scribenick Bob

<Lena> I am trying to call hcls but getting the message "the conference is restricted at this time"

Lena - try HCLS2

<Lena> what is the #?

<michel> 42572

<Lena> got it :)

<Lena> yes

Joanne: pharmacogenomics, AMIA, AOB

<michel> agenda:1. AMIA presentation

Joanne: Just got slides from students, can use as basis for TMO presentation

Michel: Susie will present on TMO too

<michel> personal genome project website - 10 genomes

<matthias_samwald> http://www.personalgenomes.org/

Joanne: Can we find APOE allele?

Michel: Looking at data now.

Joanne: 10 people, starting w. George Church.

<matthias_samwald> e.g. http://www.personalgenomes.org/public/1.html

<Lena> one example - https://my.personalgenomes.org/profile/huCF2688

Matthias: Can also see microarray data here

<Joanne> Here are the slides https://docs.google.com/present/edit?id=0ARi7AC7gwFMMZGhja3J0NTRfMjgyaGM2Nnp3ZnE&hl=en&authkey=CPmgvdUG

Joanne: Gave the students the paper cold, so there's no bias
... merge this w. Susie's presentation?

Michel: Let's use W3C templates if we can find them.

Scott: Been invited to Tokyo re HCLS; interested in Joanne and Susie's presentations
... not quite doable to have a standard slide set

Michel: Pharmacogenomics; looked at some of the resources
... start crafting a compelling use case for making data available
... primarily interested in support of HC; but also re-usable for clincial and LS research

<michel> http://www.w3.org/wiki/HCLSIG/TranslationalMedicine/pharmacogenomics

<Joanne> this was probably captured earlier in the chat, but I suggest we utilise the data at http://www.personalgenomes.org/

Michel: focussed on high-level resources
... also try to identify papers for insight into clinical trials, freq of alleles etc.

<Joanne> Have to go now. Send me comments on the TMO/TMKB presentation as well as working in the google doc. THANKS!

<Joanne> scott, have a wonderful trip!

Michel: also interested in support for recording in EHRs
... Adrian Coulet SOPHARM shows how SNPs can be represented in OWL
... SOPHARM loads a number of other ontologies; gets quite large

Bosse(?): Proprietary systems for gen. info

<michel> matthias - commercial systems should be incorporated in the survey

<michel> ... partners health care - center for personalized medicine - linked to harvard

<matthias_samwald> http://pcpgm.partners.org/it-solutions/geneinsight

Matthias: Harvard, Center for Personalized Genetic Medicine

Scott: Susie mentioned biobanking in i2b2

<mscottm> BBMRI

Scott: Biobanking .. research infrastructure
... there is consistent interest in i2b2; how to handle SNPs
... microarray data heavy duty; we'd rather get patient centric SNP data
... one of the key applications: kidney transplant unit, w SNPs for patients, use as biomarkers for successful transplant
... plus tie in to chemo effectiveness

<mscottm> http://nlp.dbmi.pitt.edu/report_repository.html

Scott: BluLab NLP repository
... Richard Boyce at Pitt might have SNPs

<michel> i need to reconnected

Scott: look for gene expression biomarkers; interesting for IO Informatics w ontological framework for data

Michel: Pitt clinical report

Scott: Has gotten IRB approval for himself, but not for web
... has given example reports in google doc; using as an example for info extract, text mining, for meaningful RDF

<mscottm> http://nlp.dbmi.pitt.edu/images/RAD.xml

Scott: radiology example sould be on the website

<epichler> another example: http://nlp.dbmi.pitt.edu/images/HP.xml

Scott: engagement has been mostly w. LODD group
... opportunity to tie Term, LODD, TM all together
... maybe get IO Informatics data, already been freed-up and post-competitive
... maybe put into Indivo pipeline
... More of a reach: i2b2, starts w. Oracle.
... getting IO data into Indivo, then get SNPs would be the approach
... IO data not on web; but there are examples of patient RDF
... IO interested in LODD and TM agenda

Michel: What datasources to consider? Availability?

Scott: Immediate gap is SNPs or any form of biomarker; we could do something w. gene expression data
... Gene Atlas will present on re RDF; working to provide for restricted datasets

<mscottm> http://www.ebi.ac.uk/gxa/

<mscottm> James Malone will present about Gene Atlas RDF on Monday's BioRDF call.

Matthias: Want to focus on simple stuff like SNPs, or include more complicated gene expression, etc
... would like to focus on pharmaco data that have relevance

Michel: SNP data should be the ones that have clinical significance
... can identify trials w this?

Matthias: Yes, valuable to include clincial trials

Michel: Animals models, sometimes do have genetic variants homolog to human

Lena: Yes, animal models before clincial trials
... sequences too
... Sequences are concise, more so than RNA expression

Michel: OMIN has been RDF-ized?

<Lena1> (sequencing mRNA - rather than hybridizing it - is becoming increasingly relevant and car provide cues about the actual amount of mRNA on the cell)

Scott: Creating URIs for SNPs; dbSNP maybe create a semantic view of dbSNP or other relational DBs

<Lena1> e.g. http://www.ncbi.nlm.nih.gov/pubmed/19949700

<mscottm> http://www.ncbi.nlm.nih.gov/projects/SNP/

<Lena1> another intersting source of data - http://web.mit.edu/sirna/

<Lena1> RNA is the "new" DNA ;-)

This is scribe.perl Revision: 1.135  of Date: 2009/03/02 03:52:20  
Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

No ScribeNick specified.  Guessing ScribeNick: Bob
Inferring Scribes: Bob

WARNING: No "Topic:" lines found.

Default Present: 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
Present: 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

WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting


WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 17 Feb 2011
Guessing minutes URL: http://www.w3.org/2011/02/17-hcls2-minutes.html
People with action items: 

WARNING: No "Topic: ..." lines found!  
Resulting HTML may have an empty (invalid) <ol>...</ol>.

Explanation: "Topic: ..." lines are used to indicate the start of 
new discussion topics or agenda items, such as:
<dbooth> Topic: Review of Amy's report