Scientific Discourse Meeting, January 23, 2012

Notes:

1. Use case 1 status, Rich Boyce:

gearing up for the C-SHALS presentation
in abstract we talked about a conceptual prototype for 2 packages, this is now available
Now going through the process of building a linked data set and revamping prototype in Linked Data standard
Current prototype: what does Package Insert enhanced with scientific literature look like? Now, want to mark up a paper, take annotations and bring into Linked Data graph and link to section in Package insert for two drugs
code will be posted here
Project page for the code here
Road map with milestones, are dividing among themselves
Now have all the structured product labels in the code repository and scientific articles for 2 drugs at C-SHALS
Met with Pieder Caduff to discuss XPharm/Pharmapendium to discuss details; figuring out protocol for this
Should talk to Provenance group; as Elsevier opens up Pharmapendium we should bring in some provenance markup to identify where data comes from - is Satellite standard compliant with new provenance standard?

Anita to do: look at Satellite and PROV overlap Rich: at noon I will have a few full-text annotated with Sapienta will send it around

2. Use case 2 , David Shotton -

Stripped out information re. infectious disease - diagram mibio.png sent around earlier
Form to fill in is here can generate a report in the middi format in XML; recently at a hackathon people repurposed this format to describe cancer research papers
Now want to share with rest of the team and see what next steps are

Q Anita how can this be used? A: david: can accompany article as a supplementary file; can be published separately e.g. as a pointer to the article or as a submission to e.g. Dryad or other data repository

Questions: 1) Are these the right things you want to add 2) How/where is it added?
Anita: suggest also looking at Rutgers research data metadata

3. Use case 3

No news, ask Joanne Luciano for update next general meeting

4. Next calls:

We'll keep 4-week general call schedule
Next general call February 20: Anita will invite someone from the PROV group to present [1]
Next week (January 30, 2012): Paolo Ciccarese will present re. DOMEO

Agenda:

1. Enhance Drug-mechanism Knowledge in Drug Product Labels

Team: Richard Boyce, Maria Liakata, Jodi Schneider, Mike Taylor, Anita de Waard

2. Defining core metadata for describing biomedical investigations

Team: Tim Clark, Susanna-Assunta Sansone, David Shotton, Philippe Rocca-Serra

3. Mining Treatment Outcomes

Team: Joanne Luciano, Anita de Waard

4. Any other business, next calls.

Dial-in & IRC Information:

Time: 10:00 EDT
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Duration: 1hr