warn about disallowed relations in FYPO extensions

[pombase-admin]

Allowable extensions for phenotype annotations are listed in this file in the PomBase SourceForge subversion repository, which gets loaded anyway:

pombase/phenotype_ontology/supplemental_files/fypo_extension_relations.obo

We'd like warnings in a log for any extensions on FYPO annotations that use relations not in that file.

thanks!

Original comment by: mah11

[pombase-admin]

Unknown extension relations should be warned about already, including for FYPO. Do you have an example of a missing warning?

You should see messages like this for curation sessions: error in b42a7324f08b6a24: DBIx::Class::Schema::txn_do(): can't find relation cvterm for: phosphorylated_by (from the log files that like like: log.2014-04-28-12-54-28.curation-tool-data-load-output)

Or like this for the contig files: failed to add annotation extension to SPBC649.04 <-> mRNA level: can't find relation cvterm for: in_response_to (from the qualifier_problems.txt file)

Original comment by: kimrutherford

[pombase-admin]

• status: open --> closed-works-for-me

Original comment by: mah11

[pombase-admin]

hmm, something prompted me to open this ticket, but now I can't remember what. (Going by the creation date, it may have been jet lag.)

I'll close it, and reopen if I do spot something that should've spawned a warning but didn't.

Original comment by: mah11

[pombase-admin]

I vaguely remember we had used some extensions (like "during" or whatever) with phenotype terms, and they didn't spawn a warning.

Original comment by: ValWood