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Extend form to include standard GO-CAM model fields #12

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kltm opened this Issue Sep 22, 2017 · 3 comments

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kltm commented Sep 22, 2017

From @thomaspd on September 22, 2017 0:55

On the form interface for Noctua, we could add two additional fillable fields for each line (MF, BP, CC):

MF: [has_input (gene product)] [occurs_during (biological phase)]
This would give the added triplets MF—(has_input)—>gene product, and MF—(occurs_during)—> phase

CC: [part_of (cell type)] [part_of (anatomy term)]
This would give CC—(part_of)—>cell type, and cell type—(part_of)—>anatomy

BP: [part_of (BP')] [part_of (BP")].
This would give BP—(part_of)—>BP', and BP'—(part_of)—>BP"

All the triplets from a given line would be associated with the same evidence.

This way, one could enter all the parts of a standard annoton from a single form, as defined in our upcoming GO-CAM paper:
screen shot 2017-09-21 at 5 28 20 pm

This will be a great help for ensuring that users build models that adhere to our standard as much as possible, and should help with at least some of the usability issues.

Copied from original issue: geneontology/noctua#499

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kltm Sep 22, 2017

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Looping @thomaspd back in after move.

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kltm commented Sep 22, 2017

Looping @thomaspd back in after move.

@kltm kltm changed the title from Extending form editor to include standard GO-CAM model fields to Extend form to include standard GO-CAM model fields Sep 22, 2017

@kltm kltm added the enhancement label Sep 22, 2017

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krchristie Sep 22, 2017

Just to confirm that I understand this part:

MF: [has_input (gene product)] [occurs_during (biological phase)]
This would give the added triplets
MF—(has_input)—>gene product, and MF—(occurs_during)—> phase

CC: [part_of (cell type)] [part_of (anatomy term)]
This would give CC—(part_of)—>cell type, and cell type—(part_of)—>anatomy

BP: [part_of (BP')] [part_of (BP")].
This would give BP—(part_of)—>BP', and BP'—(part_of)—>BP"

All the triplets from a given line would be associated with the same evidence.

By triplets from a given line, you mean each series of extensions in a single aspect, so if I put cell type and anatomy into my CC line all of these things get the same evidence.

This would be great!

krchristie commented Sep 22, 2017

Just to confirm that I understand this part:

MF: [has_input (gene product)] [occurs_during (biological phase)]
This would give the added triplets
MF—(has_input)—>gene product, and MF—(occurs_during)—> phase

CC: [part_of (cell type)] [part_of (anatomy term)]
This would give CC—(part_of)—>cell type, and cell type—(part_of)—>anatomy

BP: [part_of (BP')] [part_of (BP")].
This would give BP—(part_of)—>BP', and BP'—(part_of)—>BP"

All the triplets from a given line would be associated with the same evidence.

By triplets from a given line, you mean each series of extensions in a single aspect, so if I put cell type and anatomy into my CC line all of these things get the same evidence.

This would be great!

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thomaspd Sep 23, 2017

Yes, you understand correctly, glad it would work for you! :)

thomaspd commented Sep 23, 2017

Yes, you understand correctly, glad it would work for you! :)

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