Software Group Progress Report Q2 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)
Authentication / Auth
- Gathering requirements at CalTech hackathon
- Implementing persona integration in Noctua
- Authentication YAML for Noctua specified
Noctua
- CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua
- Documentation of 3 components: Noctua, Barista and Minerva
- Implemented LEGO->GPAD in OWLTools JIRA GO-288
Transition to OWL
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
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)
Priorities for Q3
WebSite
- Drupal and AmiGO 2 client running in cloud?
- AmiGO AmiGO_2#Timeline
- Selenium test framework (Mary)
- AmiGO 2.2 July
- AmiGO 2.3 Oct
Noctua
Top-level ticket: GO-255
- Working prototype of Capella-Noctua integration noctua-51
- SETH TO ADD
- import from Reactome (Chris)
Infrastructure
- Migrate MGI GAF->GPAD scripts to OWLTools (Mary)
- Refactor Golr loading (Seth, Heiko, Chris)
- Migrate crons to Jenkins JIRA GO-99
MySQL retirement
- Replace go-db-perl code with owltools code (Kalpana)
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