Semantic resources project/Meeting notes/2009-08-27

= Notes from August 27 meeting =

Taken by: Kaitlin Thaney

Attendees: Alan Ruttenberg, Elizabeth Wu, Jonathan Rees, Paolo Ciccarese, Kaitlin Thaney, Tim Danford

I. Welcome Tim!

'''II. PRO meeting debrief'''


 * Met with Darren Natale in early August. Gave Darren a presentation on a protein important to Alzheimer's Disease. EW also laid out all the things needed for AlzForum that PRO is not handling as individual records, and also gained a better understanding of proteins and peptides. Discussion about how isoforms, variants and fragments are being curated.
 * Action Items:
 * Darren would give first attempt at using APP as an example, create an ontology, and report back.
 * Alan will translate Darren's file in OWL, and will review the draft ontology with Gwen and Elizabeth.
 * EW to get in touch with Marco - Darren wants a dump of proteins from SWAN in order to use as a resource to include into PRO.

'''III. Develop Work Plan'''

From the proposal, we're responsible for (by the end of 2009):

1. Prepare 2-3 scientific cases, gather infrastructure level requirements, design draft architecture

- have discussed architecture - worthwhile exercise to document.

- Neurocommons extension and annotation project, NC installations - current state of discussion re: Drupal RDF - Web services - New terms

- 2-3 scientific cases - APP integration with PRO - Alan's CHDI work - idea that when people are doing experiments on Huntington fragments, want to make sure fragments survive. (epitope info and antibody resources)

2. Develop 5-6 biomedical data resources together with infrastructure needed to support their use.

a) Antibodies 	 b) PRO c) Mouse Models 	 d) Cell Types? - Have Coriell catalog that TimD and Alan can use as a starting point (possibly Paolo when done with antibody work)

- Harvard Stem Cell researchers had a diagram of stem cell types. Would be perfect input ala LSEs. Not sure if it can be shared.

e) Protocols? Action item: AlanR to review AlzForum DB on protocols.

f) Annotations?

g) Sequence level data - sequence coordinates - suggestion from TimD - Take array designs, use case: start with gene or something annotated against gene, go down sequence, find things that are expressed spatially close but may not be annotated against.

AlanR - idea of a resource that's spatially based seems too big, may be somewhat unwieldy

JAR - but benefit would be that it's a rich resource.

AlanR - perhaps (to TimD) think more narrowly to transcription factors, binding and hypotheses.

Action Item: TimD to draft one page proposal for this spatial data resource focusing on relevance to stem cells. Include what you think the content could be, some sample queries, then present to the group

h) AlzGene - Alzheimer disease pathway resources Action Item: AlanR to review content from AlzGene, then review with members of the team in terms of IDO work already being done.

3. Complete Integration of 1-2 biomedical data resources.

'''IV. Antibodies'''

- AlzForum is in process of migrating to Drupal, moved and cleaned. during this the antibody DB has changed a little bit.

- AlanR curious about criteria / process for cleaning, directly relevant to the project. Human cleaning.

- Concern over data munging and corruption during the translation period, due to past experience where corruption is difficult to correct and recover.

- Need to coordinate with person cleaning the DB.

- PC - concern over Don Hatfield's comments re: SWAN and AlzForum, comes off as that being 2 separate KBs.

V. Action Items (Including ones listed above) :


 * TC and SD: Finalize TimD's hiring paperwork and setup.
 * Gwen and Alan: translate the result to OWL (Darren's file is in OBO 1.0) and then review.
 * EW: to get in touch with Marco - Darren wants a dump of proteins from SWAN in order to use as a resource to include into PRO.
 * TimD: draft one page proposal for this spatial data resource focusing on relevance to stem cells. Include what you think the content could be, some sample queries, then present to the group
 * AlanR: review AlzForum DB on protocols.
 * AlanR: review content from AlzGene, then review with members of the team in terms of IDO work already being done.
 * SD: Getting Stem Cell Ontology into the cell type resource.
 * AR/JAR/KT: ask SD specifically about requirement documents or use cases that are used in SCF development, specifically StemBooks and PD Online.
 * EW: work on getting search logs again.
 * Alan Bawden: evaluate search logs, if and when obtained. Could consider setting up pipeline so NLM updated nightly /frequently. Maybe even have an escape hatch for queries.
 * KT: craft outline of report
 * EW: Connect AR with person cleaning AlzForum database.
 * JTW: talk to Eve Nichols about AlzForum's antibody ToU re: interoperability and integration concerns.
 * KT: Ping group on NC installation at SCF.

Adjourned