15:55:42 <RRSAgent> RRSAgent has joined #HCLS
15:55:42 <RRSAgent> logging to http://www.w3.org/2012/02/14-HCLS-irc
15:56:18 <michel> Meeting: W3C HCLS – Life Sciences Forum
15:56:21 <ericP> Zakim, this will be hcls
15:56:21 <Zakim> ok, ericP; I see SW_HCLS()11:00AM scheduled to start in 4 minutes
15:56:23 <michel> Chair: michel
15:56:33 <Zakim> SW_HCLS()11:00AM has now started
15:56:34 <michel> zakim, this is hcls
15:56:34 <Zakim> michel, this was already SW_HCLS()11:00AM
15:56:35 <Zakim> +EricP
15:56:35 <Zakim> ok, michel; that matches SW_HCLS()11:00AM
15:57:36 <Zakim> +[IPcaller]
15:57:46 <michel> zakim, [IPcaller] is michel
15:57:46 <Zakim> +michel; got it
16:00:32 <amrapali> amrapali has joined #hcls
16:00:37 <jun> jun has joined #hcls
16:01:38 <Zakim> + +1.510.541.aaaa
16:01:45 <Helena> Helena has joined #hcls
16:01:53 <Zakim> + +1.832.386.aabb
16:02:16 <Zakim> +Joseph_Scheuhammer
16:02:26 <Zakim> +ScottB
16:02:33 <JP> JP has joined #HCLS
16:02:44 <Zakim> + +1.215.239.aacc
16:02:51 <iker> iker has joined #hcls
16:03:03 <ericP> Zakim, aacc is iker 
16:03:03 <Zakim> +iker; got it
16:03:04 <michel> zakim, +1.215.239.aacc is iker
16:03:05 <Zakim> sorry, michel, I do not recognize a party named '+1.215.239.aacc'
16:03:15 <Zakim> +[IPcaller]
16:03:24 <jun> zakim, [IPcaller] is jun
16:03:24 <Zakim> +jun; got it
16:03:34 <ericP> Zakim, who is here?
16:03:34 <Zakim> On the phone I see EricP, michel, +1.510.541.aaaa, +1.832.386.aabb, Joseph_Scheuhammer, ScottB, iker, jun
16:03:36 <mscottm2> mscottm2 has joined #hcls
16:03:37 <Zakim> On IRC I see iker, JP, Helena, jun, amrapali, RRSAgent, Zakim, michel, MacTed, egonw_, ericP
16:03:38 <epichler> epichler has joined #HCLS
16:03:50 <Helena> zakim, +1.832.386.aabb is me
16:03:50 <Zakim> +Helena; got it
16:04:34 <matthias_samwald> matthias_samwald has joined #hcls
16:05:22 <Zakim> +[IPcaller]
16:05:35 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
16:05:35 <Zakim> +matthias_samwald; got it
16:05:38 <Helena> http://www.w3.org/2011/prov/wiki/Main_Page
16:05:51 <mscottm2> Have been trying to dialin but keep getting "This passcode is not valid."
16:06:29 <Zakim> + +31.62.427.aadd
16:06:51 <mscottm2> Zakim, +31.62.427.aadd is mscottm2
16:06:51 <Zakim> +mscottm2; got it
16:06:53 <matthias_samwald> "hcls" passcode worked for me
16:07:11 <matthias_samwald> oh, you made it by now.
16:07:37 <mscottm2> Yeah, 4x a charm. :)
16:08:39 <Zakim> +Philippe
16:08:43 <Zakim> -EricP
16:08:57 <mscottm2> http://www.w3.org/TR/2012/WD-prov-primer-20120110/
16:10:02 <michel> lena: can use provenance model on tcga dataset 
16:11:04 <Zakim> + +1.514.864.aaee
16:13:16 <mscottm2> Zakim, who is making noise?
16:13:32 <Zakim> mscottm2, listening for 13 seconds I heard sound from the following: michel (65%), ericP (7%)
16:16:52 <mscottm2> From Richard Boyce: For the SciDisc Use Case, we have created a set of web pages that show a very basic demo of one way that a drug package insert might be flagged to claims present in the other knowledge sources on the semantic web.
16:16:52 <mscottm2> http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/outfiles/
16:16:52 <mscottm2> Each web page shows DailyMed Structured Product Label sections (posted on the new linkedSPL endpoint <http://tinyurl.com/7b5rtpk>) that have been linked to 1) claims present in the linked data version of the Drug Interaction Knowledge Base (http://dbmi-icode-01.dbmi.pitt.edu:2020/) and 2) published results from studies involving the drug's active ingredient that have been registered in clinicaltrials.gov (via LinkedCT). I will discuss the use case and demo at
16:17:39 <michel> https://02.chat.mibbit.com/?server=irc.w3.org:6665&channel=%23hcls
16:18:02 <michel> http://goo.gl/RPjOE
16:18:19 <junz> junz has joined #hcls
16:19:05 <jun> that link works fine for me. just tested it
16:20:29 <michel> mscottm2: biordf group - expression rdf w3c note
16:21:32 <michel> ... gives guidelines for producing rdf on differentially expressed genes, experimental conditions
16:22:00 <michel> ... getting people around the table fged, arrayexpress, more confidence in rdf created
16:22:23 <michel> ... workshop article shows show to interconvert between representations
16:23:27 <michel> ... tutorial aspect needs to be developed in the note - R script from jim mccusker to generate the rdf; python scripts from io informatics; other tools
16:24:11 <michel> ... rdf representation + how to use it with other tools to perform analysis; take the results and do something with it
16:25:09 <Zakim> -ScottB
16:25:15 <michel> ... looking at putting a SPARQL interface to synapse (API from sage bionetworks)
16:26:18 <michel> ... includes snp data, patient data
16:27:15 <michel> matthias: seems that main access is now api, no file download
16:28:18 <michel> mscottm2: are they interested in linked open data? further discussion required
16:28:40 <michel> ... focus on network biology
16:28:52 <michel> ... goals are close; should be possible to work together
16:29:23 <michel> ... stephen friend has raised some $16M in a years time, sage bionetworks have many partners in pharma
16:30:42 <mscottm2> i did get a chance to talk with mike about synapse and the semantic web.
16:30:42 <mscottm2> if i understood him right, currently he doesn't believe there really is a
16:30:42 <mscottm2> good use case to making the data available as a sparql end point.  i kind
16:30:42 <mscottm2> of agree that HCLS hasn't made a compelling case for this yet.  but, on
16:30:42 <mscottm2> the other hand, mike is working with NCBO in developing an ontology that
16:30:43 <mscottm2> describes and drives how synapse works, which will be published via
16:30:45 <mscottm2> bioportal.  this concept is like what i worked on with mike at teranode,
16:30:47 <mscottm2> where our customers (who, sadly, never came to be) would describe their
16:30:49 <mscottm2> business process (how the drug pipeline worked, who reported to who,...)
16:30:51 <mscottm2> and that would drive the UI and what options users had.
16:31:18 <mscottm2> http://synapse.sagebase.org/#DatasetsHome:0
16:31:23 <mscottm2> http://sagebase.org/research/Synapse1.php
16:32:07 <Zakim> - +1.514.864.aaee
16:34:43 <mscottm2> re:eric's comments - I was hoping for a database connector (as usual :) )
16:34:52 <ericP> naturally
16:35:23 <michel> mscottm2: lodd
16:36:02 <michel> ... paper in journal of web semantics - should be published soon 
16:36:17 <michel> ... w3c note derived from this without the use cases
16:36:28 <michel> ... solicited comments, got a few
16:37:15 <michel> ... pretty close to being done
16:37:19 <michel> ... more comments welcome
16:37:45 <michel> ... next discussion will be about future work
16:37:51 <michel> ... and approval
16:37:55 <iker> @scott, could you send the link to the note please?
16:38:20 <michel> http://goo.gl/r15nL
16:38:25 <iker> thanks
16:39:56 <michel> mscottm2: biohackathon 2011 got some people together to come up with a vocabulary to describe datasets (beyond void, etc)
16:40:22 <Helena> (i think the  document is ready for publication as a working draft or something of the sort )
16:42:39 <Helena> (that would actually push us to finalize it, I think :) )
16:43:02 <iker> q+
16:44:19 <michel> ack
16:44:37 <michel> ack iker
16:46:17 <mscottm2> https://docs.google.com/document/d/1qVSZ1n334fTTchCWS2tOaEL6z-H12pcqty98jQIg6nw/edit
16:47:45 <Helena> q+
16:48:25 <Helena> q-
16:48:41 <Helena> (never mind, was going to mention void, but now i saw it there in the document :) )
16:49:11 <Zakim> -Joseph_Scheuhammer
16:51:25 <michel> lena: signaling pathway leads to death; take list of proteins, go in tcga by exposing the data as rdf, snps/expression. idea is to look at what is happening in the pathway at several layers of biological info, see if the changes are localized
16:51:41 <michel> ... gene, protein, snps, epigenetics
16:52:18 <ericP> agenda+ bio-hackathon around BOS
16:53:14 <michel> ... patterns were previously uncovered; 1st layer epigenetics, 2nd layer snps, 3rd layer gene expression
16:53:32 <michel> ... 4th layer protein expression 
16:54:48 <michel> ... lots of  data (terabytes?), better to target specific data
16:55:47 <Helena> https://sites.google.com/site/simsciencesnuig/project-ssg--004
16:56:08 <iker> IMO sounds really interesting!!
16:56:45 <iker> @michel, do you have a couple of minutes after the call?
16:56:45 <mscottm2> Persons who discover new tools relevant to the HCLSIG can Tweet it using the hashtag #hclstool and I will periodically aggregate tweets with that hashtag and add these tools to the HCLSIG wiki <http://www.w3.org/wiki/HCLSIG/Tools>.
16:57:40 <michel> ericP: biohackathon in Boston in June?
16:58:45 <Helena> Yes!
16:59:56 <jun> Will try if I can get the visa for another meeting in June in USA
17:00:44 <iker> @ericP could you send a link to the Biohackathon website?
17:01:48 <jun> How about having one in Europe too?:)
17:02:12 <mscottm2> Ideas for experts: Paul Groth - http://www.youtube.com/OpenPHACTS
17:02:27 <mscottm2> Lee Harland (Pistoia, OpenPHACTS tech lead)
17:02:33 <Zakim> - +1.510.541.aaaa
17:02:37 <Zakim> -Helena
17:02:41 <Zakim> -matthias_samwald
17:02:43 <Zakim> -jun
17:02:43 <Zakim> -ericP
17:08:39 <mscottm2> http://www.ebusiness-unibw.org/tools/goodrelations-annotator/
17:09:14 <michel> rrsagent, draft minutes
17:09:14 <RRSAgent> I have made the request to generate http://www.w3.org/2012/02/14-HCLS-minutes.html michel
17:09:20 <michel> rrsagent, make log world-visible
17:12:47 <Zakim> -iker
17:12:48 <Zakim> -mscottm2
17:12:48 <Zakim> -michel
17:12:50 <Zakim> SW_HCLS()11:00AM has ended
17:12:50 <Zakim> Attendees were EricP, michel, +1.510.541.aaaa, Joseph_Scheuhammer, ScottB, +1.215.239.aacc, iker, jun, Helena, matthias_samwald, mscottm2, +1.514.864.aaee
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