Add and update resource descriptors using bioregistry conventions

[sjm41]

Summary

• Add new resource descriptor entries for biocyc, cazy, kegg.pathway, merops.family, and wikipathways
• Update existing TCDB entry to use bioregistry prefix (tcdb), identifier pattern, and resolution URL
• All new/updated entries use bioregistry.io resolution URLs and identifier patterns sourced from https://bioregistry.io

Test plan

• Verify YAML syntax is valid
• Confirm each new gid_pattern matches its corresponding example_gid
• Confirm each default_url resolves correctly when the example identifier is substituted

🤖 Generated with Claude Code

[sjm41]

Note: the old (existing) TCDB entry was not based on bioregistry, and its gid pattern only allowed full 4-character IDs. The new pattern comes from bioregistry and allows for xrefs to 1-, 2- or 3- character IDs as well as full 4-character IDs.

[sjm41]

Another note:
I added a new 'kegg.pathway' entry based on https://bioregistry.io/registry/kegg.pathway.

There is one existing KEGG entry in the yaml file that looks like this:

 - db_prefix: KEGG
    name: Kyoto Encyclopedia of Genes and Genomes
    example_id: KEGG:05220
    gid_pattern: "^KEGG:\\w*:*\\d+$"
    default_url: http://www.genome.jp/dbget-bin/www_bget?map[%s]
    pages:
      - name: ontology_provided_cross_reference
        url: http://www.genome.jp/dbget-bin/www_bget?map[%s]

That entry doesn't look right, so I asked Claude:

Can you tell what the pre-exisitng KEGG entry was meant to represent? The details don't look good to me.

Looking at the existing entry:

• db_prefix: KEGG
  name: Kyoto Encyclopedia of Genes and Genomes
  example_id: KEGG:05220
  gid_pattern: "^KEGG:\w*:*\d+$"
  default_url: http://www.genome.jp/dbget-bin/www_bget?map[%s]
  pages:
  • name: ontology_provided_cross_reference
    url: http://www.genome.jp/dbget-bin/www_bget?map[%s]

It looks like it was meant to represent KEGG pathways, based on:

• The URL uses map[%s] — the map prefix is KEGG's convention for pathway maps
• 05220 is a KEGG pathway number (likely hsa05220 = "Proteoglycans in cancer")

But there are several problems:

1. Incomplete example ID — KEGG:05220 is missing the organism prefix (e.g. hsa05220)
2. Sloppy gid_pattern — ^KEGG:\w*:*\d+$ is very loose, allowing optional characters and colons in odd places
3. Outdated URL — uses http://www.genome.jp rather than the current https://www.kegg.jp
4. Only used for ontology_provided_cross_reference — likely added to resolve cross-references from disease ontologies (like DOID) pointing to
   KEGG pathways

It seems like the new kegg.pathway entry we just added is a proper replacement. Would you like to remove this old KEGG entry?

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This PR doesn't delete that existing KEGG entry, because I wasn't sure exactly what "ontology_provided_cross_reference" might be using it. But I suspect Claude is right, and it should be deleted (and my new kegg.pathway entry used instead.