Closed gocentral closed 9 years ago
Hi Emily,
I'm ready to add the constraint you suggest, however based on what the file currently has for plastid:
[Term] id: GO:0009536 name: plastid relationship: never_in_taxon NCBITaxon:33208 {id="GOTAX:0000491", source="PMID:21311032"} ! Metazoa relationship: never_in_taxon NCBITaxon:4751 {id="GOTAX:0000499", source="PMID:21311032"} ! Fungi relationship: never_in_taxon NCBITaxon:28009 {id="GOTAX:0000500", source="PMID:21311032"} ! Choanoflagellida relationship: never_in_taxon NCBITaxon:554915 {id="GOTAX:0000501", source="PMID:21311032"} ! Amoebozoa
I'm wondering if we might prefer to add instead, for consistency,
never_in_taxon Bacteria never_in_taxon Archea ?
I appreciate that your suggested rule would be more inclusive. I'll assign this to Becky in case she has any comments, as she did some work on the plastid rule previously. Becky, you may assign this to me afterwards.
Thanks! Paola
Original comment by: paolaroncaglia
Original comment by: paolaroncaglia
A summary of my previous edits:
Plastids used to have the taxon restriction: only_in_taxon NCBITaxon:33090 ! Viridiplantae
This original rule was updated because plastids are found in both green plants and several algae. The common taxon restriction for these is Eukaryota, so Emily's suggestion is obviously correct...... however, for annotation purposes we thought it would be more useful to add never_in_taxon restrictions so the plastid terms weren't used for mammals etc.
Paola's suggestion of the extra two 'never_in' rules looks good to me.
thanks, Becky
Original comment by: rebeccafoulger
Brilliant, thanks this works for me. Sorry, I was looking at a out-of-date view of the taxon file, so hadn't realized the additional rules for plastid had been added.
Cheers, Emily
Original comment by: edimmer
I've added two new 'never_in' taxon checks for plastid ; GO:0009536:
relationship: never_in_taxon NCBITaxon:2 ! Bacteria relationship: never_in_taxon NCBITaxon:2157 ! Archaea
Let us know if it's still not covering all the restrictions you need. cheers, Becky
Original comment by: rebeccafoulger
Original comment by: rebeccafoulger
Could you please add the following rule into:
ftp://ftp.geneontology.org/pub/go/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo
[Term] id: GO:0009536 name: plastid relationship: only_in_taxon NCBITaxon:2759 {id="GOTAX:NEW",source="PMID:22531210"} ! Eukaryota
Thanks, Emily
Reported by: edimmer
Original Ticket: geneontology/ontology-requests/9562