17:02:52 <RRSAgent> RRSAgent has joined #hcls2
17:02:52 <RRSAgent> logging to http://www.w3.org/2011/02/17-hcls2-irc
17:03:05 <michel> zakim, this is tmo
17:03:06 <Zakim> ok, michel; that matches SW_HCLS(TMO)11:00AM
17:03:26 <Zakim> + +1.518.276.aaaa
17:03:42 <Bob> scribenick Bob
17:04:06 <Zakim> +??P27
17:04:24 <michel> zakim, ??P27 is michel
17:04:24 <Zakim> +michel; got it
17:04:32 <Lena> I am trying to call hcls but getting the message "the conference is restricted at this time"
17:04:37 <Zakim> +pchampin
17:04:47 <Zakim> +??P35
17:04:51 <matthias_samwald> matthias_samwald has joined #hcls2
17:05:01 <Bob> Lena - try HCLS2
17:05:01 <Zakim> + +1.832.386.aabb
17:05:22 <Lena> what is the #?
17:05:36 <michel> 42572
17:05:53 <epichler> epichler has joined #HCLS2
17:06:00 <Zakim> - +1.832.386.aabb
17:06:32 <Zakim> + +31.62.427.aacc
17:06:34 <Zakim> + +1.832.386.aadd
17:06:38 <Lena> got it :)
17:07:11 <Lena> yes
17:08:07 <Bob> Joanne: pharmacogenomics, AMIA, AOB
17:08:42 <michel> agenda:1.  AMIA presentation
17:09:38 <Bob> ... Just got slides from students, can use as basis for TMO presentation
17:11:02 <Bob> Michel: Susie will present on TMO too
17:11:44 <michel> personal genome project website - 10 genomes
17:11:55 <matthias_samwald> http://www.personalgenomes.org/
17:12:15 <Bob> Joanne: Can we find APOE allele?
17:13:11 <Bob> Michel: Looking at data now.
17:13:30 <Bob> Joanne: 10 people, starting w. George Church.
17:13:57 <matthias_samwald> e.g. http://www.personalgenomes.org/public/1.html
17:14:02 <Zakim> - +31.62.427.aacc
17:14:19 <Lena> one example - https://my.personalgenomes.org/profile/huCF2688
17:14:23 <Zakim> + +31.62.427.aaee
17:14:30 <Joanne> Joanne has joined #hcls2
17:15:03 <Bob> Matthias: Can also see microarray data here
17:15:07 <Joanne> Here are the slides https://docs.google.com/present/edit?id=0ARi7AC7gwFMMZGhja3J0NTRfMjgyaGM2Nnp3ZnE&hl=en&authkey=CPmgvdUG
17:16:53 <Bob> Joanne: Gave the students the paper cold, so there's no bias
17:17:34 <bbalsa> bbalsa has joined #HCLS2
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17:18:21 <Bob> ... merge this w. Susie's presentation?
17:19:41 <Bob> Michel: Let's use W3C templates if we can find them.
17:21:50 <Bob> Scott: Been invited to Tokyo re HCLS; interested in Joanne and Susie's presentations
17:22:47 <Bob> ... not quite doable to have a standard slide set
17:25:21 <Bob> Michel: Pharmacogenomics; looked at some of the resources
17:25:36 <Bob> ... start crafting a compelling use case for making data available
17:26:02 <Bob> ... primarily interested in support of HC; but also re-usable for clincial and LS research
17:26:06 <michel> http://www.w3.org/wiki/HCLSIG/TranslationalMedicine/pharmacogenomics
17:26:32 <Joanne> this was probably captured earlier in the chat, but I suggest we utilise the data at http://www.personalgenomes.org/
17:26:49 <Bob> ... focussed on high-level resources
17:28:16 <Bob> ... also try to identify papers for insight into clinical trials, freq of alleles etc.
17:28:43 <Joanne> Have to go now.  Send me comments on the TMO/TMKB presentation as well as working in the google doc.  THANKS!
17:29:18 <Joanne> scott, have a wonderful trip!
17:29:38 <Zakim> - +1.518.276.aaaa
17:29:55 <Bob> ... also interested in support for recording in EHRs
17:30:58 <Bob> ... Adrian Coulet SOPHARM shows how SNPs can be represented in OWL
17:31:22 <Bob> ... SOPHARM loads a number of other ontologies; gets quite large
17:32:54 <Bob> Bosse(?): Proprietary systems for gen. info
17:33:03 <michel> matthias - commercial systems should be incorporated in the survey
17:33:42 <michel>  ... partners health care - center for personalized medicine - linked to harvard
17:33:43 <matthias_samwald> http://pcpgm.partners.org/it-solutions/geneinsight
17:34:11 <Bob> Matthias: Harvard, Center for Personalized Genetic Medicine
17:35:10 <Bob> Scott: Susie mentioned biobanking in i2b2
17:35:31 <mscottm> BBMRI
17:35:55 <Bob> ... Biobanking .. research infrastructure
17:36:43 <Bob> ... there is consistent interest in i2b2; how to handle SNPs
17:37:14 <Bob> ... microarray data heavy duty; we'd rather get patient centric SNP data
17:38:20 <Bob> ... one of the key applications: kidney transplant unit, w SNPs for patients, use as biomarkers for successful transplant
17:38:31 <Bob> ... plus tie in to chemo effectiveness
17:38:44 <Zakim> -michel
17:39:01 <mscottm> http://nlp.dbmi.pitt.edu/report_repository.html
17:39:15 <Zakim> +??P1
17:39:31 <Bob> ... BluLab NLP repository
17:39:54 <Bob> ... Richard Boyce at Pitt might have SNPs
17:40:23 <michel> i need to reconnected
17:40:36 <Bob> ... look for gene expression biomarkers; interesting for IO Informatics w ontological framework for data
17:40:53 <Bob> Michel: Pitt clinical report
17:41:15 <Bob> Scott: Has gotten IRB approval for himself, but not for web
17:41:53 <Bob> ... has given example reports in google doc; using as an example for info extract, text mining, for meaningful RDF
17:42:09 <mscottm> http://nlp.dbmi.pitt.edu/images/RAD.xml
17:42:15 <Bob> ... radiology example sould be on the website
17:42:37 <epichler> another example: http://nlp.dbmi.pitt.edu/images/HP.xml
17:42:52 <Bob> ... engagement has been mostly w. LODD group
17:43:22 <Bob> ... opportunity to tie Term, LODD, TM all together
17:44:20 <Bob> ... maybe get IO Informatics data, already been freed-up and post-competitive
17:44:34 <Bob> ... maybe put into Indivo pipeline
17:44:54 <Bob> ... More of a reach: i2b2, starts w. Oracle.
17:45:21 <Bob> ... getting IO data into Indivo, then get SNPs would be the approach
17:45:52 <Bob> ... IO data not on web; but there are examples of patient RDF
17:48:23 <Bob> ... IO interested in LODD and TM agenda
17:48:49 <Bob> Michel: What datasources to consider?  Availability?
17:49:54 <Bob> Scott: Immediate gap is SNPs or any form of biomarker; we could do something w. gene expression data
17:50:33 <Bob> ... Gene Atlas will present on re RDF; working to provide for restricted datasets
17:50:51 <Zakim> - +1.832.386.aadd
17:51:25 <mscottm> http://www.ebi.ac.uk/gxa/
17:51:32 <Zakim> + +1.832.386.aaff
17:52:16 <mscottm> James Malone will present about Gene Atlas RDF on Monday's BioRDF call.
17:52:16 <Lena1> Lena1 has joined #hcls2
17:53:28 <Bob> Matthias: Want to focus on simple stuff like SNPs, or include more complicated gene expression, etc
17:53:50 <Bob> ... would like to focus on pharmaco data that have relevance
17:54:38 <Bob> Michel: SNP data should be the ones that have clinical significance
17:54:57 <Bob> ... can identify trials w this?
17:55:16 <Bob> Matthias: Yes, valuable to include clincial trials
17:56:04 <Bob> Michel: Animals models, sometimes do have genetic variants homolog to human
17:56:23 <Bob> Lena: Yes, animal models before clincial trials
17:56:40 <Bob> ... sequences too
17:57:14 <Bob> Lena: Sequences are concise, more so than RNA expression
17:57:39 <Bob> Michel: OMIN has been RDF-ized?
17:58:18 <Lena1> (sequencing mRNA - rather than hybridizing it - is becoming increasingly relevant and car provide cues about the actual amount of mRNA on the cell)
17:59:48 <Bob> Scott: Creating URIs for SNPs; dbSNP maybe create a semantic view of dbSNP or other relational DBs
18:00:10 <Lena1> e.g. http://www.ncbi.nlm.nih.gov/pubmed/19949700
18:00:32 <mscottm> http://www.ncbi.nlm.nih.gov/projects/SNP/
18:01:08 <Zakim> -??P35
18:01:10 <Zakim> - +1.832.386.aaff
18:01:11 <Zakim> - +31.62.427.aaee
18:01:12 <Zakim> -Bob_Powers
18:01:13 <Zakim> -??P1
18:01:13 <Zakim> -Christi
18:01:18 <Zakim> -pchampin
18:01:19 <Zakim> SW_HCLS(TMO)11:00AM has ended
18:01:21 <Zakim> Attendees were Bob_Powers, Christi, +1.518.276.aaaa, michel, pchampin, +1.832.386.aabb, +31.62.427.aacc, +1.832.386.aadd, +31.62.427.aaee, +1.832.386.aaff
18:02:46 <Lena1> another intersting source of data - http://web.mit.edu/sirna/
18:03:04 <Lena1> RNA is the "new" DNA ;-) 
18:03:16 <matthias_samwald> rrsagent, draft minutes
18:03:16 <RRSAgent> I have made the request to generate http://www.w3.org/2011/02/17-hcls2-minutes.html matthias_samwald
18:03:32 <matthias_samwald> rrsagent, make log world-visible
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