Software Group Progress Report Q2 2014: Difference between revisions
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== Progress Report Q2 == | == Progress Report Q2 == | ||
=== | === Website === | ||
* Drupal Rollout: migrated to | * Drupal | ||
* AmiGO 2.0 released in March | ** Drupal Content: migration complete (Moni, Seth, Rama, ...) | ||
* AmiGO 2.1 in testing May | ** Drupal Rollout: migrated to AWS, still testing (Seth, Stuart) [https://www.ebi.ac.uk/panda/jira/browse/GO-106 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 / | === Authentication / Authorization === | ||
* Gathering | * Gathering requirements at CalTech hackathon | ||
* Persona | * Implementing Persona authentication into Noctua | ||
== Noctua == | === LEGO: Noctua/Barista/Minerva === | ||
* | * Implemented prototype system, 3 components: | ||
** Noctua: client component | |||
* Implemented LEGO->GPAD in OWLTools | ** Barista: messaging/session layer | ||
** Minerva: OWLServer | |||
* CalTech hackathon, discussed integration between Capella (text span annotation tool) and Noctua [https://github.com/kltm/go-mme/issues/51 noctua-51] | |||
* Implemented v1 of LEGO->GPAD/GAF in OWLTools [https://www.ebi.ac.uk/panda/jira/browse/GO-288 JIRA GO-288] | |||
== Transition to OWL == | === Transition to OWL and ontology support === | ||
* 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 | ||
* TG templates (HEIKO TO ADD) | |||
* ... | |||
== GPAD/GPI | === GPAD/GPI === | ||
* GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS) | * GPAD 1.1 spec (Tony, Heiko, Chris, DavidOS) | ||
* Added 2-way converters to OWLTools (Heiko) | * Added 2-way converters to OWLTools (Heiko) | ||
* GPI exports direct from MGI (Mary) | * 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 == | == Priorities for Q3 == | ||
=== | === Website === | ||
* | * Attempt further virtualization/distribution of AmiGO 2 client | ||
* AmiGO 2.3 | ** 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 | |||
=== LEGO === | |||
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] | |||
==== Noctua ==== | |||
=== | |||
* | |||
* 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) | |||
==== Minerva ==== | |||
* Import from Reactome (Chris) | |||
* Pipeline for GAF/GPAD output (Heiko) | |||
=== Paper Viewer === | |||
* Capella->Noctua integration [https://github.com/kltm/go-mme/issues/51 noctua-51] pushed to Q4 | |||
=== Infrastructure === | === Infrastructure === | ||
* Refactor | |||
* 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] (Heiko, Mike) | |||
* GPAD submission and verification pipeline (Heiko) --- May be bumped to Q4 | |||
=== MySQL retirement === | === MySQL retirement === | ||
* Replace go-db-perl code with | * Replace go-db-perl code with OWLTools code (Kalpana) [https://www.ebi.ac.uk/panda/jira/browse/GO-282 JIRA GO-282] | ||
=== Transition to OWL === | === Transition to OWL === | ||
* 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]] | |||
Latest revision as of 10:58, 18 June 2014
Progress Report Q2
Website
- 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/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
- 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
LEGO
Top-level ticket: GO-255
Milestone in github: Q3
Noctua
- 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)
Minerva
- Import from Reactome (Chris)
- 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