15:55:37 <RRSAgent> RRSAgent has joined #hcls
15:55:37 <RRSAgent> logging to http://www.w3.org/2010/12/02-hcls-irc
16:04:15 <Susie> Susie has joined #hcls
16:05:14 <Joanne> Joanne has joined #hcls
16:05:33 <Joanne> I couldn't get on the mbit client
16:07:29 <mscottm> Zakim, pick a victim
16:07:29 <Zakim> sorry, mscottm, I don't know what conference this is
16:07:35 <mscottm> zakim, this is hcls
16:07:35 <Zakim> ok, mscottm; that matches SW_HCLS()11:00AM
16:07:36 <mscottm> Zakim, pick a victim
16:07:36 <Zakim> Not knowing who is chairing or who scribed recently, I propose +1.610.651.aacc
16:07:48 <ericP> Zakim, please dial ericP-office
16:07:48 <Zakim> ok, ericP; the call is being made
16:07:50 <Zakim> +EricP
16:08:26 <ericP> Zakim, who is here?
16:08:26 <Zakim> On the phone I see +1.860.440.aabb, mscottm, +1.610.651.aacc, epichler, +1.518.276.aadd, ??P7, EricP
16:08:31 <Zakim> On IRC I see Joanne, Susie, RRSAgent, Zakim, mscottm, ericP
16:08:40 <Zakim> +Bob_Powers
16:08:48 <Susie> Scott gives update on BioRDF
16:08:50 <Joanne> I'm 518
16:09:02 <Zakim> + +1.617.947.aaee
16:09:16 <ericP> Zakim, please mute +1.617.947.aaee
16:09:16 <Zakim> +1.617.947.aaee should now be muted
16:09:41 <Susie> Presentation from Adrian Coulet
16:09:56 <Susie> Did work on text mining using PharmGKB
16:10:01 <Bob> Bob has joined #hcls
16:10:08 <michel> michel has joined #HCLS
16:10:12 <Susie> And created an ontology from that data
16:10:32 <Susie> Also presentation from Dietrich RS on SESL
16:10:45 <Zakim> - +1.617.947.aaee
16:10:47 <Susie> It has many ties to what we are doing
16:11:07 <Zakim> + +1.617.947.aaff
16:11:37 <Susie> Using microarrays in both projects
16:11:53 <Susie> We've been looking at federation with SPARQL
16:12:06 <Susie> Will give tutorial on this topic at SWAT4LS next week
16:12:06 <ericP> Zakim, please mute +1.617.947.aaff
16:12:06 <Zakim> +1.617.947.aaff should now be muted
16:12:19 <Susie> EricP will dial in remotely for this
16:12:21 <michel1> michel1 has joined #HCLS
16:12:57 <Susie> Will use Uniprot and GO annotations from UCSC
16:13:30 <Susie> Similar to what we started to do with the microarray data
16:14:11 <Susie> Continue to work on type of RDF to represent microarray data
16:14:32 <Susie> Will work with scientific discourse and array express
16:15:06 <ericP> Zakim, unmute +1.617.947.aaff
16:15:06 <Zakim> +1.617.947.aaff should no longer be muted
16:15:20 <Susie> Tim talks about scientific discourse
16:16:02 <Susie> one thread align swan, obi and myexperiment with microarray representation
16:16:09 <Susie> using mged and obi for that
16:16:41 <Susie> set up relationship with Susanna Santone at University of Oxford, and Philippe
16:17:01 <Susie> being done with swan, myexperiment and obi
16:17:25 <Susie> will be able to represent experiments using genetic epidemiology or population studies
16:17:48 <Susie> Have the data in private db and then release publicly when ready
16:17:52 <mscottm> ISATAB - ISATools, ISACreator, etc.
16:18:11 <Susie> columns are aligned to identifiers in ontologies
16:18:23 <Susie> excel workbook with tabs for entities 
16:18:38 <mscottm> http://www.slideshare.net/proccaserra/hcls-sci-discisa2rdf
16:19:24 <Susie> also working on rhetorical document structure which is lead by Anita de Waard
16:19:34 <Susie> Has sub-comments, 1 is orb
16:19:54 <Susie> Tudor Groza is working on an HCLS note on that topic
16:20:10 <Susie> Also a mid-grain ontology in a draft form, which was proposed by Elsevier
16:20:22 <Susie> Fine grained ontology by David Shotton and others
16:20:41 <Susie> Moving towards supporting the text mining community
16:21:11 <Bob> Tim: supporting the text-mining community is a good way to advance linked data
16:23:32 <Susie> Ontologies are beginning to form a nice dense web of models
16:25:00 <Susie> Scott talks about terminology
16:25:11 <Susie> Progress on mamagram use case
16:25:47 <Susie> Talk about ways to prototype ideas relating to discrepancies between reports
16:26:05 <Susie> John Madden has reports in XML that he's seeing if we can start with
16:26:32 <Susie> Aiming to put in an NIH grant, but will need to have finished prototyping in order to write it up
16:26:47 <Susie> Eric gives update on COI
16:27:24 <Susie> NCI work on adding semantics to web services is happening in COI wiki space
16:27:40 <Susie> Hasn't started his contract there yet
16:28:07 <Susie> NCBO seminar yesterday that referenced this work
16:29:01 <Susie> Susie update on LODD
16:29:05 <Bob> "Google it up" is now a verb.
16:29:11 <mscottm> scribenick: mscottm
16:29:17 <ericP> -> http://www.bioontology.org/webinar-series NCBO webinar list
16:29:30 <mscottm> Susie: We're working to finish the paper for J. of Cheminformatics
16:29:48 <mscottm> ..will refer to recent RDF data, and the Allen Brain Atlas work.
16:30:13 <mscottm> ..Still interested in writing a Best Practices document. We'll move to that as soon as the paper is done.
16:30:18 <ericP> -> http://www.bioontology.org/sites/default/files/NCBO_Webinar_20101201_caBIG_DavidHau.pdf slides for Dav Hau's NCI webinar at NCBO
16:30:47 <mscottm> ..We will also consider the role of LODD. One role: LODD could be a useful place for people to publish their data.
16:31:02 <Joanne> thanks Eric (you're faster than I am - I was just back to the window to paste!)
16:31:07 <mscottm> ..With time, I think that there should be more effective search mechanisms but this is a good start.
16:31:45 <mscottm> ..With my role in PRISM, we are interested in creating a document about our data needs for distribution to NCI, NCBI, and Pistoia.
16:32:10 <mscottm> ..Interested in working with other organizations to create quality standards for linked data.
16:32:33 <mscottm> Joanne: RPI is involved with U.S. and UK gov linked data.
16:33:00 <mscottm> Susie: PRISM is interested in creating quality standards for Pharma.
16:33:01 <michel> question: what does "high quality" mean
16:33:24 <mscottm> scott's definition: annotated with provenance
16:33:51 <mscottm> Joanne: RPI would be interested in any service of URIs and linked data.
16:33:52 <ericP> -> https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=46376657&rKey=21d56b8b169a3a31 WEBEX recording on Dav Hau's NCI webinar at NCBO
16:34:17 <mscottm> Susie: We'll keep you posted on our progress.
16:34:59 <Bob> Susie: Quality = make sure data are linked together so makes sense
16:35:58 <Bob> ...quality also means a service level of availability
16:36:00 <mscottm> Susie: Make sure that there are links between things that are supposed to be the same.
16:36:25 <mscottm> scribenick: Susie
16:36:31 <Susie> Michel updates on TMO
16:36:39 <Susie> Submitted paper on J. Biomedical Semantics
16:36:44 <Susie> Lead by Jim and Joanne
16:37:01 <Susie> Nice section by EricP on unit testing for ontology development
16:37:34 <Susie> Considering next areas of work
16:37:45 <Susie> Representing genetic variations is of intrest
16:37:58 <Susie> Want to represent htis information accurately
16:38:06 <Susie> Want to do more work to integrate with other ontologies
16:38:14 <Susie> Want working eHR system
16:38:36 <Susie> Should look at options that are free and available, that have web interface, support for terminology
16:39:09 <ericP> Zakim, who is making noise?
16:39:13 <mscottm> Zakim, who is making noise?
16:39:22 <Zakim> ericP, listening for 12 seconds I could not identify any sounds
16:39:34 <Zakim> mscottm, listening for 10 seconds I could not identify any sounds
16:39:50 <Susie> joanne: we still have some clean up work for the paper
16:40:09 <Susie> joanne: want to work with a hospital or ctsa center
16:41:06 <ericP> q+ to talk about i2b2
16:41:15 <Bob> Susie: Been pondering collaborating w i2b2, Kohane's lab
16:41:43 <michel> q+ to talk about openmrs
16:41:44 <Bob> ...there is ontology hive inside i2b2
16:41:59 <Susie> joanne: want to make a valuable contribution
16:42:59 <Bob> Susie: We have agreed to share our extended i2b2 platform
16:44:02 <Bob> Scott: Any EHR project in IMI?
16:44:29 <Susie> JJ& is involved in the UBIOPRED and BTCure projects, and also one in oncology
16:44:31 <mscottm> I know of EHR4CR
16:44:40 <ericP> q?
16:45:20 <Bob> Scott: OPS Open Pharmacological Space
16:46:46 <Bob> Susie: Integrating omics data for clinical trials, etc, rather than for patient records per se
16:46:48 <ericP> q!
16:47:23 <ericP> Zakim, ack 
16:47:23 <Zakim> I don't understand 'ack', ericP
16:47:24 <ericP> Zakim, ack me
16:47:24 <Zakim> ericP, you wanted to talk about i2b2
16:47:25 <Susie> tranSMART
16:47:26 <Zakim> I see michel on the speaker queue
16:48:07 <Susie> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914663/
16:48:34 <mscottm> Zakim, ack michel
16:48:34 <Zakim> michel, you wanted to talk about openmrs
16:48:35 <Zakim> I see no one on the speaker queue
16:50:13 <Bob> Michel: We seem to be fragmenting among various task forces
16:50:52 <Bob> Eric: Where would we develop interface code? Which source do we acquire first?
16:50:55 <Susie> Michel: could we use i2b2 as a rally point?
16:51:56 <Susie> Eric: best value is in showing we can work with both i2b2 and indivo, and that they couldn't easily work together without us
16:53:31 <Susie> Scott: if we had pathology report that fits in indivo that could enable connect to other tasks
16:53:42 <Susie> Michel: absolutely what should happen
16:53:59 <Susie> Scott: anonymized data would be ideal
16:54:51 <Bob> (Chime is at Cleveland Clinic)
16:55:18 <Susie> BioRDF could be a consumer of text mined data
16:55:55 <Susie> Scott: please share other thoughts about connection points
16:56:33 <Bob> Scott: Biobanking is a great platform, tends to get wet-lab scientists excited, for search as a first step
16:57:18 <Bob> Susie: i2b2 has interest in support for biobanking, along w. omics
16:57:54 <Bob> ...Crimson hive in i2b2 is for biobanking
17:00:19 <mscottm> David Cox (Pfizer) 
17:00:33 <Zakim> - +1.518.276.aadd
17:00:34 <Zakim> - +1.610.651.aacc
17:00:34 <Zakim> -??P7
17:00:35 <Zakim> - +1.617.947.aaff
17:00:37 <Zakim> -epichler
17:01:10 <Zakim> -Bob_Powers
17:02:30 <Zakim> -EricP
17:02:32 <Zakim> -mscottm
17:02:39 <michel> michel has left #HCLS
17:02:40 <Zakim> - +1.860.440.aabb
17:02:42 <Zakim> SW_HCLS()11:00AM has ended
17:02:48 <Zakim> Attendees were +1.617.947.aaaa, +1.860.440.aabb, mscottm, +1.610.651.aacc, epichler, +1.518.276.aadd, EricP, Bob_Powers, +1.617.947.aaee, +1.617.947.aaff
17:02:51 <mscottm>   RRSAgent, please draft minutes
17:02:51 <RRSAgent> I have made the request to generate http://www.w3.org/2010/12/02-hcls-minutes.html mscottm
17:03:04 <mscottm>   RRSAgent, please make log world-visible
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