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tair / toastdos-back

The back-end system for the GOAT community annotation tool
GNU General Public License v3.0
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Add evidence field to annotation #185

Closed bgrawi closed 6 years ago

bgrawi commented 7 years ago

A submitter should be able to add supporting evidence to an annotation for certain annotation types (TBD).

This field will be shown next to the other annotation fields and will validate against other locus types.

Acceptance Criteria:

tberardini commented 7 years ago

After discussion with @lreiser, we need to modify the schema to allow for more than one locus identifiers to be used as supporting evidence. Currently, the GeneTermAnnotation table models only ONE evidence_id (this is the key for supporting evidence, refers to Locus table). However, sometimes, more than one evidence_id needs to be added.

Suggested solution:

Update schema to add a linking table between GeneTermAnnotation (GTA) and Locus. Remove evidence_id from GTA table.

tberardini commented 7 years ago

Also, enable usage of CheBI id/s for chemicals in the evidence_with. This is as an alternative to being able to use locus id/s.

http://purl.obolibrary.org/obo/chebi.obo

lreiser commented 6 years ago

Evidence with needs to allow for AND/OR relationship. So when a user is prompted to add evidence with for an IGI or ProteinProtein (IPI )annotation AND there is more than one evidence with they are also able to choose (via drop down selector) if it is AND or OR.

This also affects the export of Evidence With (which still needs to be done) in the data export.#241 The AND relation is indicated with a comma (eg. AGI_LocusCode:AT1G02300, AGI_LocusCode:At5G01010) The OR relation is indicated with a pipe (e.g. UniProtKB:Q34T68|UniProtKB:J45H89)

GavinNishizawa commented 6 years ago

Should it be possible to have something such as UniProtKB:Q34T68,UniProtKB:Q10T01|UniProtKB:J45H89 ? In other words, should AND and OR relations be able to "mix" ? e.g. "X is related to U or V and W and Y or Z"

tberardini commented 6 years ago

Checking with GO experts. I'll post the response when I get one.

tberardini commented 6 years ago

After checking - it is better to NOT allow mixing and matching of AND and OR relations.

lreiser commented 6 years ago

@tberardini thanks for checking.. I 'd never seen one in combination so that makes sense.