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(BJ) RNA types #17

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

Queries on RNA types retrieve no data. RNA types should be included in the json file @kimrutherford ?

includes tRNA snRNA snoRNA rRNA

ValWood commented 2 years ago

This might be becasue SO term identifiers are not loading? Only SO terms names are visible. The visible set is only a subset of the ones we use related to the annotation objects in the sequence contig files.

We also add SO terms to features (like RNAs) to describe their type. @kimrutherford can confirm if these are exported.

kimrutherford commented 2 years ago

We also add SO terms to features (like RNAs) to describe their type. @kimrutherford can confirm if these are exported

The SO term names of each gene are exported in the "feature_type" field, kind of. The term name we use has a space instead of an underscore ("snRNA gene" instead of snRNA_gene for SO:0001268). We don't currently export the SO term ID, but that's straightforward to add.

https://github.com/pombase/pombase-chado/issues/842

rachellyne commented 2 years ago

I'm not sure why these haven't loaded. We have added a feature type attribute to the gene class but it's empty! I think it should be a simple fix.

danielabutano commented 2 years ago

yes, my fault. Instead to take the "feature_type" field I used "featureType". I will fix it. Only a question. when we have 2 values (e.g. mRNA gene) do you want both ?

kimrutherford commented 2 years ago

Only a question. when we have 2 values (e.g. mRNA gene) do you want both ?

I think we should have the whole string "mRNA gene" because that's similar to the term name in SO.

ValWood commented 2 years ago

Yes. IIRC the cognate SO terms always have an underscore mRNA_gene (which always confuses me- most ontologies don't do this)

danielabutano commented 2 years ago

Fixed!