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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 ;-)
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