Semantic resources project/Meeting notes/2010-04-08

April 8

Participants: Tim Danford, Elizabeth Wu, Paolo Ciccarese, Jonathan Rees, Kaitlin Thaney

Notes taken by: Kaitlin Thaney

Alz Resource


 * Discussion of format issues (currently represented in HMTL table, TD to scrape and represent in tabular format)


 * Annotations in PATO (phenotypic quality ontology)?


 * Talk about citation
 * AlzForum has citation database (paper of the week, in PubMedID)
 * at the very least, AlzForum to provide set of correspondences between POW IDs and PMIDs - in index form / dump.

Antibody Tool


 * Continue testing.


 * New menu item "Read Data sheet" opens URL behind the scenes, not in browser, pulls text (word, hmtl, pdf) and displays in a separate window. allows you to highlight and pull into main window and create new fields associated with the antibody and those themselves can be annotated.


 * What's missing from the tool?

Mouse Models


 * Discussion on the mouse-strain mailing list right now:
 * how the resource going to be maintained / managed in the long term -- property longevity issue.


 * question of strains, genotypes, what these terms actually mean


 * when Alan provide copy of JAX data dump
 * what's already on jax site already and to what extent does the workflow align with the existing antibodies workflow - or differ.


 * Need to create model and infrastructure (manipulation of MGI, provide some RDF for MGI) - low level requirements from PDOnline.


 * Set of possible goals for mouse models resource


 * Trying to define a model (MGI or JAX as a start) and see what we can get out of that, without involving community process, see what we can gain. Once we prove that we can use that as the goods to exchange / propose to wider community.


 * Scrape AlzForum for basic information, do a join based on PubMed ID - integration.


 * TD to work on getting a dump from MGI, work on that.

5th resource possibilities


 * Decision/Consensus by May 1 on what this resource will be, what the strategy is.


 * Cell lines


 * Mutation Database from AlzForum


 * Pathways

Action Items


 * TD: scrape and represent in tabular format the AlzForum HTML table.


 * Look at single behavioral phenotype and see how far away it is in PATO, how to annotate in AlzForum, gain better understanding.


 * TD/ PC/ EW/ JAR: Continue testing antibodies software.


 * Alan / JAR - get data dump from MGI for TD / team


 * TD: Send Alan example of 10 antibodies for example of model


 * TD/ EW/ JAR/ PC: Make sure annotation tool is installed, working, updated on Paolo, Elizabeth, JAR's machine


 * TD/ JAR: Integration / hook up of annotation framework / annotation tool with triplestore


 * PC and Alan: Mouse models - discuss what strategy is and how to move forward.


 * PC to discuss with Alan next Monday