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geneontology / noctua-form-legacy

Simple annoton editor workbench for Noctua.
BSD 3-Clause "New" or "Revised" License
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Allow additional interacting taxon ID #89

Closed cmungall closed 4 years ago

cmungall commented 5 years ago

This is only used when a curator is annotating an inter-species interaction

This will essentially act as an extra level of partonomy:

CC -po-> cell type -po-> gross anatomical structure -po-> taxon

in practice this will frequently be short-circuited, direct CC to taxon

tmushayahama commented 5 years ago

@thomaspd Can you explain this one

thomaspd commented 5 years ago

This would be another level of nesting of the CC context. Right now in the form, it is MF occurs in CC part of CC part of cell type part of anatomy

We would add the ability to include one more level of nesting at the end of that chain: part of organism

It could be implemented in Noctua form under the ... button at the end of any of the fields above (for example "part of CC"). The text could be "Specify interacting organism". When the user selects this option, another field is added right under the "part of anatomy" line. The autocomplete of the new field uses the same closure as the "organism" filter in Amigo. When making this into a model, you would use the same rule as for the other fields in this part of the form: if there are fields above it that are left blank, you connect it (with part of) to the last one that was filled in (and if none are filled in, it gets connected directly to MF using occurs in).

vanaukenk commented 5 years ago

This is accounted for in the current specs:

https://github.com/geneontology/GO_Shapes/blob/master/shapes/go-cam-shapes.shex

tmushayahama commented 5 years ago

@cmungall @vanaukenk @kltm any idea of how to autocomplete taxon id and short of long taxon names on neo?

cmungall commented 5 years ago

I suggest we just do this in a generic fashion. Do not implement any specific code. Currently the curator must know the 4 letter code but when we have so many organisms this is unwieldy we will just add synonymy info to neo

On Tue, Jul 30, 2019 at 3:53 PM Tremayne notifications@github.com wrote:

@cmungall https://github.com/cmungall @vanaukenk https://github.com/vanaukenk @kltm https://github.com/kltm any idea of how to autocomplete taxon id and short of long taxon names on neo?

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vanaukenk commented 5 years ago

@kltm - has confirmed that the NCBI slim taxon is loaded in neo. What is the source of the NCBI slim taxon?

An alternative source of species information is the BioLink API. The source of data here would be the species list in AmiGO (annotated species OR ontology taxon slim).

Ideally, curators would be able to autocomplete on taxon id or name or substring of a name.

For now, curators will just copy and past the numerical NCBI taxon ID but, in the future, we will implement autocomplete that will show the label.

cmungall commented 5 years ago

(Apologies my previous comment didn't make sense as I thought we were talking about filtering genes by taxon)

taxslim is the subset used by various ontologies for taxon constraints plus the set used for manual curation in GO. If we want to be sure any taxon can be used we can just include the full ncbitaxon in the import chain

On Tue, Aug 6, 2019 at 10:45 AM vanaukenk notifications@github.com wrote:

@kltm https://github.com/kltm - has confirmed that the NCBI slim taxon is loaded in neo. What is the source of the NCBI slim taxon?

An alternative source of species information is the BioLink API. The source of data here would be the species list in AmiGO (annotated species OR ontology taxon slim).

Ideally, curators would be able to autocomplete on taxon id or name or substring of a name.

For now, curators will just copy and past the numerical NCBI taxon ID but, in the future, we will implement autocomplete that will show the label.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/geneontology/simple-annoton-editor/issues/89?email_source=notifications&email_token=AAAMMOPNBHKVOEJDULAQS6TQDG2CDA5CNFSM4GP7CMXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3V5QSY#issuecomment-518772811, or mute the thread https://github.com/notifications/unsubscribe-auth/AAAMMOOEX7OHLPZPZQRCFHDQDG2CDANCNFSM4GP7CMXA .

vanaukenk commented 4 years ago

@tmushayahama - can we close this now that we have organism in the CC annotation extensions on the Noctua 2.0 form?