Taxon Editing Workflow after 12th June 2009
The editing workflow has now been simplified as we only now keep checked links in the file, and so do not need to mark unchecked links with a dbxref.
Edit as follows:
1) Load these files:
go/ontology/editor/gene_ontology_write.obo (the latest copy) go/scratch/go-taxon/ncbitax-slim.obo go/scratch/go-taxon/TaxonGOLinksFile.obo go/scratch/go-taxon/UnionTerms.obo
2) Edit sensu synonyms and taxon links at the same time to avoid thinking about each term twice.
3) Save the whole dataset out as all_files_mid_edit.obo. Do not check this into cvs. It takes ages.
4) Run the scripts TaxonLinkedTerms.pl and RetainTaxonLines.pl.
5) Check in the master files go/scratch/go-taxon/TaxonGOLinksFile.obo and go/ontology/editor/gene_ontology_write.obo. The union file only needs to be checked in if new union terms have been added.
6) Check that no links have been made that restrict an ancestor term to a smaller taxonomic group than the group to which a descendent term is restricted.
- Load the above files into OBO-Edit.
- Run the RuleBasedReasoner.
- Open the link search tool
- Run the search: [self][have][is redundant]
- All the search results are situations where either a term has a link to the same taxonomic grouping as its ancestor term, or situations where a term has a link to a broader taxonomic grouping than its ancestor term. These can be very clearly seen in the graphviz component.