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

[caufieldjh]

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

kgx/kgx/utils/kgx_utils.py

Lines 412 to 432 in 6645182

	def get_prefix_prioritization_map() -> Dict[str, List]:
	"""
	Get prefix prioritization map as defined in Biolink Model.
	Returns
	-------
	Dict[str, List]
	"""
	toolkit = get_toolkit()
	prefix_prioritization_map = {}
	# TODO: Lookup via Biolink CURIE should be supported in bmt
	descendants = toolkit.get_descendants("named thing")
	descendants.append("named thing")
	for d in descendants:
	element = toolkit.get_element(d)
	if element and "id_prefixes" in element:
	prefixes = element.id_prefixes
	key = format_biolink_category(element.name)
	prefix_prioritization_map[key] = prefixes
	return prefix_prioritization_map

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.

[cmungall]

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. — Reply to this email directly, view it on GitHub <#369>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOKFSCGOUBVT6OFY23DUVW6TNANCNFSM5LZT5W3Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>