Taxon Editing Workflow after 12th June 2009

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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)

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 and

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.