Software Group progress report for 2009

Progress report for the software group, 2009

OBO-Edit

• Released OBO-Edit 2.0
• Improvements in the following components:
  • Cross Product Editor
  • Assert Implied Links Panel (used frequently as part of regulates work)
  • Remove Redundant Links Panel
  • Parent Editor
  • Graph Editor -- Improved editing and display features
• Hands on-training for working with Cross-products in OBO-Edit
  • Finding xp terms, searching, recognizing, constructing and manipulating xps
• Reasoner improvements
  • Rewrote reasoner to handle relation chain axioms for regulates
  • Ability to perform incremental reasoning and step-wise reasoning on large ontologies.
• Saving
  • added save-isa-closure option (required for Cross-Products
  • Ability to save filtered OBO files based on user defined constraints.
• November 2009: Working on version 2.1beta2 and plan to implement a two week release cycle December 2009 onwards.

List of Bug fixes: Tracker on sourceforge: https://sourceforge.net/tracker/?group_id=36855&atid=418257

AmiGO

• AmiGO_1_6 released.
  • Community annotation / GONUTs integration
  • RefG support
  • various misc.
• AmiGO_1_7 released.
  • uses Google analytics
  • IEA support
  • new graphics backend, integrated with term enrichment
  • various new requested features, bug fixes
  • OpenSearch plugins
• AmiGO_1_8 - in beta, many prototype components are in use
  • Matrix queries
  • Lucene-based search

Ongoing:

• Starting to replace old infrastructure with new (graphing)
• More work on:
  • core perl API
  • JSAPI

PAINT

• prototyped web-based implementation of PAINT viewer
• SUZI TO ADD

Database/Infrastructure

• Implemented ontology checks and managed move to automated checking system
• Various changes to publishing pipeline. See Media:go-infrastructure-2009.pdf
  • Managed move to GAF2.0 - MGI now publishing 2.0
  • Advocacy for Annotation Cross Products column
• Prototype new compositional term request system - http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=xp_term_request_client
• Rewrote go-perl from scratch to be better equipped for GO in 2010. Uses Moose framework. GO_Moose
  • map2slim being ported
  • GAF Inference now uses this -- http://www.geneontology.org/scratch/gaf-inference/
  • Taxon checks now use this -- http://www.geneontology.org/scratch/go-taxon/
• Database extended to handle phylogenetic trees (for PAINT-derived data)

Support

• Answered queries on go-help
• Provided custom SQL queries for GOC members for use in GOOSE
• Extensive reasoner / scripting support for regulates work. 1000s of broken links fixed
• Maintenance of news site

Software/Ontology cross-over

• Ongoing work on cross-products
  • Cross-products paper published as ICBO proceedings and submitted as full article to JBI
  • Writing custom scripts to detect GO/CHEBI inconsistencies
  • Cross-product work used in 2 papers from Hunter Lab:
• Ongoing work on improving Reactome-GO integration
  • Using XPs to partially automate assigning GO-Reactome xrefs

Production

• IEAs from main organisms now loaded into AmiGO database