SWUG:Report 200905
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