Update foreign SSSOM sets from the ontology. #3415
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The `group` element in the XML catalog contains a `xml:base` attribute with an empty value (`xml:base=""`). It is unclear whether an empty value is legal (though the XML Base specification [1] does not seem to explicitly forbid it), but in any case it does not make any sense, and some XML Catalog parsers barf upon encountering such an attribute. So here we simply remove it. This has (as expected) no effect on the parsing of the catalog by both Protégé and ROBOT. [1] https://www.w3.org/TR/xmlbase/
When importing an externally maintained SSSOM set (the FBbt mapping set and the Biomappings set), check them against Uberon to (1) remove any mapping to an Uberon entity that does not exist or is deprecated, and (2) add any missing label for Uberon entities.
Recent changes in the SSSOM pipelines require SSSOM-CLI's `--update-from-ontology` option which was added in SSSOM-Java 0.7.9, which itself was included in ODK 1.5.3.
matentzn
approved these changes
Nov 11, 2024
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This PR amends the rules that refresh the externally maintained SSSOM mapping sets (the FBbt set and the Biomappings set) to include a step that check those sets against the current version of the ontology to
(1) remove any mapping to a Uberon entity that does not exist or is deprecated;
(2) add any missing label, using the labels found in the ontology.
This necessitates, as a preliminary:
(1) making sure we are using ODK 1.5.3, as previous versions do not include a recent enough version of SSSOM-Java;
(2) removing a bogus empty
xml:baseattribute in the XML catalog, that preventssssom-clifrom reading it.