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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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plastids only in eukaryota rule #9769

Closed gocentral closed 9 years ago

gocentral commented 12 years ago

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

gocentral commented 12 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

gocentral commented 12 years ago

Original comment by: paolaroncaglia

gocentral commented 12 years ago

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

gocentral commented 12 years ago

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 Sorry, I was looking at a out-of-date view of the taxon file, so hadn't realized the additional rules for plastid had been added.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

gocentral commented 12 years ago

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

gocentral commented 12 years ago

Original comment by: rebeccafoulger