Semantic resources project/Meeting notes/2009-10-29

= Notes from October 29 meeting =

Taken by: Kaitlin Thaney, Tim Danford

Attendees: Jonathan Rees, Paolo Ciccarese, Kaitlin Thaney, Tim Danford, Tim Clark (dialed in), Alan Ruttenberg

I. Establishing consensus on 5 resources:


 * Pre-established resources:
 * SWAN
 * Mouse Models
 * Antibodies
 * PRO
 * Other candidates (need 5th for reporting purposes):
 * Information from Entrez Gene
 * Pubmed article records
 * Cell lines
 * ChIP Experiments
 * Genomics experiment indexing
 * Tim C. suggests “brain regions” (but we wonder if these last two that are well-represented in NIF) This falls under the rubric of INCF that Alan is working on.
 * Alan and Tim both like the pathway idea.
 * Add Pathways as 5th resource, include cell lines and protocols in "Future Work" section of report

'''II. Discussion on Cell Signaling Dataset'''

and AF site data.
 * Discussion of going back and asking them for more data, things not included in the table (research methods to create and verify antibodies IN the table, but no Pubmed references ... though they're listed on the Web site)
 * PC, TD, AR will draft a short email asking for more information.
 * Discussion of trying to identify duplicates (antibodies and offers to sell) between this
 * PC: has identified a list of proteins related to heat-shock proteins, will go over with Don Hatfield and send them to PRO.

'''III. Discussion about antibody sources and work '''


 * Currently sources are AlzForum Antibody and Cell Signaling.


 * TC: thoughts on using Exact Antigen
 * AR: To use, there may be a cost. Would need to assess budget. Issue of false positives. Note: AR's last interaction with them was 3 years ago.
 * TC: Put in the queue to approach, see if we can work out financial issues and work something out.


 * Pulling the protein names out of the AlzForm table.
 * AR has done work on this. Built up a dictionary: NCBI, entrez gene, OMIM, uniprot; handles transliteration and families; identifies unique and ambiguous hits.
 * TWD: I will ask alan for this.
 * PC: can we encode some of the rules we’ve learned for the HSP proteins?


 * AR to approach ABCam

'''IV. Proteins Resource Discussion'''


 * PC: Talk to Don for list of proteins selected from antibody resource. EW had said they were interested in the subset of antibodies and related proteins ... perhaps they'd be interested in this? PC to make contact


 * TC: How far is this from completion?


 * PC: If you look at list they sent before, looks pretty structured. Need to ID protein and reactivity, add link to publications (which is in the table?)

'''IV. Web service'''


 * TC: Talk about the need to get a new provisional URI created, done via Web service to shorten response time. Need process to do ongoing annotation. Can we get Alan Bawden to help?


 * AR: the Web service mechanics are the easiest thing, what’s hard is getting buy-in from the back end and the process for substitution. Need to take the proteins from Alzforum, and then meet with Darren Natale (PRO) and talk with him about automating the process.
 * TWD: send mail to Darren, setting up a meeting for AR / TD / PC / JAR.

'Off phone with TC. KT leaves.'

V. Additional discussion on proteins

modified clone number -- 4F3 vs. 4F3-E8
 * AR: talks to PC with examples of the heat shock proteins.
 * discussion of "conjugated" antibodies, and how these need to be represented.
 * Spends 15 mins with PC, googling an example of an antibody with a

'''VI. Action Items'''


 * AR / TD/ PC: draft what add'l info we want from Cell Signaling Technologies, detail issue of duplicates. Send to CST.


 * PC: talk to Don Hatfield from AlzForum about the names to submit to PRO.


 * PC to then send list of proteins from antibodies in AlzForum to PRO


 * AR: send TD details and code from previous work pulling names (HCLS, MLNM work), see if TD can integrate with any of his existing work.


 * AR: follow up with ABCAM.


 * TD: draft note to send to Darren @ PRO to set up meeting (send to AR for review first). AR / TD / PC / JAR to be in attendance at PRO meeting.


 * TD: mine pathway file for protein information.


 * KT: Continue to sift through content on wiki for content that can be repurposed or a starting ground for the report.

Adjourned