Software Group Progress Report Q2 2014: Difference between revisions
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=== Website === | === Website === | ||
* Drupal Content: migration complete (Moni, Seth, Rama, ...) | * Drupal | ||
* Drupal Rollout [https://www.ebi.ac.uk/panda/jira/browse/GO-106 106] | ** Drupal Content: migration complete (Moni, Seth, Rama, ...) | ||
* AmiGO 2.0 released in March (Seth) | ** Drupal Rollout: migrated to amazon, still testing (Seth, Stuart) [https://www.ebi.ac.uk/panda/jira/browse/GO-106 JIRA GO-106] | ||
* AmiGO 2.1 in testing May (Seth, Rama) | * AmiGO | ||
** AmiGO 2.0 released in March (Seth) | |||
** AmiGO 2.1 in testing May (Seth, Rama) | |||
== Authentication / Auth == | == Authentication / Auth == | ||
* Gathering | * Gathering requirements at CalTech hackathon | ||
* | * Implementing persona integration in Noctua | ||
* Authentication YAML specified | * Authentication YAML for Noctua specified | ||
== Noctua == | == Noctua == | ||
* CalTech hackathon | * CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua | ||
* Documentation of 3 components: Noctua, Barista and Minerva | * Documentation of 3 components: Noctua, Barista and Minerva | ||
* Implemented LEGO->GPAD in OWLTools | * Implemented LEGO->GPAD in OWLTools [https://www.ebi.ac.uk/panda/jira/browse/GO-288 JIRA GO-288] | ||
== Transition to OWL == | == Transition to OWL == | ||
* Added import catalogs to OE | |||
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-222 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) | * oboeditor plugin for Protege v0.1 (Heiko, Simon J) | ||
* Fixes to obo/owl converter for never_in_taxon links | * Fixes to obo/owl converter for never_in_taxon links | ||
| Line 27: | Line 33: | ||
* GPI exports direct from MGI (Mary) | * GPI exports direct from MGI (Mary) | ||
== Retire GO Mine == | |||
* Done? (SETH/KALPANA) | |||
Retire GO Mine | |||
? | |||
== Priorities for Q3 == | == Priorities for Q3 == | ||
| Line 50: | Line 40: | ||
=== WebSite === | === WebSite === | ||
* Drupal and AmiGO 2 client running in cloud? | * Drupal and AmiGO 2 client running in cloud? | ||
* AmiGO 2.3 | * AmiGO [[AmiGO_2#Timeline]] | ||
** Selenium test framework (Mary) | |||
** AmiGO 2.2 July | |||
** AmiGO 2.3 Oct | |||
=== Noctua === | === Noctua === | ||
* Working prototype of Capella-Noctua integration | |||
Top-level ticket: [https://www.ebi.ac.uk/panda/jira/browse/GO-255 GO-255] | |||
* Working prototype of Capella-Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] | |||
* SETH TO ADD | * SETH TO ADD | ||
* import from Reactome (Chris) | |||
=== Infrastructure === | === Infrastructure === | ||
* Refactor Golr loading | * Migrate MGI GAF->GPAD scripts to OWLTools (Mary) | ||
* Refactor Golr loading (Seth, Heiko, Chris) | |||
* Migrate crons to Jenkins [https://www.ebi.ac.uk/panda/jira/browse/GO-99 JIRA GO-99] | |||
=== MySQL retirement === | === MySQL retirement === | ||
| Line 65: | Line 64: | ||
* oboeditor plugin v0.2 | * oboeditor plugin v0.2 | ||
* prototype of solution for caching inferred links (Heiko, DavidOS) | * prototype of solution for caching inferred links (Heiko, DavidOS) | ||
* Progress towards automation of integration with RHEA [https://www.ebi.ac.uk/panda/jira/browse/GO-190 GO-190] -- not enough resources to complete in Q3 | |||
* Progress towards automation of integration with IPR/PFAM -- not enough resources to complete in Q3 | |||
[[Category:Reports]] | [[Category:Reports]] | ||
Revision as of 16:51, 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)
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