<michel> scribenick Bob

<michel> zakim ??P32 is michel

Michel: Post-mortem on the paper

Joanne: Grateful to take it on; challenging w. group this size
... Jim McCusker really helped
... could bring in provenance considerations too
... late nite w. EricP and Jim
... Thanks to Michel for re-proofing
... working on section on queries, working with table
... Most of text is wrangled to the ground.
... what level of detail on the query descriptions
... second question: what to say re significance of queries

Michel: No need to discuss syntax;
... but can query with broader terms than those in the data
... describe in terms of data sources, add any discussion of real inferencing

Scott: Point out significance of being able to make general queries
... hospitals, each department having own IT dept
... point out advantages of having all patient data in one place
... plus clinical trials, plus drug and other scientific information
... tone for queries: It's about the fact that can combine info in ways not possible before
... important to remember that added value is ability to query across data sources

Joanne: Deadline has a little bit of play; reviewers get full version a little later

EricP: "It's not going to be us, is it?" :)

Michel: Great job, significant expansion of BioOnt paper
... broadness from both Joanne and Deborah, placed in context of what's important
... paper is nicely well rounded; EricP unit testing, XML to RDF
... will get some interesting feedback from reviewers

EricP: Need more co-ordination. (Giving several different views on data0

<Joanne> I sent the email to Larissa (and the other organizers) that we plan to send it later today.

EricP: representation of some of the more complex tests
... generic, vs simple pattern for units
... have not got all original XML data into Indivo

Michel: EricP and I will try to figure out the coverage and what needs to be translated
... think re how the knowledge needs to be represented, SNPs(?) etc

Joanne: Wrap up all the paper to-dos

Michel: Patient records in TMKB come from the original XML

EricP: doc files had angle brackets for XML, blue sky view of patient record
... tailor that against somebody else's blue sky, started mapping into Indivo
... pieces of these data have not made it thru the pipe
... also grddl, test data are not quite done

(would have to hear this w/o typing to grok :)

EricP: Will take back to Indivo, negotiate and address how the XML schema looks

Michel: How to involve Indivo spec to handle what we expect
... plus work with then to standarize path to RDF

Joanne: This is valuable to get Indivo on board in RDF
... important contribution from HCLS
... More than best practices, it's a requirement

<mscottm> Joanne: It's a requirement that hasn't been met.

<mscottm> +1

EricP: caMatch(?) for tracking EHR system
... for clinical trial protocol requirements

Joanne: ICD-11, any contact?

can't hear you!

<trish_whetzel> WHO is using WebProtege ->iCat to develop ICD-11

EricP: WHO contracted w Stanford for software, build ontologies

<trish_whetzel> @eric, how do you see TMO to be normative for i2b2?

Trish: Project has been iterative over that last year plus.

Scott: Nice part of pushing semweb forward

<trish_whetzel> iCat development has been an iterative process to include new features as requested by WHO

Scott: IMI got $2B, there are 3 IMIs, w Open Pharma Space
... will use semweb. Plus math modeling, plus EHR stuff, all supposed to co-ordinate
... large pressure to move in the direction of our paper
... people talking, throwing money. But we did it.
... Leaking over to us; room to hire possibly W3C folks
... nice piece of news: Cannot get around RDF to manage resources
... and there are 3 IMIs that all need to co-ordinate.

<trish_whetzel> Thoughts on submitting to Spring AMIA TBI or CRI

<trish_whetzel> AMIA Deadline is Dec. 15

Joanne: query 12, how to tell whether using inferencing

<Joanne> http://esw.w3.org/HCLSIG/PharmaOntology/Queries

<Joanne> Are there any AD patients without the APOE4 allele as these would be good candidates for the clinical trial involving Bapineuzumab?

<Joanne> Which existing marketed drugs might potentially be re-purposed for AD because they are known to modulate genes that are implicated in the disease?

Query 6: Are there any AD patients...

Query 12: pharmgkb manually curated

Scott: reasoning has already been done in pharmgkb
... relates genes and drugs to diseases
... a bit like diseaseome. Win here is that the interesting relations are already there.

<trish_whetzel> Need to move to next call. Bye

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