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13:48:55 <RRSAgent> logging to http://www.w3.org/2011/04/07-hcls2-irc
13:50:02 <ericP> Zakim, space for 10 for 90 minutes?
13:50:05 <Zakim> sorry, ericP; could not schedule an adhoc conference; passcode overlap; if you do not have a fixed code you may try again
13:51:59 <ericP> Zakim, space for 10 for 70 minutes?
13:52:01 <Zakim> sorry, ericP; could not schedule an adhoc conference; passcode overlap; if you do not have a fixed code you may try again
13:52:05 <ericP> Zakim, space for 10 for 65 minutes?
13:52:08 <Zakim> ok, ericP; conference Team_(hcls2)13:52Z scheduled with code 42572 (HCLS2) for 65 minutes until 1457Z; however, please note that capacity is now overbooked
14:01:07 <Zakim> Team_(hcls2)13:52Z has now started
14:01:15 <Zakim> +mscottm
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14:02:04 <Zakim> + +44.453.083.aaaa
14:02:14 <Zakim> + +1.631.444.aabb
14:03:34 <Zakim> +??P18
14:03:43 <matthias_samwald> matthias_samwald has joined #hcls2
14:04:14 <Zakim> + +1.647.839.aacc
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14:07:55 <AndreaS> Hi
14:08:41 <Zakim> + +1.781.431.aadd
14:09:42 <mscottm> hi
14:13:33 <Zakim> + +44.754.501.aaee
14:14:11 <Zakim> +EricP
14:15:18 <Zakim> -EricP
14:15:22 <Zakim> +EricP
14:15:28 <mscottm> Zakim, pick a victim
14:15:28 <Zakim> Not knowing who is chairing or who scribed recently, I propose +1.781.431.aadd
14:15:53 <mscottm> Zakim, pick a victim
14:15:54 <Zakim> Not knowing who is chairing or who scribed recently, I propose ??P18
14:15:58 <Zakim> -EricP
14:16:22 <matthias_samwald> scribenick: matthias_samwald
14:16:37 <matthias_samwald> zakim, who is on the call?
14:16:37 <Zakim> On the phone I see mscottm, +44.453.083.aaaa, +1.631.444.aabb, ??P18, +1.647.839.aacc, +1.781.431.aadd, +44.754.501.aaee
14:17:02 <matthias_samwald> janos: started when i looked into a database called Biogrid
14:17:08 <mscottm> Andrea: briefly: involved in BioPax and semantic web aspects of BioPax
14:17:14 <Zakim> +EricP
14:17:25 <matthias_samwald> ... interesting, curated database
14:17:36 <matthias_samwald> ... protein-protein interactions from many organisms
14:18:12 <matthias_samwald> ... i downloaded a dataset, loaded it into MySQL
14:18:28 <matthias_samwald> ... i saw potential for linking it to LODD  -- pubmed IDs, gene ids etc.
14:18:40 <mscottm> janos - your voice is dropping out for me. is it only for me?
14:19:02 <matthias_samwald> ... searching for 'biogrid' and 'owl' gave some results in google
14:19:19 <matthias_samwald> ... pathway commons, for example. they have Biogrid in BioPAX format.
14:19:33 <matthias_samwald> ... so it was available in OWL, but not as linked data.
14:19:58 <Zakim> + +20416aaff
14:20:01 <matthias_samwald> ... i downloaded the BioPAX OWL file, loaded it into triple store
14:20:05 <Zakim> -mscottm
14:20:45 <ericP> ericP has changed the topic to: Experiences with http://thebiogrid.org/ , slides: http://www.w3.org/wiki/images/3/30/BioGrid2RDF.pdf
14:20:47 <mscottm> Zakim, +20416aaff is mscottm
14:20:47 <Zakim> +mscottm; got it
14:21:02 <ericP> -> http://www.w3.org/wiki/images/3/30/BioGrid2RDF.pdf Experiences with http://thebiogrid.org/
14:21:05 <matthias_samwald> ... qustion is: can we take something in this format an link it to other resources on the Semantic Web?
14:21:37 <matthias_samwald> ... i chose to work with the tabular raw data
14:23:07 <matthias_samwald> ... for example, with PubMed ID you can easily link to Bio2RDF URIs
14:24:41 <matthias_samwald> ... slide 8: for example, you can put a gene name into NCBO annotator, it will correctly give you the gene ID
14:25:41 <matthias_samwald> scott: i have a question. it looks interesting for setting up a script that does that for each item in the column to retrieve PURLs. could you do that?
14:26:55 <matthias_samwald> janos: can be done
14:28:33 <matthias_samwald> janos: i am now working on a version of UMLS that includes CUIs as well as other identifiers
14:28:43 <matthias_samwald> ... can facilitate alignment
14:29:16 <matthias_samwald> ... Bio2RDF also has Entrez Gene IDs, this is another opportunity for linking
14:30:19 <matthias_samwald> ... on the final slide: an example of a detail in the UMLS metatheasaurius
14:30:35 <matthias_samwald> ... you can see that is also has PubMed IDs, but not linked to external resources
14:30:48 <matthias_samwald> ... the project is in an early phase.
14:31:04 <matthias_samwald> any questions?
14:31:43 <matthias_samwald> scott: the interactions are between what types of entities?
14:32:01 <matthias_samwald> janos: data comes from high-throughput screening of protein interactions
14:32:27 <matthias_samwald> ... protein is coded via gene, but data is about protein interactions
14:33:04 <matthias_samwald> ... data is manually curated
14:34:44 <matthias_samwald> ... i am also working on a project that is part of VIVO
14:35:20 <matthias_samwald> ... could also be used to connect researchers working on strongly related proteins
14:37:53 <matthias_samwald> ... i don't want to re-do what Pathway Commons did. Rather, I annotate the data that they already have.
14:40:15 <matthias_samwald> andrea: could you identify any limitations of the approach? you also worked with the tabbed format -- why that instead of BioPAX?
14:41:07 <matthias_samwald> janos: i have not done an exact comparison between the two. I suspected that the different formats did not contain exactly the same version of the data.
14:41:27 <matthias_samwald> andrea: did you check the consistency of the BioPAX file?
14:42:33 <matthias_samwald> janos: no
14:44:43 <matthias_samwald> andrea: UMLS is not completely free, can you directly use it?
14:45:09 <matthias_samwald> janos: they have different levels of restrictions, i only used level 0 (freely available) subsets of the UMlS
14:45:47 <matthias_samwald> ... as long as it is level 0 you can publish it as RDF
14:46:31 <matthias_samwald> eric: if i map something from SNOMED CT to something else, i am not allowed to recapitulate it... but can i use the terms from SNOMED CT in my alignment at all?
14:47:12 <matthias_samwald> janos: if you only use the identifiers and not the original wording of the descriptions... there might be a problem
14:48:18 <matthias_samwald> scott: john madden believed that it was no problem to use the terms. the problem is when you make the entirety of SNOMED available for download on your website.
14:49:05 <matthias_samwald> ... for the Shared Names initiative i wanted to be able to serve PURLs for SNOMED terms
14:49:44 <matthias_samwald> ... what we came away with was that it should be possible to server the PURLs/identifiers, but you should not make it possible to download the entire SNOMED vocabulary from your site
14:51:25 <matthias_samwald> claus: i am looking at the BioGrid web page. data is available in many formats. maybe we could talk to them to serve RDF as well?
14:51:54 <matthias_samwald> janos: i have not contacted them yet. what i wanted to do so far is to add the annotations to the web of linked data. but it could be good to talk to them.
14:52:35 <matthias_samwald> scott: lets get back to the topic of the W3C note
14:53:09 <matthias_samwald> ... if we were to produce a not with a step-by-step guide for publishing linked data in the life science domain, which timeline would we be looking at?
14:53:28 <matthias_samwald> eric: the social process is hard to predict.
14:53:48 <matthias_samwald> ... figuring out how to reach consensus
14:56:30 <matthias_samwald> scott: i was suggesting that we could take material from the best practices document we recently submitted, revise and reformat it -- then we could see how it looks and decide how to proceed further. This could be done rather easily.
14:57:01 <Zakim> This conference is in overtime; all ports must be freed
14:58:15 <matthias_samwald> eric: the process for a recommendation would also include peer review, reference implementations. this would take one year at least.
15:00:03 <matthias_samwald> zakim, please draft minutes
15:00:03 <Zakim> I don't understand 'please draft minutes', matthias_samwald
15:00:24 <Zakim> - +1.647.839.aacc
15:00:25 <Zakim> -mscottm
15:00:27 <Zakim> - +44.453.083.aaaa
15:00:27 <Zakim> - +1.631.444.aabb
15:00:29 <Zakim> -EricP
15:00:33 <Zakim> - +44.754.501.aaee
15:00:36 <Zakim> -??P18
15:00:37 <Zakim> - +1.781.431.aadd
15:00:40 <Zakim> Team_(hcls2)13:52Z has ended
15:00:42 <Zakim> Attendees were mscottm, +44.453.083.aaaa, +1.631.444.aabb, +1.647.839.aacc, +1.781.431.aadd, +44.754.501.aaee, EricP
15:02:52 <matthias_samwald> RRSagent, please draft minutes
15:02:52 <RRSAgent> I have made the request to generate http://www.w3.org/2011/04/07-hcls2-minutes.html matthias_samwald
15:03:00 <matthias_samwald> RRSagent, please make minutes world-visible
15:03:00 <RRSAgent> I'm logging. I don't understand 'please make minutes world-visible', matthias_samwald.  Try /msg RRSAgent help
15:04:59 <matthias_samwald> RRSAgent, please make logs world-visible
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16:04:16 <matthias_samwald> will join the call in a minute... 
16:05:21 <michel> dd
16:05:37 <michel> zakim, this is tmo
16:05:37 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
16:06:06 <mscottm> congrats
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16:06:11 <mscottm> nope
16:06:59 <Zakim> +[IPcaller.a]
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16:08:12 <Zakim> +epichler
16:08:13 <Bob> scribenick Bob
16:08:31 <michel> scott: collabrx - mike travers no longer working there, but is available to chat
16:08:58 <mscottm> Jeff Shrager
16:09:17 <michel>  .. AI guy
16:09:22 <Bob> Scott: Jeff is LISP/AI guy
16:09:44 <Bob> ... :-) have internalized the LOD cloud
16:10:08 <Bob> ... converatons wiki-style about patients, alleles
16:10:27 <Bob> ... We could try for 2 weeks
16:10:49 <Bob> ... Adrian Coulet on the 14th
16:11:11 <Bob> Michel: Will try to get Jeff in for the 21st
16:12:29 <Bob> ... 21st is Harmony meeting NYC. I'll be attending
16:12:41 <michel> https://docs.google.com/document/d/1lKdDSb2uBBIeTEQAv2CyTHN_aVW63k9si1hmmilOMi0/edit?hl=en&authkey=CJGUtcwF#
16:12:58 <Bob> Michel: Paper. Matthias has looked thru instructions for authors
16:13:42 <Zakim> +Joanne
16:15:20 <Bob> Matthias: J. Fut. Med.? research article, create our own ontologies or focus on...
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16:16:34 <Bob> Michel: Scott invited to contribute to J.Pharmacogenomics, initially for review paper
16:17:14 <Bob> ... advanges/disadvantages of different approaches, ultimately get to ontology
16:17:41 <Bob> ... consider conceptualization in ontological approach
16:17:50 <Bob> ... May 3 time frame
16:18:13 <Bob> Scott: skype conversation here:
16:19:14 <Bob> ... sopharm, nanopubs, review of technologies and how they have been used to date
16:19:22 <mscottm> Review of representation in SO-Pharm, PGx knowledge, Nanopub, anonymous
16:19:31 <mscottm> Pharma co., relational in general, tables to RDF and OWL, identifiers, + proposal
16:19:39 <mscottm> review of representation of PGx knowledge
16:19:52 <mscottm> from relational database to logic-based representations#
16:20:00 <mscottm> identifiers, terminology, database cross-references
16:20:05 <mscottm> entity-relation models
16:20:12 <michel> https://docs.google.com/present/edit?id=0AYy0zfdRviKsZGM5cWM1OXRfMTAwZzlycmJjZmI&hl=en&authkey=CKXAsvMI
16:21:42 <Bob> Scott: From last week, discussion of how we want to represent real data
16:22:27 <Bob> Mihel: We have specific use cases to draw from
16:23:44 <Bob> Michel: We need descriptions of resources; three use cases, one of which is diagnostics
16:24:17 <Bob> ... another use case for clinical trials, id genetic cohorts, side effects
16:24:28 <Bob> ... 3rd use case research
16:25:49 <Bob> Joanne: Diagnostics and treatment not nec coupled
16:27:02 <Bob> Matthias: Narrow down on pharmacogenomics, want to focus
16:27:47 <Bob> Joanne: Don't want to lose sight of the bigger picture.
16:28:09 <Bob> Scott: Idea of using molecular characterization for stratification of patient
16:28:24 <Bob> ... use semweb rep to do patient stratification
16:28:47 <Bob> ... tangible form of example for everybody
16:29:08 <Jluciano> (I find it amusing to hear that patitent startification is the new buzz --- I presented a way to use Nerual Nets to do this in Sept 1994 at an Irish Neural Net conference.
16:29:17 <Bob> Michel: Patient-centrict is most appropriate,  add to TMO work
16:30:07 <Bob> Joanne: Data from IO Informatics, yes it has genetic data
16:30:21 <Bob> ... genes, biomarkers, blood
16:30:42 <Bob> Michel: But link to PGx outcome?
16:31:07 <mscottm> http://www.genomeweb.com/dxpgx/systems-biology-fights-cancer
16:31:13 <Bob> ... HCLS wiki page for translational medicine, links to FDA alerts
16:31:26 <Bob> ... time frame short for IO data, maybe later
16:32:16 <Bob> ... need someone to develop this patient-centric use case
16:33:10 <Bob> (got the link?)
16:33:37 <matthias_samwald> here is the list of FDA drugs with pharmacogenomic-relevant info: http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083378.htm
16:33:53 <Jluciano> who's voice is that?
16:34:13 <michel> http://www.w3.org/wiki/HCLSIG/PharmaOntology/UseCases
16:34:24 <mscottm> Bosse
16:34:36 <Jluciano> Thanks!
16:34:54 <Bob> Bosse: Chris had a lot of use cases, including PGx
16:35:25 <Bob> Michel: We had developed a use case; maybe look into this one!
16:35:52 <Bob> ... need validation on treatment option, etc
16:36:27 <Bob> Scott: I have contact info from founder of Co. making chemo chip, using biomarkers
16:36:57 <Bob> ... can contact radiologist in NL w. data
16:37:20 <Bob> ... siimilar to OncoDx
16:38:17 <Bob> Joanne: We can get warfarin data, synthetic?
16:38:30 <Zakim> -[IPcaller]
16:38:42 <Bob> ... probably available today
16:38:53 <Zakim> +??P1
16:39:11 <Bob> Scott: Can we follow the whole (life cycle) of a (patient encounter)?
16:39:55 <Zakim> -??P1
16:40:00 <Bob> OK: Not whole scenario!  Just do you have genomic info, sufficient to stratify
16:40:21 <Bob> (I overstated Scott's proposal!)
16:40:21 <Jluciano> Here appears to be clinical avatar data:  http://lpm.hms.harvard.edu/sites/default/files/cairodemodata.tar_.gz
16:41:26 <Jluciano> the clinical avatar data is on warfarin
16:41:41 <Bob> Matthias: Draft OWL ont for treatment decisions
16:41:45 <janos> janos has left #HCLS2
16:42:05 <Bob> ... separate ontology, maybe could be integrated w. what we need for PGx
16:42:34 <Jluciano> from Peter Tonellato's group at Harvard Laboratory for Personalized Medicine.
16:42:42 <Bob> Scott: Represent rules for this? or sparql?
16:43:26 <Bob> Matthias: Looking at SPIN too, haven't fixed on how to pursue decision support
16:43:40 <Bob> (don't let me overstate all this :-)
16:44:12 <Bob> Matthias: Maybe can offer a prototype that could be a start for work
16:44:23 <Bob> Michel: can you hear us?
16:44:37 <mscottm> Matthias: What I could offer now is a prototype that hasn't left the lab
16:44:40 <Bob> probably not :(
16:45:07 <Bob> Scott: What kind of decision support?
16:45:49 <Bob> Matthias: Start, mostly focus on order entry. Medication to recommendation, warnings, etc
16:46:13 <mscottm> What's your number? I'll try to dial you in.
16:46:16 <Bob> ... focussing on the the process of specific medication as it applies to a patient
16:46:37 <Bob> Scott: Not a larger scale disease frame?
16:46:45 <Jluciano> http://clinicalavatars.org/#/menu_model
16:47:01 <Bob> Matthias: Not at the moment. But looking at neurological diseases and cancer.
16:47:27 <Jluciano> http://clinicalavatars.org/#/menu_model/menu_doWhat?model=warfarin
16:47:37 <Bob> Joanne: Breast cancer and warfarin use case in this clinicalavators.org
16:47:46 <Bob> ... can use tools to create datasets
16:48:37 <Jluciano> AGE	GENDER	RACE	HEIGHT	WEIGHT	SMOKER	DVT	AMI	CYP2C9	VKORC1 >64	F	White	<58 in	<100 lbs	N	N	Y	1/1	B/B >64	F	White	60	250 to 259	N	Y	N	1/1	B/B 25 to 44	M	White	66	180 to 189	Y	N	N	1/1	A/A <18	F	White	73	150 to 159	N	N	N	1/1	B/B <18	F	White	64	120 to 129	N	N	N	1/1	B/B 45 to 64	F	White	72	160 to 169	Y	N	N	1/1	A/B <18	M	White	<58 in	130 to 139	N	N	N	1/1	B/B 45 to 
16:49:44 <Bob> Joanne describing how to build your own avatar
16:50:46 <Jluciano> http://clinicalavatars.org/?sid=doseDiagnose&preConfig=warfarin&downloadAvatarsFileName=/tmp/AVATAR3fk535
16:51:37 <Bob> Michel: Don't know what headers are, etc
16:52:35 <Bob> Joanne: pasting info now...
16:52:42 <Jluciano> Warfarin is the most widely used anticoagulant in the world. However, its narrow therapeutic window results in a relatively high risk of bleeding when over-dosed or an increased risk of thrombosis when under-dosed. Furthermore, the wide-range of dose response for an individual is heavily influenced by variants in the CYP2C9 and VKORC1 genotypes that control w
16:52:56 <Jluciano> Chih-Lin Chi, Ph.D.1, Prasad Patil, B.S.1, Vincent A. Fusaro, Ph.D.1, Peter J. Kos, M.S.3, Rimma Pivovarov, B.S.1, Charles F. Contant, Ph.D.2, Peter J. Tonellato, Ph.D.1,3 1Center for Biomedical Informatics, Harvard Medical School; 2TIMI Study Group 3School of Public Health, Univ. of WI-Milwaukee 
16:53:23 <Jluciano> Our clinical trial simulation design consists of four steps. First, we identify variables from a literature review to create the stochastic model that produces clinical avatars based on statistical characteristics of a population and variable dependencies. Second, we predict an initial dose for each avatar using dosing algorithms from literature. We then appl
16:53:41 <Jluciano> protocols used in clinical trials and other studies as guidelines for daily dose, dose adjustment, and INR measurement schedule. Fourth, we conduct randomized trial simulations on clinical avatars. In our clinical trial simulation, we randomly assign clinical avatars to different treatment protocol groups and compare the TTR between different groups.   
16:58:29 <Bob> Michel: Start by creating diagrams, writing descriptive axioms
16:59:27 <Jluciano> INR Response --- 	International Normalized Ratio (for blood clotting time)
16:59:35 <Bob> ... can make diagrams on Google docs
17:00:42 <Bob> Scott: We can make diagram for INR-warfarin in google doc
17:01:05 <Bob> Michel: Dosage, compostion, diagnostic, outcomes
17:01:27 <Bob> ... extend w. gene-drug relations
17:02:07 <Bob> ... Note that you can also put comments in google doc, w. a little bubble
17:02:31 <Bob> Joanne: Settled on warfarin?
17:02:44 <Bob> Michel: Yes, very well understood.
17:03:17 <Bob> Joanne: we could switch over to breast cancer
17:03:49 <Bob> Scott: Already working on breast cancer, have some resources
17:05:07 <Jluciano> http://clinicalavatars.org/?preConfig=gailRosner&pid=generate&preConfigured=GailRosnerUSMixedCPT&numAvatars=100&submit.x=152&submit.y=35
17:05:13 <Bob> Joanne: Link for breast cancer above
17:06:43 <Bob> Michel: Will create the diagram.
17:07:07 <Zakim> -epichler
17:07:09 <Zakim> -bbalsa
17:07:09 <Zakim> -Bob_Powers
17:07:11 <Zakim> -[IPcaller.a]
17:07:12 <Zakim> - +62427aaaa
17:07:13 <michel> rrsagent, draft minutes
17:07:13 <RRSAgent> I have made the request to generate http://www.w3.org/2011/04/07-hcls2-minutes.html michel
17:07:22 <epichler> epichler has left #HCLS2
17:07:22 <michel> rrsagent, make log world-visible
17:12:12 <Zakim> disconnecting the lone participant, Joanne, in SW_HCLS(TMO)11:00AM
17:12:16 <Zakim> SW_HCLS(TMO)11:00AM has ended
17:12:18 <Zakim> Attendees were Bob_Powers, +62427aaaa, bbalsa, [IPcaller], epichler, Joanne
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