02 Dec 2010

See also: IRC log


+1.617.947.aaaa, +1.860.440.aabb, mscottm, +1.610.651.aacc, epichler, +1.518.276.aadd, EricP, Bob_Powers, +1.617.947.aaee, +1.617.947.aaff
mscottm, Susie


<Joanne> I couldn't get on the mbit client

<Susie> Scott gives update on BioRDF

<Joanne> I'm 518

<Susie> Presentation from Adrian Coulet

<Susie> Did work on text mining using PharmGKB

<Susie> And created an ontology from that data

<Susie> Also presentation from Dietrich RS on SESL

<Susie> It has many ties to what we are doing

<Susie> Using microarrays in both projects

<Susie> We've been looking at federation with SPARQL

<Susie> Will give tutorial on this topic at SWAT4LS next week

<Susie> EricP will dial in remotely for this

<Susie> Will use Uniprot and GO annotations from UCSC

<Susie> Similar to what we started to do with the microarray data

<Susie> Continue to work on type of RDF to represent microarray data

<Susie> Will work with scientific discourse and array express

<Susie> Tim talks about scientific discourse

<Susie> one thread align swan, obi and myexperiment with microarray representation

<Susie> using mged and obi for that

<Susie> set up relationship with Susanna Santone at University of Oxford, and Philippe

<Susie> being done with swan, myexperiment and obi

<Susie> will be able to represent experiments using genetic epidemiology or population studies

<Susie> Have the data in private db and then release publicly when ready

<mscottm> ISATAB - ISATools, ISACreator, etc.

<Susie> columns are aligned to identifiers in ontologies

<Susie> excel workbook with tabs for entities

<mscottm> http://www.slideshare.net/proccaserra/hcls-sci-discisa2rdf

<Susie> also working on rhetorical document structure which is lead by Anita de Waard

<Susie> Has sub-comments, 1 is orb

<Susie> Tudor Groza is working on an HCLS note on that topic

<Susie> Also a mid-grain ontology in a draft form, which was proposed by Elsevier

<Susie> Fine grained ontology by David Shotton and others

<Susie> Moving towards supporting the text mining community

<Bob> Tim: supporting the text-mining community is a good way to advance linked data

<Susie> Ontologies are beginning to form a nice dense web of models

<Susie> Scott talks about terminology

<Susie> Progress on mamagram use case

<Susie> Talk about ways to prototype ideas relating to discrepancies between reports

<Susie> John Madden has reports in XML that he's seeing if we can start with

<Susie> Aiming to put in an NIH grant, but will need to have finished prototyping in order to write it up

<Susie> Eric gives update on COI

<Susie> NCI work on adding semantics to web services is happening in COI wiki space

<Susie> Hasn't started his contract there yet

<Susie> NCBO seminar yesterday that referenced this work

<Susie> Susie update on LODD

<Bob> "Google it up" is now a verb.

<mscottm> scribenick: mscottm

<ericP> NCBO webinar list

Susie: We're working to finish the paper for J. of Cheminformatics
... will refer to recent RDF data, and the Allen Brain Atlas work.
... Still interested in writing a Best Practices document. We'll move to that as soon as the paper is done.

<ericP> slides for Dav Hau's NCI webinar at NCBO

Susie: We will also consider the role of LODD. One role: LODD could be a useful place for people to publish their data.

<Joanne> thanks Eric (you're faster than I am - I was just back to the window to paste!)

Susie: With time, I think that there should be more effective search mechanisms but this is a good start.
... With my role in PRISM, we are interested in creating a document about our data needs for distribution to NCI, NCBI, and Pistoia.
... Interested in working with other organizations to create quality standards for linked data.

Joanne: RPI is involved with U.S. and UK gov linked data.

Susie: PRISM is interested in creating quality standards for Pharma.

<michel> question: what does "high quality" mean

scott's definition: annotated with provenance

Joanne: RPI would be interested in any service of URIs and linked data.

<ericP> WEBEX recording on Dav Hau's NCI webinar at NCBO

Susie: We'll keep you posted on our progress.

<Bob> Susie: Quality = make sure data are linked together so makes sense

<Bob> ...quality also means a service level of availability

Susie: Make sure that there are links between things that are supposed to be the same.

<scribe> scribenick: Susie

Michel updates on TMO

Submitted paper on J. Biomedical Semantics

Lead by Jim and Joanne

Nice section by EricP on unit testing for ontology development

Considering next areas of work

Representing genetic variations is of intrest

Want to represent htis information accurately

Want to do more work to integrate with other ontologies

Want working eHR system

Should look at options that are free and available, that have web interface, support for terminology

joanne: we still have some clean up work for the paper
... want to work with a hospital or ctsa center

<Bob> Susie: Been pondering collaborating w i2b2, Kohane's lab

<Bob> ...there is ontology hive inside i2b2

joanne: want to make a valuable contribution

<Bob> Susie: We have agreed to share our extended i2b2 platform

<Bob> Scott: Any EHR project in IMI?

JJ& is involved in the UBIOPRED and BTCure projects, and also one in oncology

<mscottm> I know of EHR4CR

<Bob> Scott: OPS Open Pharmacological Space

<Bob> Susie: Integrating omics data for clinical trials, etc, rather than for patient records per se

<ericP> q!

<Zakim> ericP, you wanted to talk about i2b2



<Zakim> michel, you wanted to talk about openmrs

<Bob> Michel: We seem to be fragmenting among various task forces

<Bob> Eric: Where would we develop interface code? Which source do we acquire first?

Michel: could we use i2b2 as a rally point?

Eric: best value is in showing we can work with both i2b2 and indivo, and that they couldn't easily work together without us

Scott: if we had pathology report that fits in indivo that could enable connect to other tasks

Michel: absolutely what should happen

Scott: anonymized data would be ideal

<Bob> (Chime is at Cleveland Clinic)

BioRDF could be a consumer of text mined data

Scott: please share other thoughts about connection points

<Bob> Scott: Biobanking is a great platform, tends to get wet-lab scientists excited, for search as a first step

<Bob> Susie: i2b2 has interest in support for biobanking, along w. omics

<Bob> ...Crimson hive in i2b2 is for biobanking

<mscottm> David Cox (Pfizer)

Summary of Action Items

[End of minutes]

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Present: +1.617.947.aaaa +1.860.440.aabb mscottm +1.610.651.aacc epichler +1.518.276.aadd EricP Bob_Powers +1.617.947.aaee +1.617.947.aaff

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Got date from IRC log name: 02 Dec 2010
Guessing minutes URL: http://www.w3.org/2010/12/02-hcls-minutes.html
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