SWUG:Meeting 2010 09 28

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
  • increased emphasis on reuse
  • Transition to OWL
• 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