<matthias_samwald> high five!

scribe Bob

<mscottm> scribenick Bob

Automate radiologists and pathologists communication

Formulate appropiate queries, whether reports are consonant or dissonant

Scott: Been involved in DERI project, we have put that use case front and center
... can use that as a use case to leverage w. Terminology
... Pink Ribbon project in Netherlands
... might look for connection w. Pink Ribbon on breast cance
... breast cancer is a familiar area for radiologists, paths

Some RDF infrastructure is already in place for this use case

scribe: also have some XML data

Scott: Last HCLS call, agenda re i2b2, relevance, demos etc.
... also talking about EPRs
... Indivo has been sorted out by ericP

EricP: i2b2 is in triple format, combo of concept code, value, unit
... a bit of structure for describing events, facts

<mscottm> Sorry - that was me I solved it

EricP: working w. Dave Connally(?) to take RDBS

<ericP> connolly

EricP: Question: go to i2b2, Indivo datastores

<mscottm> KUMC = Kansas University Medical Center

EricP: Work is happening KUMC

Scott: Looking for connections w. particular task forces

EricP: Working w. proposals for funding

Scott: Productive fun, get that going

Tim: Sci Discourse, last call Dec 20
... Working on a number of related threads:
... rhetorical document structure; There are a number of efforts in the group to bring one model together
... working to put a spec together: ORB Ontology of rhetorical blocks
... similarities and differences; Want semweb representation independent of order of entities
... Also bibliographic references and citations
... want to satisfy library requirements
... FRBR Functional requirements for biblographic records
... want to satisfy FRBR, SWAN and others
... paper coming in J. BioMed. Sem.
... Also Data interpretations: OBI, myExperiment and SWAN
... no paper yet; we have a first cut OWL model
... Annotation ontology, now being extended(?)
... Scientific article of the future: Status is that nobody has done anything yet :-)
... interesting workshop: Beyond PDF
... this workshop is very relevant to our group
... We started several different threads at the beginning of last year
... code is coming around some of these threads

Scott: BioRDF last couple of months submitted to Problems workshop
... microarray studies; also text mining
... most recent call, started looking at how to build on microarray work
... important: re-using existing microarray analyses
... RDF analogue of what Gene Atlas already does
... hoping by creating another pub, show how to issue sparql requests

Q: How far away from having stack for GeneLib?

Scott: Number of people think that it's fairly trivial
... it's already tabular
... another step is to take it to publishers; important to upload data
... see if we can get this moving. It is an inevitability.
... trying to create infrastructure
... much of the data is already in json

Tim: Would really like to see a spec on this!

Scott: OBI reps of experimental conditions; but our scope is somewhat larger

EricP: Would a simple spec be sufficient?
... trying not to volunteer :-)

Tim: Would like to see a capstone, b/c other people could use the representation
... carve out a subset of OBI
... we could integrate experimental conditions from OBI, no problem

Sounding here like a big agreement on a push for this.

Scott: Capturing results of text mining --> RDF, can go full circle
... creating a M&M section; perform microarray in Traverna, store in triple store
... Tim really important angle, to plan the conclusion on this

Tim: There will be a doodle poll on how to close the gap

Scott: Article, note or practices; these are all possibilities
... COI

EricP: i2b2 stuff. The other side is Mark Wilkinson project to make web services w. graph pattern

<mscottm> re: Mark Wilkinson (and Chris Baker and Michel Dumontier) SADI project

Scott: LODD

Susie: LODD taking minimalistic approach w aggressive time frame
... document that outlines best practices for generating linked data
... people w. experiences encountering roadblock after roadblock
... need realist view of the world, or can one take shortcuts
... have identified a number of different issues
... Feb 1 deadline for a paper
... Scott is also driving the effort in describing best practices

<michel> http://linkeddata.org/guides-and-tutorials

<johnM> guys, I've got to go. Talk soon, Scott.

<mscottm> Thanks for coming John.

Michel: Important that any document also goes to the link above

Scott: Michel on TM

Michel: Demo, still a few issues on patient records, EricP, Joanne, Tim
... a bit akin to what we were talking about with Tim above
... keen to know about overlaps in healthcare. EricP is bridging groups
... would make sense for COI to be brought into TMO?

EricP: COI happening independent of calls.

Michel: EHR stuff is happening in TM. Records, datasets

EricP: COI is acting as clients of TM, no modeling suggestions

Michel: Wonder if we should consider to revive COI?

EricP: Indivo and i2b2 integrated w. workflow will add momentum

Scott: 1) COI coming back?
... 2) TM is going inevitably into patient records
... should make it clear outside that TM is doing this work, more prominent

EricP: All for it.

Scott: Re-frame the work of TM, make patient records more front and center?

Michel: Have an opportunity to showcase; want a revived, active group.
... brother is at McMaster, work going on there about Indivo.

Scott: Good to be transparent from main web page; TM doing stuff w. patient records, COI in sleep mode.

Michel: Planning F2F before EO charter??

Scott: F2F has been un-planned.
... has been judged not be important. But worth considering again; it is getting late.

Michel: Have been discussing HCLS re-chartering with some people.

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