Allow new entities in the "with/from" field (e.g. "FISH" at ZFIN)

[sabrinatoro]

(following the annotation call of 03/12/2019): We discussed allowing other entities which have stable IDs in the with/from field.

ZFIN would like to add "FISH" (ZFIN:ZDB-FISH-####). Other entities mentioned in the call: alleles, variants

[vanaukenk]

Thanks @sabrinatoro It would be helpful to know what defines a "FISH", e.g. genotype, environmental conditions, etc. to make sure we capture what would be useful in an entity file.

[sabrinatoro]

FISH = Genotype + Sequence targeting reagent

We currently submit Genotype and Sequence targeting reagent (morpholino, CRISPR, TALEN) separately in the with/from field. FISH is an entity which brings these two entities together.

For example: https://zfin.org/ZDB-FISH-150901-10657 This FISH combines genotype ZFIN:ZDB-GENO-980202-957 and morpholino ZFIN:ZDB-MRPHLNO-050729-2

[suzialeksander]

I'm looking at the GPAD 2.0 and I don't see any defined restrictions on what's even allowed, or not. Not sure if this has been changed since 2019, but do we need to clarify the docs @vanaukenk ? GAF 2.2 has a list of examples but it reads more as curation guidance than specs.

https://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8

https://github.com/geneontology/go-annotation/blob/675cca2d171507d13675eb7616df1d55743a826b/specs/gpad-gpi-2-0.md

https://geneontology.org/docs/gene-product-association-data-gpad-format-2.0/

[suzialeksander]

@sramachand do you know if this problem still exists, that is: are you currently able to add the entities you need in the with/from?

[suzialeksander]

Note from chatting with @pgaudet -if needed, the language at https://geneontology.org/docs/gene-product-association-data-gpad-format-2.0/#7-with-or-from can be expanded a bit.