Allow search to filter diseases only in OMIM

[kshefchek]

For example, @iimpulse would like to search for diseases only in OMIM, such as:

https://api.monarchinitiative.org/api/search/entity/marf?prefix=OMIM&rows=20&start=0&minimal_tokenizer=false

But this returns nothing.

First we'll need to make sure the equivalent id list is reflexive, so that we can put the filter on this field instead of id. This might also be potentially confusing to users, as they would get back Mondo as a primary id when searching for OMIM

[pnrobinson]

It would be useful to have a query that would return MONDO is for a given OMIM query. If this is not possible please let us know and we will look for another solution -- this is currently a blocker!

[kshefchek]

if you have an OMIM id, you can get the linked MONDO id via bioentity/{id}, eg https://api.monarchinitiative.org/api/bioentity/OMIM:154700

[pnrobinson]

@kshefchek that seems very useful. Are these 1:1 OMIM<->MONDO mappings?

[kshefchek]

to follow up here, the original ticket was to add support for limiting autocomplete to only diseases in OMIM, which would require some updates to our solr schema and the solr loader code. There are some additional requirements for poetry, such as mapping an OMIM 1:1 mapping to Mondo, and also to get all superclasses. I think we support both these but need to check.

Another route is to expand out the on demand ontology endpoints in /ontol and /ontology which run fetch the latest ontology using the obo purl. See https://ontobio.readthedocs.io/en/latest/inputs.html (although no obvious from the docs how this works)

[monicacecilia]

372 is a "superticket" keeping track of all three requests. Feel free to remove / edit (either ticket) as needed.

[kshefchek]

I've added two new params to autocomplete that will support this: include_eqs= true|false, when filtering in/out a prefix include equivalent identifiers exclude_groups=true|false, exclude classes with children, ie only return leaf classes

I've also updated the response to include equivalent identifiers so that the Mondo ID can be mapped to OMIM ID without making a second call to bioentity

example: https://api.monarchinitiative.org/api/search/entity/autocomplete/marf?category=disease&prefix=OMIM&include_eqs=true&rows=20&start=0&exclude_groups=true