Software Group progress report for 2010: Difference between revisions
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*[http://wiki.geneontology.org/index.php/OBO-Edit_Release_Timeline Release Tracker] | *[http://wiki.geneontology.org/index.php/OBO-Edit_Release_Timeline Release Tracker] | ||
*[http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418257&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Bug tracker] | *[http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418257&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Bug tracker highlighting upcoming fixes based on priority] | ||
*2010 fixes, features and updates [[2.1 fixes and updates]] | |||
=== Transition to OWL === | === Transition to OWL === |
Revision as of 16:12, 1 December 2010
Management
- Created a timeline SWUG_Timeline_2010-2011
Annotation Support
Database
Production (Stuart, Gail, Ben, Mike C)
- Rebuilt goweb-dev (not replaced)
- Upgraded OS from RH 32-bit -> RH 64bit
- Upgraded mysql from 5.0 -> 5.1
- Replaced GO loading machine
- (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks
- (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)
- sucessfully tested loading on claret
- have also done initial testing on load-qfo replacement for loading sequences into godb
- Ordered 2 machines to replace GO frontends, goweb1/goweb2
- Anticipated that these machines will be into production by the end of 2010.
- During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.
- Worked on testing and installing of Amigo 1.8 (required 64bit OS for clucene-based searching)
- Made several upgrades to GAF filtering script
- update from GAF 1.0 -> 2.0
- added the following feature_types
- gene_product
- polypeptide
- added the following evidence codes: IMR, IRD
- added qualifier 'rapid_divergence'
- Put in place filter-paint-associations.pl script
Schema Overhaul
- SQL schema creation into postgres through a java program
- generation of TSV files through Schema_Overhaul#OBO_Access_Layer except the following tables (in progress)
- ontology_imports, ontology_subset, all_only_relationship, never_some_relationship , relation_chain
- Schema_Overhaul#OBO_Access_Layer is in progress
- loading of TSV files into postgres
- incremental update of the GOLD database (in progress)
- Command Line Interface is built
- Basic Admin servlet interface is built to run the db operations through a web interface (in progress)
(this may belong in a separate report - add here for now anyway)
Annotation QC
- v1 of [[Taxon_Constraint_Check_Engine] in production. v2 (java rewrite) in progress
- Function_to_Process_Inference_Engine in production
- Annotation_Rule_Engine
- current and proposed checks now captured in the annotation xml file
AmiGO
- See AmiGO_1_9
- See Full_Text_Indexing_Progress
Website
- Overhaul with different layout, some organisational changes, more easily accessed menu navigation, vertical rhythm
- New documentation for ontology relations, structure
- Updating of tools list (hampered by lack of new tool submissions)
Workflow Support
- Created a basic GO_Galaxy_Environment
- integrated map2slim
- integrated slim-creator
- integrated enrichment tools
- GO TermFinder
- Ontologizer
MOOSE libraries
- Ontology slimmer
- Ontology and annotation slimmer (map2slim)
- Added algorithms of transitive closure and transitive reduction for use by slimming scripts
- Started some preliminary support for basic boolean logic (for creating bucket terms)
Reference Genome Support
RefG in AmiGO
- Loading Trees (SVEN)
- Matching IDs
- Currently ~64% of of the ids are being matched after the new QFO load.
- Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.
- Report Pages
- 2. Concurrent annotation: Code written, not part of load yet.
- Some group name in file provided by Pascale Gaudet are not in group list. Informed Paul Thomas.
- 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is
- 2. Concurrent annotation: Code written, not part of load yet.
- Matching IDs
- js phylo views: work in progress on dev machine (nothing public yet, rapidly changing alpha versions). See: AmiGO_Phylotrees.
- existing refg pages: to be dropped--no further work
- AmiGO_and_QuickGO_Integration SETH/TONY
MARY TO FILL IN
Paint
SUZI TO FILL IN
Ontology Support
TermGenie
See Compositional_Term_Submission_Tool
- Created initial prototype, in use by ontology group and annotators
- Integrated autocomplete
- Added involved_in template
OBO-Edit
- Release Tracker
- Bug tracker highlighting upcoming fixes based on priority
- 2010 fixes, features and updates 2.1 fixes and updates
Transition to OWL
- Initiated plan for ontology support in next cycle Software_Group_2010_Future_Plans#Plan
- first draft of obof1.4 guide http://www.geneontology.org/GO.format.obo-1_4.shtml
- formal spec of obo syntax and owl mapping: http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html
- rewritten parser and obo2owl converter, 100% java http://code.google.com/p/oboformat/