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NCATS-Tangerine / biothings-explorer-beacon

A beacon wrapper for the Biothings Explorer API
MIT License
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Prefixes to use for OMIM #4

Open cmungall opened 5 years ago

cmungall commented 5 years ago

works:

https://kba.ncats.io/beacon/biothings-explorer/concepts/OMIM.GENE%3A138140

but this doesn't:

https://kba.ncats.io/beacon/biothings-explorer/concepts/OMIM%3A138140

This is not an easy one to resolve, as we have an impedance mismatch with ID spaces here. We treat OMIM as one prefix, biothings breaks it down by type, which I think overloads prefix

lhannest commented 5 years ago

I think this translation between different forms of namespaces should be something that the beacon aggregator handles. The aggregator can hold each beacon's kmap in memory and use it to determine which beacons can handle which namespaces, and what format to use for those namespaces. When querying across all beacons for OMIM:138140 it should see that biothings-explorer only recognizes omim.gene and automatically substitute omim.gene:138140 for OMIM:138140. Similarly it can translate between PubMed and PMID, NCBIGene and NCBIGENE and so on, so that individual beacons needn't stick to any particular namespace convention.