Software Group Progress Report Q2 2014

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Progress Report Q2


  • Drupal
    • Drupal Content: migration complete (Moni, Seth, Rama, ...)
    • Drupal Rollout: migrated to AWS, still testing (Seth, Stuart) JIRA GO-106
  • AmiGO
    • AmiGO 2.0 released in March (Seth)
    • AmiGO 2.1 in testing May (Seth, Rama)
  • Term Enrichment
    • Panther services integrated (Anushya, Seth)

Authentication / Authorization

  • Gathering requirements at CalTech hackathon
  • Implementing Persona authentication into Noctua

LEGO: Noctua/Barista/Minerva

  • Implemented prototype system, 3 components:
    • Noctua: client component
    • Barista: messaging/session layer
    • Minerva: OWLServer
  • CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua noctua-51
  • Implemented v1 of LEGO->GPAD/GAF in OWLTools JIRA GO-288

Transition to OWL and ontology support

Top-level ticket: GO-222

  • Berkeley OWL hackathon (with David and Tanya): gathered requirements, tested roundtripping, reasoning etc
  • Added import catalogs to OE (this allowed us to add all logical defs to main ontology)
  • oboeditor plugin for Protege v0.1 (Heiko, Simon J)
  • Fixes to obo/owl converter for never_in_taxon links
  • TG templates (HEIKO TO ADD)
  • ...


  • GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS)
  • Added 2-way converters to OWLTools (Heiko)
  • GPI exports direct from MGI (Mary)

Retire GO Mine

  • Done? (SETH/KALPANA)


  • Paint v1.0 release (Suzi)
  • JsPAINT prototype (Mitch, Seth)

Priorities for Q3


  • Attempt further virtualization/distribution of AmiGO 2 client
    • Image deployment at production?
    • Test feasibility of AmiGO 2 client running in in hosted or PaaS?
      • PaaS may require rewrite of some high-level bits
  • AmiGO AmiGO_2#Timeline
    • Selenium test framework (Mary, JuanCarlos)
    • AmiGO 2.2 July
    • AmiGO 2.3 Oct
    • Matrix improvements


Top-level ticket: GO-255

Milestone in github: Q3


  • Authorization
  • Authentication
  • Semi-permanent layout
  • Undo (push to Q4?)
  • Showing inference
  • Improved front-end
  • Species selector for new models & Filter search for appropriate genes/proteins
  • Dev instance up and running at CalTech (JuanCarlos, Raymond)
  • OA-type editor in Noctua (Juancarlos)


  • Import from Reactome (Chris)
  • Pipeline for GAF/GPAD output (Heiko)

Paper Viewer

  • Capella->Noctua integration noctua-51 pushed to Q4


  • Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
  • Refactor GOlr loading (Seth, Heiko, Chris)
  • Migrate crons to Jenkins JIRA GO-99 (Heiko, Mike)
  • GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4

MySQL retirement

  • Replace go-db-perl code with OWLTools code (Kalpana) JIRA GO-282

Transition to OWL

  • oboeditor plugin v0.2
  • prototype of solution for caching inferred links (Heiko, DavidOS)
  • Progress towards automation of integration with RHEA GO-190 -- not enough resources to complete in Q3
  • Progress towards automation of integration with IPR/PFAM -- not enough resources to complete in Q3