Taxon-GO Implementation April 2009 onwards

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1st April 2009

This work has been on hold for a while as we were waiting for more sophisticated filtering in OBO-Edit to let all editor edit the file while doing normal live file editing. However Chris has asked that we push on without the filtering for a while.


Loaded the files in OE2 and found some file problems. The UnionTerm stanzas were a bit messed up, but were fixed by adding a Typedef for the the union_of relationship, and removing the top term.

Other file errors found and fixed:

Two entire taxa had gone missing from the taxon slim, and we had also lost a union_of term from the UnionTerms file. I do not know how that happened but I have replaced them.

Midori had added a new only_in_taxon link to a union_of term that did not exist. I have made the union_of stanza and added it to the file. I should talk with Midori about how to edit these files. I did not know she had started.

I have recommitted the edited source files and also saved out and recommitted the all_files_mid_edit.obo file. I did not make any edits so the perl scripts do not need to be run.

Fixed this misformed tag 'name: synonym: "synonym: "synonym: "'in both edit file and source.

Set up WinXP laptop to run the perl scripts to generate the tab delimited file that the users need to act on these links.

TODO: There are a bunch of terms that currently have two only_in_taxon links and they mess up the converstion to tab-delimited. Need to resolve these relationships. Have deleted them from the file for now.