finalize the decision on which examples and datasets we will show in the paper.
15:30:25 <matthias_samwald> jun: lena shared the SPARQL endpoint, i can identify other examples while she is away.
15:30:45 <matthias_samwald> kei: i think the RDF representation is very close to final
15:31:02 <matthias_samwald> ... based on that gene list representation we could come up with some examples
15:34:27 <matthias_samwald> scott: queries could be restricted based on projects and consortiums
15:36:24 <matthias_samwald> jun: maybe scott could write these down (e.g. in the motivation section)
15:37:36 <matthias_samwald> scott: also basic information such as "how many statements are in the graph" etc.
15:38:19 <matthias_samwald> kei: maybe we could have an extra call
15:39:19 <matthias_samwald> kei: whoever can join an extra call later this week (e.g. wed/thur) would help
15:39:27 <matthias_samwald> scott: i can make it on those days
15:40:00 <ericP> Zakim, please dial ericP-office
15:40:00 <Zakim> ok, ericP; the call is being made
15:40:01 <Zakim> +EricP
15:40:15 <matthias_samwald> michael: i can make some comments
15:41:06 <matthias_samwald> jun: maximum number of pages is 6
15:41:52 <matthias_samwald> jun: maybe we can delete some of the figures if the page number is exceeded
15:42:13 <matthias_samwald> jun: we can discuss on call later this week
15:42:22 <matthias_samwald> jun: feel free to cut my text if needed.
15:45:36 <matthias_samwald> __ the group agrees to have another teleconference on thursday 26. __
15:46:31 <matthias_samwald> scott: is all the data in the dropbox?
15:46:37 <matthias_samwald> eric: i believe so.
15:48:06 <Zakim> -EricP
15:50:48 <matthias_samwald> scott: simon twigger has done some very good work for microarrays, he is part of NCBO, gave presentation at C-SHALS
15:51:08 <matthias_samwald> ... close to the work we are doing, but we haven't gotten to the level of exchanging RDF graphs
15:52:18 <matthias_samwald> michael: could you please add this to the discussion section?
15:52:22 <matthias_samwald> scott: i will.
15:55:13 <Zakim> - +1.206.605.aaaa
15:55:19 <Zakim> -[IPcaller]
15:55:20 <Zakim> -Kei_Cheung
15:55:22 <matthias_samwald> rrsagent, create minutes
15:55:22 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/23-hcls-minutes.html matthias_samwald
15:55:33 <Zakim> -mscottm
15:55:41 <michael> michael has left #hcls
15:56:39 <matthias_samwald> rrsagent, set logs world-visible
15:57:23 <matthias_samwald> rrsagent, create minutes
15:57:23 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/23-hcls-minutes.html matthias_samwald
15:58:22 <Zakim> -??P11
15:58:28 <matthias_samwald> Meeting: BioRDF
15:58:38 <matthias_samwald> Chair: Kei Cheung
15:58:42 <matthias_samwald> Scribe: Matthias Samwald
15:59:22 <matthias_samwald> rrsagent, create minutes
15:59:22 <RRSAgent> I have made the request to generate http://www.w3.org/2010/08/23-hcls-minutes.html matthias_samwald
15:59:54 <matthias_samwald> zakim, bye
15:59:54 <Zakim> leaving.  As of this point the attendees were Kei_Cheung, +1.206.605.aaaa, [IPcaller], mscottm, EricP
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