Semantic resources project/Meeting notes/2009-05-22

Notes from May 22 meeting
Taken by: Kaitlin Thaney, edited by Alan Ruttenberg

Attendees: Alan Ruttenberg, Elizabeth Wu, Sudeshna Das, Jonathan Rees

I. Discussion of JSON / SPARQL - broader interoperability issue.

Joined by telecon: Stephane Corlosquet, from DERI Ireland. writing RDF proxy module for SCF/Drupal.

Discussion of RDF/JSON format for SPARQL results. Alan to investigate matter with Virtuoso.


 * AR discusses potential interoperability issues suggested by SPARQL CONSTRUCT query mentioned above.
 * AR: Related to first specific aim of our proposal Develop procedures for the translation of SWAN/SCF objects to and from RDF so that SWAN/SCF knowledge can be made available and integrated with the KB and other Semantic Web content.
 * AR: If schema for gene in NeuroCommons is different from schema for gene in SCF then the there are potentially two ways to query for the same information. Advise is to not have different vocabulary.
 * SC: Mapping of RDF to RDF is generic part of Drupal RDF architecture. Export would not expose the internal schema.
 * SD: Questions whether there is really an interoperability issue here.
 * AR: Raises issue of open source development of SCF and embedded SPARQL queries and maintains concern. Asks to learn more so that assessment can be made.
 * Action: SC to send further information on architecture and requirements that he's trying to address in Drupal for SCF to our mailing list. This will give us better material to form a basis of discussion about whether interoperability will in fact be a concern, and if so, discuss ways of moving forward in that address both existing requirements and address these concerns.

II. Review of antibody action items from May 18


 * EW met with Don Hatfield, antibody curator for AlzForum.
 * EW and AR have been reviewing desparatelyseekingantibodies, see Semantic_resources_project/Antibodies
 * Still trying to get the search logs for AlzForum
 * Observations:
 * Terminology issue on the free text field in desparatelyseeking. need controlled vocabulary
 * Might use text information retrieval tech to get some information on epitopes
 * EW notes that Don has moved from comprehensively gathering antibodies to more targeted selection of research relevant ones. We might pursue same strategy in prioritizing work.
 * Action: Schedule information gathering meeting: AR, EW, JAR and Don Hatfield - goal: familiarization, talk about IDs, epitope, examples of papers he's pulled antibody info from, get from Don some knowledge about what kind of info he's using and looking for so we get a better idea of how to approach this part of the project.

III. Hiring

Feedback from AR and JR on discussion with candidate.

IV. SWAN / AlzForum interaction

Brief check in on status of SWAN/Interaction with our project.

V. PRO next step

Action: AR and EW slim down presentation for PRO meeting. Alan to ask PRO folks when they can meet.

General discussion


 * Mention of bugtracker system to track / manage tasks -- bugs.neurocommons.org. Action for Sudeshna to inform SCF team about its existence.
 * Discussion of goals of the project and role of proposal in guiding project planning. More discussion needed as we don't all share the same views as yet.