<michel> scribenick bob

Michel: Review for the special issue
... deadline will be Feb 7, must include revised version and replies to reviewers

<michel> http://esw.w3.org/HCLSIG/PharmaOntology/Publications/JBMS-reviews

Michel: Review #1 How do patient records reflect...

<michel> ACTION: item to chris to address "realism" of the synthetic patient records [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action01]

Chris: Want to tackle this; Michel's point about patient records being a bridge is good
... Albany Med has various different medical records
... each version has an abridged version

Michel: We should deal w. issue, but thought we already addressed it

Joanne: Write up separate sections before integrating into google doc?

Michel: Making action items for people in irc
... Next point is security and patient confidentiality
... how do we deal w, in semweb approach and our approach?
... add a section wrt privacy/security
... there has been some work on triple store security

Joanne: Will ask ericP plus RPI

<michel> ACTION: item to add section detailing security/privacy of patient records using SW technologies -> Joanne + ericP [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action02]

Some kind of anonymization, will that be covered in the paper?

Joanne: We do not discuss anonymization in paper.

Michel: Next, longitudinal data does not seem to be addressed

Scott: Ex BP, checked at each visit.

(sorry!)

Joanne: Longitudinal connections are being done at the app level

Chris: These connections are best left to the clear objective data

<michel> how do we address the representation of longitudinal data

Michel: Collection of events ordered by time, we deal w. simply
... sparql over events thru time would connect things longitudinally

Elgar: (some subtle objection here)

Michel: This is a domain of information artifacts w. time stamps
... we are not formally treating the timestamping of events
... Will work w. ericP to look at time stamps
... then there's ordering as an important value add

<michel> ACTION: item to longitudinal data - michel, chris and ericP ; find interesting longitudinal query to ask using SPARQL [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action03]

Chris: Trying to keep it very simple
... send Chris example queries re medical or clinical

Michel: Next, assigned to Joanne, Tim and ericP

<michel> ACTION: item to sparql example that identifies AD patients "without the apoe4 allele" seems to only performs a string match against the value of the apoe4 property. [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action04]

Michel: Review #2 w 8 points
... Do we have enough characteristics to make it clinically interesting
... move AD stuff from footnote in methods up into text

<michel> ACTION: item to move AD use case details from methods to use case section - bosse [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action05]

<michel> ACTION: item to Ontology Design section points to “research questions” but wrong table is listed - elgar [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action06]

<michel> ACTION: item to remove reference to "real world entities", as this is not of interest to us - michel [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action07]

<michel> ACTION: item to cite the relation ontology paper - http://genomebiology.com/2005/6/5/R46 - joanne [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action08]

<michel> ACTION: item to Figure 3 in the current version of the manuscript seems to have nothing to do with mappings. This looks like the wrong figure was uploaded ?? - Joanne [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action09]

<mscottm> I don't understand what it means - which questions are being referred to?

<michel> ACTION: item to bring unit testing and data mapping into the use case - elgar + others working on use case [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action10]

<michel> ACTION: item to queries were included as supplementary data - elgar [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action11]

<michel> elgar - add 'queries operational as of XXXX'

<michel> add the answers to the supplementary data document

<michel> ACTION: item to fix first sentence of the SPARQL queries section to 14 listed questions: joanne [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action12]

Michel: What else should we do for this paper?

Joanne: AMIA asks for a demo, address this later

<michel> ACTION: item to prepare response to reviewers - michel [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action13]

Michel: Will create a response-to-reviewers doc
... also need dedicated reviewers
... Scott and Elgar will give the first big read

<michel> ACTION: item to review the paper - matthias, scott [recorded in http://www.w3.org/2011/01/20-hcls2-minutes.html#action14]

Joanne: Will put in a fresh google doc

<michel> response to reviewers - https://docs.google.com/document/d/1XoRj-Ysxa0xOX2n3MBNcG7_dT7cEA4C3ITKn3z1rCPc/edit?hl=en&authkey=CJXJhtsP

Michel: Trying to schedule a meeting w. EHR Oscar(?)

<matthias_samwald> i will probably not be available on Tuesday evening.

<matthias_samwald> yeah :)

Michel: Poster presentations for AMIA

Joanne: We are podium too

<mscottm> Congrats!

Joanne: AZ is interesting for AMIA and would make a good demo
... CSHALS meeting, RPI/W3C doing demo, will show mash-ups, sparql etc

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