Cross-map protein structure features to UniProt feature CV

Add UniProt core ontology (purl.uniprot.org/core) cross-mappings to the
protein_structure_features value sets, complementing the OBO-first SO
meanings:
- Secondary structure: broad_mappings to Helix_Annotation /
  Beta_Strand_Annotation (UniProt is 3-state vs SS8 8-state); TURN
  exact_mapping to Turn_Annotation.
- Sites/modifications: Coiled_Coil_Annotation (exact), Active_Site_Annotation
  (related), Binding_Site_Annotation (broad, for protein- and metal-binding
  sites), Disulfide_Bond_Annotation (exact).
Declare the uniprot_core prefix. Geometric surface features (pocket, cleft,
elbow, etc.) remain unmapped as neither SO nor UniProt provides terms.

Author: claude

src/valuesets/schema/bio/protein_structure_features.yaml

@@ -22,6 +22,7 @@ prefixes:
   linkml: https://w3id.org/linkml/
   SO: http://purl.obolibrary.org/obo/SO_
   EDAM: http://edamontology.org/
+  uniprot_core: http://purl.uniprot.org/core/
   valuesets: https://w3id.org/valuesets/
   orcid: https://orcid.org/
   valuesets_meta: https://w3id.org/valuesets/meta/
@@ -51,33 +52,43 @@ enums:
         title: alpha helix
         description: Right-handed alpha helix (3.6 residues/turn, i to i+4 hydrogen bonding)
         meaning: SO:0001117
+        broad_mappings:
+        - uniprot_core:Helix_Annotation
         annotations:
           dssp_code: H
           ss8_class: H
       THREE_TEN_HELIX:
         title: 3-10 helix
         description: 3-10 helix (3 residues/turn, i to i+3 hydrogen bonding)
         meaning: SO:0001119
+        broad_mappings:
+        - uniprot_core:Helix_Annotation
         annotations:
           dssp_code: G
           ss8_class: G
       PI_HELIX:
         title: pi helix
         description: Pi helix (4.1 residues/turn, i to i+5 hydrogen bonding)
         meaning: SO:0001118
+        broad_mappings:
+        - uniprot_core:Helix_Annotation
         annotations:
           dssp_code: I
           ss8_class: I
       BETA_STRAND:
         title: beta strand
         description: Extended beta strand participating in a beta sheet
         meaning: SO:0001111
+        broad_mappings:
+        - uniprot_core:Beta_Strand_Annotation
         annotations:
           dssp_code: E
           ss8_class: E
       BETA_BRIDGE:
         title: isolated beta bridge
         description: Residue in an isolated single-pair beta bridge
+        broad_mappings:
+        - uniprot_core:Beta_Strand_Annotation
         annotations:
           dssp_code: B
           ss8_class: B
@@ -86,6 +97,8 @@ enums:
         title: hydrogen-bonded turn
         description: Hydrogen-bonded turn reversing backbone direction over <=4 residues
         meaning: SO:0001128
+        exact_mappings:
+        - uniprot_core:Turn_Annotation
         annotations:
           dssp_code: T
           ss8_class: T
@@ -145,6 +158,8 @@ enums:
         title: coiled coil
         description: Two or more alpha helices wound together like strands of a rope
         meaning: SO:0001080
+        exact_mappings:
+        - uniprot_core:Coiled_Coil_Annotation
       HELIX_CAP:
         title: helix cap
         description: N-cap or C-cap residue terminating an alpha helix
@@ -154,20 +169,28 @@ enums:
         title: catalytic residue
         description: An amino acid residue directly involved in enzyme catalysis (active site)
         meaning: SO:0001104
+        related_mappings:
+        - uniprot_core:Active_Site_Annotation
       PROTEIN_BINDING_SITE:
         title: protein binding site
         description: A site that interacts selectively and non-covalently with polypeptide molecules
         meaning: SO:0000410
+        broad_mappings:
+        - uniprot_core:Binding_Site_Annotation
       DISULFIDE_BOND:
         title: disulfide bond
         description: A covalent S-S bond between two cysteine residues
+        exact_mappings:
+        - uniprot_core:Disulfide_Bond_Annotation
         annotations:
-          ontology_gap: 'true'
+          obo_gap: 'true'
       METAL_BINDING_SITE:
         title: metal binding site
         description: A local site coordinating one or more metal ions
+        broad_mappings:
+        - uniprot_core:Binding_Site_Annotation
         annotations:
-          ontology_gap: 'true'
+          obo_gap: 'true'
       POCKET:
         title: binding pocket
         description: A concave, solvent-accessible surface depression that can accommodate a ligand