Bioinformatics TC Agenda July 18, 2013

  1. Speakers for HPP sessions Yokohama (Young-Ki Paik and Gilbert Omenn).
  2. Plan for a working session at Yokohama for chr. Teams to update sections of the Wiki (Peter Horvatovich) see under the following link.
  3. High confidence phosphoylation sites listed in GPM in a set of files located at the following ftp server and acetylation protein N-terminal acetylation information on the following link , as well as the latest on missing or 'black" proteins (click here for more details).
  4. Progress with Submission of data sets to Proteome Exchange (all)
  5. Status for submissions to JPR special issue for 2014 (manuscripts being received, requirement for data uploading at time of submission, acetylation and phosphoprotein identification encouraged in this year's report).
  6. Updates from PRIDE, Peptide Atlas, GPMDB, web browsers for special issue
  7. Submission of special data sets to Wiki.
  8. Yokohama program:
    • Initiative Session 3 (Sun)
    • Joint PSI / ProteomeXchange / KBpC
    • Initiative Session 12 (Tues)
    • C-HPP (part III)
    • Will be a joint C-HPP and Bioinfomatics session
  9. Metrics for special issue in JPR
    • Ensembl Gene annotation for genome metrics (newest v.72)
    • neXtProt gold
    • Peptide Atlas canonical
    • GPMDB green
  10. The list of "Gold" phosphoproteins according to neXtProt is available here. The listed 6831 entries have at least 1 experimental phosphosite annotated as "GOLD" in the current neXtProt version (neXtProt release 2013-07-15). This list could be used as a starting point to consider PTMs in C-HPP.