Terms under photoreceptor morphogenesis

[gocentral]

The terms under photoreceptor morphogenesis (GO:0046461) need to be reorganized - the relationships aren't analogous to those between other morphogenesis/differentiation/development/ commitment terms.

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/491":https://sourceforge.net/p/geneontology/ontology-requests/491

[gocentral]

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There are also problems with non-true paths wrt eye and non-eye photoreceptors. Might be a good idea to add "eye" to the existing terms that refer to the eye in the def.

Original comment by: girlwithglasses

[gocentral]

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Attached proposed rearrangement of the photoreceptor terms in the process ontology. Term name changes: GO:0007459: photoreceptor commitment (sensu Drosophila) --> eye photoreceptor commitment (sensu Drosophila) GO:0008594: photoreceptor morphogenesis (sensu Drosophila) --> eye photoreceptor morphogenesis (sensu Drosophila)

All the other changes are rearrangements.

Original comment by: girlwithglasses

[gocentral]

Cut down process ontology with exciting photoreceptor changes.

Original comment by: girlwithglasses

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There are some weird characters at the beginning and end of the file. I had to edit them out by hand before I could load them in DAG-edit, also had to check the allow dangling parent box.

I looked at the highest level terms as I'm really not a eye morphogenesis guru. Having said that, here are my comments:

In current:

development -I-cell fate commitment ----P-cell fate determination ----P-cell fate specification -I-differentiation -I-morphogenesis

You have:

photoreceptor development -I-eye photoreceptor development -I-non-eye photoreceptor development -I-photoreceptor differentiation ----I-photoreceptor commitment ----I-photoreceptor differentiation (sensu Drosophila) -I-photoreceptor morphogenesis

I think that you're right in moving the photoreceptor development up as a direct child of development because we can't put it exclusively under either embryonic or post- embryonic development.

I'm wondering whether photoreceptor commitment should be a partof photoreceptor differentiation in this case. The example of cell ate commitment/differentiation may not apply in this case. What do you think?

BTW: We need to change the definition on non-eye photoreceptor development. Photoreceptors in plants are not cells or groups of cells, they are proteins with chromophores, hence, they don't develop, they are synthesized and that's about it. Currently, the definition is: "Development of non-eye photoreceptors, sensory cells or groups of cells [sic] react to the presence of light, e.g. the photoreceptors responsible for phototropism in higher plants."

I'd be ok with "Development of non-eye photoreceptors (sensory cells or groups of cells which react to the presence of light).

Original comment by: tberardini

[gocentral]

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Just a tiny comment from me: Please could R7 cell fate commitment ; GO:0007465 be made a child of R7 development ; GO:0045467

Thanks!

Becky

Original comment by: beckyfoulger

[gocentral]

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Amelia,

Could you take care of Becky's request while you're revamping this section? The relationship should be isa.

Thank you!

Tanya

Original comment by: tberardini

[gocentral]

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Done that and changed the def of non-eye photoreceptor development. Any objections to the rearrangement of photoreceptor development or can I implement it?

Original comment by: girlwithglasses

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From my perspective, I think the rearrangement looks great- no objections from me.

Becky

Original comment by: beckyfoulger

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David and I are still wrestling with this. Please don't commit the changes yet. I'll cc you our current conversation.

Tanya

Original comment by: tberardini

[gocentral]

• assigned_to: girlwithglasses --> tairtb

Original comment by: girlwithglasses

[gocentral]

• status: open --> closed-fixed

Original comment by: jl242