diff --git a/src/valuesets/schema/bio/protein_structure_features.yaml b/src/valuesets/schema/bio/protein_structure_features.yaml new file mode 100644 index 00000000..1b4aac56 --- /dev/null +++ b/src/valuesets/schema/bio/protein_structure_features.yaml @@ -0,0 +1,235 @@ +name: protein_structure_features +title: Protein 3D Local Structure Feature Value Sets +description: 'Value sets describing fine-grained, local three-dimensional features of protein + structures: per-residue secondary structure states, super-secondary structural motifs, + functional sites, and local geometric features (pockets, clefts, elbows). + + + These provide a curated, human-interpretable, ontology-mapped counterpart to the learned + per-residue feature vocabularies produced by protein language models -- e.g. the 8-state + secondary structure (SS8) track and structure-token codebook of ESM3, and the ~16,000 + sparse-autoencoder feature dictionaries served per-residue by interpretability APIs + (InterPLM; the Biohub/EvolutionaryScale ESMC SAE, model + biohub/ESMC-6B-sae-layer60-k64-codebook16384). Where curated ontology terms exist they + are mapped via ``meaning:``; geometric surface features (pocket, cleft, cavity, elbow, + groove, tunnel) currently have no suitable OBO term and are flagged as gaps. + + ' +id: https://w3id.org/valuesets/bio/protein_structure_features +imports: +- linkml:types +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/ +default_prefix: valuesets +slots: + secondary_structure: + description: Per-residue secondary structure state + range: SecondaryStructureType + local_structural_feature: + description: Local 3D structural feature, motif, site, or geometric feature + range: LocalStructuralFeature +enums: + SecondaryStructureType: + title: Secondary Structure Type + description: 'Per-residue secondary structure assignment. The permissible values + correspond to the canonical DSSP 8-state (SS8) classification, which is also the + secondary-structure track vocabulary used by protein language models such as ESM3. + The single-letter DSSP code is recorded in the ``dssp_code`` annotation.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + ALPHA_HELIX: + 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 + ontology_gap: 'true' + TURN: + 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 + BEND: + title: bend + description: Region of high backbone curvature without regular hydrogen bonding + annotations: + dssp_code: S + ss8_class: S + ontology_gap: 'true' + COIL: + title: coil / loop + description: Irregular, unstructured backbone region (loop / random coil) + meaning: SO:0100012 + annotations: + dssp_code: C + ss8_class: C + aliases: loop, random coil, blank + LocalStructuralFeature: + title: Local Structural Feature + description: 'Fine-grained local three-dimensional features of protein structures, + spanning super-secondary structural motifs, functional sites, and local geometric + surface features. This is the curated, ontology-mapped analogue of the learned + per-residue feature vocabularies produced by protein language models and their + sparse-autoencoder interpretations. Members marked with the ``ontology_gap`` + annotation have no suitable OBO term and are candidates for new ontology terms.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + POLYPEPTIDE_STRUCTURAL_MOTIF: + title: polypeptide structural motif + description: A recurring 3D structural element within the chain that does not form + a stable globular unit (the general parent class for local motifs) + meaning: SO:0001079 + BETA_HAIRPIN: + title: beta hairpin + description: Two adjacent antiparallel beta strands connected by a short loop or turn + annotations: + ontology_gap: 'true' + BETA_BULGE: + title: beta bulge + description: A local disruption of beta-sheet hydrogen bonding across three residues + meaning: SO:0001107 + ASX_MOTIF: + title: asx motif + description: A five-residue motif nucleated by an Asp/Asn side chain (Asx) + meaning: SO:0001106 + NEST: + title: polypeptide nest motif + description: A motif of two consecutive residues forming an anion-binding concavity + meaning: SO:0001120 + COILED_COIL: + 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 + annotations: + ontology_gap: 'true' + CATALYTIC_RESIDUE: + 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: + 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: + obo_gap: 'true' + POCKET: + title: binding pocket + description: A concave, solvent-accessible surface depression that can accommodate a ligand + annotations: + ontology_gap: 'true' + related_edam: EDAM:data_1542 + CLEFT: + title: cleft + description: An elongated surface groove between structural elements or domains + annotations: + ontology_gap: 'true' + CAVITY: + title: interior cavity + description: An enclosed, solvent-inaccessible internal void within the structure + annotations: + ontology_gap: 'true' + related_edam: EDAM:data_1542 + TUNNEL: + title: tunnel / channel + description: An elongated, often buried, passage through the structure connecting two regions + annotations: + ontology_gap: 'true' + GROOVE: + title: groove + description: A surface channel, e.g. a nucleic-acid-binding groove + annotations: + ontology_gap: 'true' + ELBOW: + title: elbow / hinge + description: A localized bend or hinge between two structural elements or domains + annotations: + ontology_gap: 'true' + KINK: + title: helix kink + description: A localized bend interrupting the regular geometry of a helix + annotations: + ontology_gap: 'true' + INTERFACE: + title: interaction interface + description: A surface patch mediating contact with another chain or molecule + annotations: + ontology_gap: 'true' diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index fddac088..c948f7f2 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -18,6 +18,7 @@ imports: - bio/genome_features - bio/bio_entities - bio/structural_biology +- bio/protein_structure_features - bio/biosafety - bio/insdc_missing_values - bio/insdc_geographic_locations