Semantic resources project/Meeting notes/2010-04-15

Participants: Alan Ruttenberg, Tim Danford, Paolo Ciccarese, Kaitlin Thaney, Sudeshna Das


 * Mouse resource

- Starting point is MGI, JAR looked through it, lots of good information.

- Mouse Phenome database (also at JAX) - data is available

- List from JAX Mice Portal - subset of what's known in MGI - information on mice JAX raise (on the wiki) - includes things like price, availability.

- AlzForum mouse resource - HTML tables

- IEDB immune epitope database - has relevant mouse information, may be worth reviewing.


 * PDOnline Mouse Resource (SD)

5th Resource


 * SD Proposals


 * Cell types

Arguments for:

Community that cares about it and resources to start with. Large overlap with immunology community.

Next step : Set up meeting of AR, SD, Alex Diehl (sp? and Andres. AR and SD to exchange papers

- BioPAX issue: JAR/AR would like to stay away from it. Closed, doesn't use OWL in a reasonable way, doesn't buy into semantic web, restrictions on data models, don't use URIs properly, cannot add external info for the format - not in an extensible format, have to do virtually as much integration work with the BioPAX information as you would if you started with native format = FAIL.
 * Pathways --

- SD: need to represent edges so you can map the nodes, the claims, PubMed references


 * Mutations (ie., off AlzForum web site) - mutations, phenotypes, other descriptions and references.

- SD concern: being done in other contexts. - PC: matter of time, how reasonable is it that we could finish by november. seems like it's not huge in terms of dimension and alongside some of the mouse work.

- AR: what's the different between this and AlzGene - collection of genome wide association studies ; SD says this talks at the level of the gene where the mutations speak to the specific mutations in the gene.

- AR's gut instinct is that this would be the best to tackle, path of least resistance and profitable.

-


 * AlzGene -- lots of work.


 * Review of Antibody Resource

Action Items


 * Definitions, term requests from PRO where necessary, a relational quality to describe concentration and other aspects of the solution -- then review -- then think about automatically putting stuff into this form