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(BJ) Data to remove (PECO) and conditions #15

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

PECO is the old name for our conditions ontology. The ontology prefix should be updated to FYECO in future data releases (there was a namespace clash with PECO, the plant evidence ontology) so we needed to change it.

The data that is currently loaded is the plant evidence code ontology.

I don't think we need to include FYECO in the drop-down anyway ( this isn't a formal OBO ontology, we hide this acronym from our users, it is only really used behind the scenes.

Instead this data would be available under. the "condition" datatype (this is a more readable label).

Esentially for fission yeast FYECO/PECO(old)/condition are different ways of describing the same datatype.

rachellyne commented 2 years ago

Ahh - I think the ontology name has just been put in wrong. The data is pombe!

ValWood commented 2 years ago

Yep the terms are ours,

it is when I click on the "conditions" in the dropdown menu that I see reference to the plant PECO:

Screenshot 2022-01-24 at 15 39 27

but this should probably go away once the mine is refreshed as we will no longer reference PECO?

The label in the drop-down could be just "phenotype conditions ontology" ( instead of PECO TERM) We don't need to say FYECO as we don't make that public,and it isn't an obo foundry ontology.

rachellyne commented 2 years ago

@val I presume the ontology we now need is fyeco.obo from here: https://github.com/pombase/fypo

We have the updated term ids loaded but did not update the ontology so they have not merged.

ValWood commented 2 years ago

Yep that is the correct source.
@kimrutherford anything else Intermine need to be aware of here?

My feeling is that this should not be treated as an 'ontology' as such. It is really just a flat vocabulary. We store it in obo format for convenience. When we use 'conditions' that have more in common with annotation extensions. I guess we can wait and see what the queries look like ;)

kimrutherford commented 2 years ago

I presume the ontology we now need is fyeco.obo from here:

Hi Rachel. That's the one.

anything else Intermine need to be aware of here?

I think you've covered everything.

danielabutano commented 2 years ago

Fixed image