ID conflict for CO_334:0000272

[cooperl09]

There is a new trait in the latest version of the TD (downloaded 12-20-24):
CO_334:0000272 Shoot apex compactness, but that ID is already in use:

[Term]
id: CO_334:0000272
name: female flower number counting on all levels
namespace: cassava_trait
def: "Count the number of female flowers after the buds appear, mature, and grow in size to become distinctive at all branch levels." [CO:curators]
is_a: CO_334:0001000 ! Variables
relationship: variable_of CO_334:0000364 ! Female flower number
relationship: variable_of CO_334:0010006 ! Counting: Female flower number all levels_method
relationship: variable_of CO_334:0100606 ! flowers
created_by: aafolabi
creation_date: 2016-05-12T12:45:13Z

[nmenda]

We have in cassavabase the variable for the trait 'shoot apex compactness' https://cassavabase.org/cvterm/77155/view
but the parent term does not exist in the obo or in cassavabase. It needs to be added.

We can do one of the following

1. modify in cassavabase / obo file the existing term ( id: CO_334:0000272
   name: female flower number counting on all levels ) and give it a new ID. Not ideal, since people may have this in their lists/phenotyping files (though no trials loaded in cassavabase with this variable yet)

2. change the ID n CO , give it a new unique ID.

[cooperl09]

It looks fine in Cassavabase, as those are two different IDs:

Term id CO_334:0000270
Term name compactness of shoot apices visual 1-3
Term definition Visual assessment of the compactness of shoot apices based on how closely the shoot apices are; with 1 = loose, 2 = moderately compact, 3 = compact.

Term id CO_334:0000272
Term name female flower number counting on all levels
Term definition Count the number of female flowers after the buds appear, mature, and grow in size to become distinctive at all branch levels.

IMO- It needs to be corrected in the Trait Dictionary.
The existing term:
id: CO_334:0000272 name: female flower number counting on all levels was created back in 2016, so its likely in use in various places.

How are the changes in the Trait Dictionary and the OBO file/ Cassavabase being synchronized? It appears as thorough changes are being made in both files independently.

[nmenda]

yes, would be better to give a new ID to shoot 'apex compactness' in Trait Dictionary, and also add it to the obo file here.

It is the responsibility of Crop Ontology to apply changes made there (using TD or any other method) to the OBO file and to pull changes made to the OBO by cassavabase or other curators and merge those into Crop Ontology.

We have an issue with assigning ID ranges although we have agreed on which IDs each curator can use https://github.com/Planteome/CO_334-cassava-traits/blob/master/ontology_id_ranges

I think sometimes when another project creates a new TD they also generate their own IDs without following the guidelines here, so that needs to be resolved too for all the RTB crops