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.

Today:

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.

This term need looking at. It is jamming the script:

[Term]
id: GO:0009521
name: photosystem
relationship: only_in_taxon JD:0000006 ! Viridiplantae and Archaea and Bacteria
relationship: only_in_taxon NCBITaxon:1224 ! Proteobacteria