TO Request 12/10/07

[planteome-user]

Hi Pankaj,

I am resubmitting this because I was not logged in and therefore would not receive updates/change e-mails.

Please uploaded TO suggestions (text-file).

Best regards, Ray

Reported by: rdidonat

Original Ticket: "obo/plant-trait-ontology-to-requests/22":https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/22

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Original comment by: rdidonat

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Did you check with the Gene Ontology group. It seems all your terms are biological process that is covered by the 'gene ontology' http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?

e.g. DNA methylation (first select the filter = biological process' http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?ont=biological\_process&session\_id=7877b1202238182&action=query&query=DNA+methylation&view=query&search\_constraint=terms

If you agree, then you can use

TO = TO:0000283 | biological process related trait and use the appropriate GO annotation to tell which biological process is involved.

Let me know if it works.

Pankaj

Original comment by: nobody

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Hi Pankaj,

I did realize in submitting these that they describe biological processes, however these also have value as phenotypic terms. For example, we won't necessarily couple the TO term directly to the GO BP term.

For example, on a Gramene page, if the trait (biological process related trait) is listed, and then several GO BPs related to the protein (but not necessarily to the trait), the user won't be able to distinguish which BP corresponds to the trait. This is why it might be worth it to expand the biological process related trait hierarchy. I would say that it will probably be rare that we add biological process related traits, these few papers happened to have many but I think they are few and far between.

What are your thoughts?

Thanks :) Ray

Original comment by: nobody

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Hi Pankaj,

After considering this more, I agree about the potential for redundancy that would arise from expanding the parent term "biological process related trait" and that it makes more sense to use the corresponding BP term. Please let me know of any feedback on term suggestions which do not pertain to child terms of this TO term.

Best regards, Ray

Original comment by: rdidonat

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Logged In: YES user_id=561361 Originator: NO

added three terms [Term] id: TO:0002713 name: cell organelle development trait def: "Trait(s) associated with phenotypes observed for abnormal development of organelle structure and biogenesis." [GR:pj] narrow_synonym: "organelle biogenesis trait" [] narrow_synonym: "organelle structure trait" [] is_a: TO:0000017 ! anatomy and morphology related trait is_a: TO:0000283 ! biological process related trait is_a: TO:0000357 ! growth and development trait

[Term] id: TO:0002714 name: plastid development trait def: "Trait(s) associated with phenotypes observed for abnormal development of plastid structure and its biogenesis." [GR:pj] narrow_synonym: "plastid biogenesis trait" [] narrow_synonym: "plastid structure trait" [] is_a: TO:0002713 ! cell organelle development trait

[Term] id: TO:0002715 name: chloroplast development trait def: "Trait(s) associated with phenotypes observed for abnormal development of chloroplast structure and biogenesis." [GR:pj] narrow_synonym: "chloroplast biogenesis trait" [] narrow_synonym: "chloroplast structure trait" [] is_a: TO:0002714 ! plastid development trait

Original comment by: jaiswalp

[planteome-user]

• status: open --> closed-accepted

Original comment by: jaiswalp