SWUG:Report 200905

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details still being filled in


Commenced re-writing of go-perl using Moose framework

  • Software in geneontology svn under go-moose

Constructed new tool using new library, go-gaf-inference.pl, this currently has two capabilities

Inferring BP annotations from MF annotations using F->P links

  • input: (1) GAF(s) (2) gene_ontology_ext.obo
  • output: new GAF file with ICs
  • results: scratch/gaf-inference/

Nearly 13k new annotations in initial run. More expected as new F->P links added

Inferring Invalid Annotations from GO->Taxon links

  • input: (1) GAF(s) (2) gene_ontology.obo (3) GOTaxonLinksFile.obo (4) UnionTaxa.obo (5) ncbi_taxonomy.obo
  • output: invalid annotations in GAF
  • results: scratch/go-taxon

Initial run produced multiple violations that proved to be true positives (i.e. genuinely invalid annotations) across a variety of evidence codes, not just IEAs

Database

  • Tested load of database using new rules for populating graph_path

This will allow determination of relationship between non-directly connected terms. This allows correct behavior for regulates and future relations.

AmiGO

IEAs in AmiGO

  • performed test load of GO lite database with IEAs for core organisms (i.e. all GAFs in gene-associations minus goa_uniprot)
  • still a few tests requires

OBO-Edit

  • Bug Fixes:
    • - [ geneontology-Bugs-2750699 ] config manager memory settings option out of sync
    • - [ geneontology-Bugs-2785074 ] OBO-Edit2-rc still present
    • - [ geneontology-Bugs-2787869 ] very minor bug with saving filters
    • - Fixed bug that stopped the box at the bottom of the history browser from appearing unless another component was clicked on.
    • - Fixed the history browser html message so it shows 'name (id)' rather then 'id (id)'.
  • Features:
    • Assert Implied Links Component
    • Layout lock/unlock option
    • Incremental reasoning switch

Paint

  • produced initial formal spec for rules for term suggestion