Software Group progress report for 2010

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Revision as of 12:12, 1 December 2010 by Amina (talk | contribs) (OBO-Edit)

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Annotation Support


Production (Stuart, Gail, Ben, Mike C)

  1. Rebuilt goweb-dev (not replaced)
    • Upgraded OS from RH 32-bit -> RH 64bit
    • Upgraded mysql from 5.0 -> 5.1
  2. Replaced GO loading machine
    • (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks
    • (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)
      • sucessfully tested loading on claret
      • have also done initial testing on load-qfo replacement for loading sequences into godb
  3. Ordered 2 machines to replace GO frontends, goweb1/goweb2
    • Anticipated that these machines will be into production by the end of 2010.
  4. During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.
  5. Worked on testing and installing of Amigo 1.8 (required 64bit OS for clucene-based searching)
  6. Made several upgrades to GAF filtering script
    • update from GAF 1.0 -> 2.0
    • added the following feature_types
      • gene_product
      • polypeptide
    • added the following evidence codes: IMR, IRD
    • added qualifier 'rapid_divergence'
  7. Put in place script

Schema Overhaul

Schema Overhaul

  1. SQL schema creation into postgres through a java program
  2. generation of TSV files through Schema_Overhaul#OBO_Access_Layer except the following tables (in progress)
    • ontology_imports, ontology_subset, all_only_relationship, never_some_relationship , relation_chain
  3. Schema_Overhaul#OBO_Access_Layer is in progress
  4. loading of TSV files into postgres
  5. incremental update of the GOLD database (in progress)
  6. Command Line Interface is built
  7. Basic Admin servlet interface is built to run the db operations through a web interface (in progress)

(this may belong in a separate report - add here for now anyway)

Annotation QC



  • Overhaul with different layout, some organisational changes, more easily accessed menu navigation, vertical rhythm
  • New documentation for ontology relations, structure
  • Updating of tools list (hampered by lack of new tool submissions)

Workflow Support

  • Created a basic GO_Galaxy_Environment
    • integrated map2slim
    • integrated slim-creator
    • integrated enrichment tools
      • GO TermFinder
      • Ontologizer

MOOSE libraries

  • Ontology slimmer
  • Ontology and annotation slimmer (map2slim)
  • Added algorithms of transitive closure and transitive reduction for use by slimming scripts
  • Started some preliminary support for basic boolean logic (for creating bucket terms)

Reference Genome Support

RefG in AmiGO

  • Loading Trees (SVEN)
    • Matching IDs
      • Currently ~64% of of the ids are being matched after the new QFO load.
      • Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.
    • Report Pages
      • 2. Concurrent annotation: Code written, not part of load yet.
        • Some group name in file provided by Pascale Gaudet are not in group list. Informed Paul Thomas.
      • 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is




Ontology Support


See Compositional_Term_Submission_Tool

  • Created initial prototype, in use by ontology group and annotators
  • Integrated autocomplete
  • Added involved_in template


Transition to OWL

See Transition_to_OWL