Semantic resources project/Meeting notes/2010-09-16

Meeting : 9/16/2010
In attendance: TWD, PC, EW (by phone), AR & JAR (starting at noon)

Tau/PRO

 * PC and TWD review Tau queries with EW by skype
 * Queries broken into two categories, based on whether they are useful for antibody or disease queries
 * Antibody Queries
 * ISOFORM queries: "what are the isoforms of Human Tau? What is their exon count (parts)? Which isoform contains the fourth microtubule binding region repeat? How do the human isoforms of tau correlate to the mouse isoforms? Which human isoforms can contain the variant Ser212Arg?"
 * VARIANT queries: "At what sites does human tau contain variations?"
 * MODIFICIER queries: "At what sites does human tau bear phosphorylation marks? Which phosphorylation marks does human Tau isoform N2 R3 carry?"
 * Disease Queries:
 * Protein complexes: PHF and NFT
 * "hyper-phosphorylated tau"
 * Elizabeth points out
 * TWD needs to start examining Mouse Tau
 * Align mouse isoform and human isoform names?

Broker

 * TWD: building test suite corresponding to functional requirements, for broker
 * each protocol message gets one or more JUnit tests proving that they work
 * built around an JSON Schema validator (JSON Schema expressions form a key part of the documentation)
 * PC and AR conduct discussion over the possibility of a 'permissive' broker which does not require ontology identifiers attached to all requests
 * PC takes an AI to write up better documentation for the permissive request broker variant.

Mouse Models

 * JAR and AR finished phone conversation with Janan Eppig this morning
 * JAR's summary of that meeting to follow
 * AR: positive response from JE

Action Items

 * TWD: email to group with much smaller (2!) examples for Tau.
 * TWD: experimental regexps for Tau isoforms/variants/modifications for Tau antibody records
 * PC: write use case, task list for 'supervisor' role, associated with the resolution of ontology-ambiguous requests in a 'permissive' broker