Software Group Progress Report Q2 2014: Difference between revisions

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Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255]
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255]
Milestone in github: [https://github.com/kltm/go-mme/issues?milestone=3&page=1&state=open Q3]


* Authorization
* Authorization

Revision as of 18:58, 5 June 2014

Progress Report Q2

Website

  • Drupal
    • Drupal Content: migration complete (Moni, Seth, Rama, ...)
    • Drupal Rollout: migrated to amazon, 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 / Auth

  • Gathering requirements at CalTech hackathon
  • Implementing persona integration in Noctua

Noctua

  • Implemented Prototype system, 3 components
    • Noctua: client component
    • Barista: middleware 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/GPI

  • 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

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

Priorities for Q3

WebSite

  • Drupal and AmiGO 2 client running in cloud?
  • AmiGO AmiGO_2#Timeline
    • Selenium test framework (Mary, JuanCarlos)
    • AmiGO 2.2 July
    • AmiGO 2.3 Oct

Noctua

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
  • import from Reactome (Chris)
  • Dev instance up and running at CalTech (JuanCarlos, Raymond)
  • OA-type editor in Noctua (Juancarlos)
  • Pipeline for GAF/GPAD output (Heiko)

Paper Viewer

  • Capella-Noctua integration noctua-51 pushed to Q4

Infrastructure

  • 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