Semantic resources project/Meeting notes/2010-09-02

Broker

 * Adding better provenance for Requests/Metadata
 * creator, date on metadata
 * identity of status changes
 * /status entry for reading legal status changes.
 * TWD: needs to add an API call for getting the status changes
 * PC: will review tomorrow the unimplemented features, and assemble list of required points for hooking up the annotation framework.
 * Automatic indexing OBO ontologies from the Sparql endpoint
 * PC: going to write up the annotator's use case for adding new users, ontologies, maintainers?
 * AR: we need to add "broker maintainer" as a use case, requirements, implementations.
 * Document Review
 * change the "annotator" and "ontology maintainer" boxes to people
 * write up a use case diagram for the *annotator* escalating a request.

External Comment on Ontology Term Request Broker

 * Goal is to enable Paolo to begin hooking up Annotator to Broker some time next week
 * Hilmar sent back this link: http://phenoscape.org/wiki/ORB_term_request_prototype
 * Link for adding Lucene support on GAE: http://code.google.com/p/gaelucene/
 * Paolo Action Item: Write up broker maintainer user and requirements
 * TWD: should document these flat file formats for the wiki. Allocate 3 hours next week to doing above AI

Mouse Models
http://neurocommons.org/page/Semantic_resources_project/MouseModels/Questions
 * JAR shows notes from his, AR's call wtih Mike Sasner.
 * Goal: get a namespace of some kind (ideally: one that already exists) for mouse strains.
 * "36% of the strains listed by JAX "for sale" are not in MGI."
 * JAR has the list of missing strains, and is waiting to send them to MS.
 * next step: talk to Jannan. If that fixes the discrepancy, then another iteration is required to figure out why it doesn't match.
 * Action Item: JAR to sent  invitation to Janan after organizing questions by end of tomorrow (Friday)
 * JAR: http://sux4j.dsi.unimi.it/ has implementations of perfect hash
 * Timothy has done work on representation of strain/modifaction/phenotype
 * Action Item: Alan to review
 * After alan has reviewed, next review will be Jonathan for completeness - is it a full recipe for generating OWL from the information he has
 * Action Item: Paolo to get someone on SCF side to review the representation proposal
 * JAR: I wouldn't call it a 'proposal', it's more of a brainstorm at this point... but worth looking at anyhow
 * AR had some crtiticisms earlier that have not been adequately resolved
 * http://neurocommons.org/page/Semantic_resources_project/MouseModels/Bottom-up ( See emendations at bottom. )

Tau

 * TWD: sends an email to Gwen & EW with Tau diagrams and OBO examples.
 * AR: Tau representation has not yet been reviewed by Gwen, so not ready to send to Darren.
 * Action Item: Timothy to send mail to Gwen explaining and asking to set up meeting next week for further discussion. * Tau is highest priority after broker and we expect to work on it intensively next week, once Paolo is able to hook broker to MGH Annotation Framework.
 * Authentication: People here prefer openid. Paolo needs to discuss it with his team. AI: Report back early next week openid or not. If openid then proceed. If not, discuss at next meeting
 * AI: Paolo by end of next week to document what we need to know about how to use openid to authenticate web applications (such as our Broker) (as distinct from a user interface)

Broker Administrator Brainstorming

 * Set up the brokert to handle requests against a new ontology
 * Cover issues for installation
 * annotation interface wants 25 ontologies quickly (is this possible)
 * Two approaches for adding an ontology
 * Negotiate a bulk request format with ontology maintainers. Write new code/spec for this format.
 * If we don't negotiate, then immediately "escalate" and use email to manage request