SWUG:Meeting 2010 09 28

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Conference call details: New GOC conference call numbers:

US: 1 866 953 9688
Outside US: UK 0808 238 6001
pin: 801561


Topics

  • AmiGO_1_8 Release
    • Estimated release time
    • Release Schedule for AmiGO_1_9
  • Production_and_GO_Admin#Switch to load-qfo-seqs.pl
    • Existing sequence loading is slow and memory intensive
    • New script depends on QFO fasta files provided by EBI
    • ~60 genomes, subsumes RefG set
    • also takes care of ID mapping / gp2protein
    • Current issues:
      • latest dump excludes DB prefixes
      • ACTION: Sven, report back
  • Software_Group_2010_Future_Plans - any questions arising from presentation at GO meeting
  • Schema_Overhaul
    • ARRA Funding
    • Berkeley - one hire 1 yr, starting October. Stanford: ?
    • Proposed: Berkeley hire will focus on ontology related db elements, Stanford hire on annotations
    • New architecture: java, use of OWLAPI for ontologies
    • Dual db strategy: "gold", "lead" - bulk loading, less normalized schema, optimized for db loading and queries
    • Exploration of non-relational technology: SOLR, triplestores, QuickGO indexes
    • Emphasis on expressivity, being prepared for next 5-6 years

Idea: have SGD ARRA developer work on MART/Mine for GO? Use case: give all mammalian genes with annotations to term X