Fix vrs schema link #190
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Fix vrs schema link #190
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The parameter descriptions in the EntryTypeDefinitions schema seem somewhat hard to parse and potentially misleading - this is a go at cleaning them up a bit.
It is not clear how to use ontologyTermForThisType w/o examples (i.e. terms for biosample, individual... - added some but incomplete...) and there is also a logical duplication having a "unique" id and an ontology term. Overall this should be clarified but the current modification seems (a) sensible (step).
Update entryTypeDefinition description
for templates the format must be "uri-template".
The Beacon schema for genomic allows 3 options: * VRS MolecularVariation * VRS SystemicVariation * Beacon LegacyVariation (which adopts the VRS location object but uses separate definitions otherwise) Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a *much* better definition of "Systemic Variations" such as CNV. This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the `bycon` based implementations such as progenetix.org have been using it for their Beacons for ~2years).
The `beacon_yaml2md.pl` doc generator contains hard coded definitions to VRS 1.2 `CopyNumber` which doesn't exist in 1.3. This should be fixed separately, possibly w/ revision of the schema documentation method/engine.
update from main
VRS references from 1.2 => 1.3
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This PR is to add all the VRS link updates work we have done in #186.