IRC log of hcls2 on 2011-02-17

Timestamps are in UTC.

17:02:52 [RRSAgent]
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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]
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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]
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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]
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17:18:15 [bbalsa]
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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]
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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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