Standardize node identifiers and prefixes

[caufieldjh]

Describe the desired behavior

@LucaCappelletti94 has found that 714,403 nodes across all of KG-OBO aren't among Bioregistry prefixes. There are 695792 unique node ids in this set across 167 ontologies.

Use a prefix remapping to normalize these prefixes where possible. The curies package may help.

Additional context

• Many of these IDs are from bnodes. That's a different issue.

• Many of these IDs are URLs. Some are resolvable to known prefixes:

  https://www.ncbi.nlm.nih.gov/pubmed/15152704

  Some are clearly still IRIs but are more challenging to have a consistent prefix for:

  https://www.worldcat.org/oclc/499105143

  And still others are just everyday URLs:

  https://www.shellingmachine.com/application/pinenuts-shelling-overview.html

• Some of these are linkml classes:

  linkml:Definition
  linkml:Element
  linkml:Example
  linkml:LocalName
  linkml:PermissibleValue
  linkml:SchemaDefinition
  linkml:SlotDefinition
  linkml:abstract
  linkml:comments
  linkml:created_on
  linkml:data_collection_state
  linkml:description
  linkml:exact_mappings
  linkml:examples
  linkml:from_schema
  linkml:identifier
  linkml:imported_from
  linkml:local_name_source
  linkml:local_name_value
  linkml:local_names
  linkml:maximum_value
  linkml:meaning
  linkml:minimum_value
  linkml:multivalued
  linkml:name
  linkml:pattern
  linkml:permissible_values
  linkml:recommended
  linkml:required
  linkml:see_also
  linkml:status
  linkml:type_uri
  linkml:value
  linkml:value_description
  linkml:values_from

• Some are predicate types and may be present in multiple ontologies, so some more in-depth pattern parsing may be needed.

  results_in
  results_in_assembly_of
  results_in_development_of
  results_in_disassembly_of
  results_in_distribution_of
  results_in_fission_of
  results_in_formation_of
  results_in_maintenance_of
  results_in_specification_of

[caufieldjh]

If we drop the obvious IRIs (as per Bioregistry), there are 476687 nodes which still have non-normalized IDs.

Many are luckily prefixes we can map, e.g. from GNO:

https://gnome.glyomics.org/StructureBrowser.html?focus=G21394OM