Resource Relation Ontology and Graph

[cthoyt]

Relationships between prefixes to capture:

• Prefix has been subsumed by other prefix (lots of examples in the NIF world, some stuff with Arapidopsis gene nomenclature getting consolidated to TAIR) (unidirectional)
• Prefixes are equivalent (EC-CODE v. IntEnz) (bidirectional)
• Prefix used in resource (the ontology graph will be a fun way to show this one off) (unidirectional)

Provides

There are many nonsense prefixes minted across various registries since the resources themselves do are not nomenclature authorities. For example, ctd.chemical provides for mesh.

Part Of

There are several ways that part of relationships can be found by prefix:

• dot delimited, has a parent (e.g., kegg with kegg.pathway, kegg.ligand),
• dot delimited, no parent (e.g., insdc.cds, insdc.gca, insdc.sra),
• no dot but has common prefix, no parent (e.g., dlxb, dlxb)

import bioregistry

for prefix, entry in bioregistry.read_bioregistry().items():
    if '.' in prefix and 'part_of' not in entry:
        print(prefix, prefix.split('.')[0] in bioregistry.read_bioregistry())

[cthoyt]

This is done