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Allow user-provided SSSOM maps to be used for prefix prioritization

Open caufieldjh opened this issue 2 years ago • 1 comments

The prefix_prioritization_map defines prefixes to be used to replace others in a clique merge: https://github.com/biolink/kgx/blob/6645182e121c2e1172db862bba67cb114c963bed/kgx/utils/kgx_utils.py#L412-L432

But what if we have an exact preference for a prefix, e.g., we want all Drug nodes to have DrugCentral prefixes? (and/or we have prefixes not known to biolink-model?) It would be convenient to provide this function with a SSSOM map to use in addition to the biolink-model prefix priorities.

caufieldjh avatar Jan 12 '22 18:01 caufieldjh

another source is the biolink id_prefixes

On Wed, Jan 12, 2022 at 10:00 AM Harry Caufield @.***> wrote:

The prefix_prioritization_map defines prefixes to be used to replace others in a clique merge:

https://github.com/biolink/kgx/blob/6645182e121c2e1172db862bba67cb114c963bed/kgx/utils/kgx_utils.py#L412-L432

But what if we have an exact preference for a prefix, e.g., we want all Drug nodes to have DrugCentral prefixes? (and/or we have prefixes not known to biolink-model?) It would be convenient to provide this function with a SSSOM map to use in addition to the biolink-model prefix priorities.

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cmungall avatar Jan 12 '22 18:01 cmungall