229 lines
7.2 KiB
JSON
229 lines
7.2 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-06/schema#",
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"$id": "https://gitlab.ebi.ac.uk/pdbe-kb/funpdbe/funpdbe-schema/raw/master/funpdbe_schema.json",
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"title": "funpdbe_schema",
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"type": "object",
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"properties": {
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"data_resource": {
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"type": "string",
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"description": "Name of the database or software"
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},
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"resource_version": {
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"type": "string",
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"description": "Version of the resource"
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},
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"software_version": {
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"type": "string",
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"description": "Version of the software used"
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},
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"resource_entry_url": {
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"type": "string",
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"description": "URL linking to the entry at the partner resource"
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},
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"model_coordinates_url": {
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"type": "string",
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"description": "URL linking to a structural model at the partner resource"
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},
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"includes_het_groups": {
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"type": "boolean",
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"description": "Does this JSON include annotations of HET residues"
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},
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"release_date": {
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"type": "string",
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"description": "Release date of the annotation dd/mm/yyyy",
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"pattern": "^[0-3]*[0-9]/[0-1]*[0-9]/[1-2][0-9]{3}$"
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},
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"pdb_id": {
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"type": "string",
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"description": "PDB identifier",
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"pattern": "^[1-9][a-zA-Z0-9]{3}$"
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},
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"additional_entry_annotations": {
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"type": "object",
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"description": "Additional entry-level annotations",
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"additionalProperties": true
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},
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"chains": {
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"type": "array",
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"items": {
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"type": "object",
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"properties": {
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"chain_label": {
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"type": "string",
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"description": "PDB chain identifier"
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},
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"additional_chain_annotations": {
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"type": "object",
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"description": "Additional chain-level annotations",
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"additionalProperties": true
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},
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"residues": {
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"type": "array",
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"items": {
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"type": "object",
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"properties": {
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"pdb_res_label": {
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"type": "string",
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"description": "Author residue index from the corresponding PDB entry (a.k.a. auth_seq_id)"
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},
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"aa_type": {
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"type": "string",
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"description": "Three-letter amino acid code",
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"pattern": "^[A-Za-z0-9]+$"
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},
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"additional_residue_annotations": {
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"type": "object",
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"description": "Additional residue-level annotations",
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"additionalProperties": true
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},
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"site_data": {
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"type": "array",
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"items": {
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"type": "object",
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"properties": {
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"site_id_ref": {
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"type": "integer",
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"description": "Reference to site_id"
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},
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"raw_score": {
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"type": "number",
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"description": "Raw calculated score"
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},
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"confidence_score": {
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"type": "number",
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"description": "Confidence level of the annotation (0-1, except if the method justifies otherwise)",
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"minimum": 0.0
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},
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"confidence_classification": {
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"type": "string",
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"description": "Confidence classification of the residue",
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"enum": [
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"high",
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"medium",
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"low",
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"null",
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"curated"
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]
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},
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"aa_variant": {
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"type": "string",
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"description": "Three-letter amino acid code of variant/mutant",
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"pattern": "^[A-Za-z0-9]+$"
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},
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"aa_variant_causes": {
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"type": "string",
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"description": "The reason behind classifying a variant benign or damaging"
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}
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},
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"required": [
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"site_id_ref",
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"confidence_classification"
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],
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"additionalProperties": false
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},
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"minItems": 1,
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"uniqueItems": true
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}
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},
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"required": [
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"pdb_res_label",
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"aa_type",
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"site_data"
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],
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"additionalProperties": false
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},
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"minItems": 1,
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"uniqueItems": true
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}
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},
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"required": [
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"chain_label",
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"residues"
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],
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"additionalProperties": false
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},
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"minItems": 1,
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"uniqueItems": true
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},
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"sites": {
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"type": "array",
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"items": {
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"type": "object",
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"properties": {
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"site_id": {
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"type": "integer",
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"description": "Site identifier"
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},
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"label": {
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"type": "string",
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"description": "Site label"
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},
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"site_url": {
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"type": "string",
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"description": "URL linking to information on the functional site at the partner resource"
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},
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"source_database": {
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"type": "string",
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"description": "Name of the source database"
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},
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"source_accession": {
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"type": "string",
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"description": "Accession identifier"
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},
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"source_release_date": {
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"type": "string",
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"description": "Date of acquiring data from source",
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"pattern": "^[0-3]*[0-9]/[0-1]*[0-9]/[1-2][0-9]{3}$"
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},
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"source_version": {
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"type": "string",
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"description": "Version of the data source"
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},
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"additional_site_annotations": {
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"type": "object",
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"description": "Additional site-level annotations",
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"additionalProperties": true
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}
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},
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"required": [
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"site_id",
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"label"
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],
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"additionalProperties": false
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},
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"minItems": 1,
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"uniqueItems": true
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},
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"evidence_code_ontology": {
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"type": "array",
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"items": {
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"type": "object",
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"properties": {
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"eco_term": {
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"type": "string",
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"description": "Evidence Code Ontology (ECO) term - http://www.evidenceontology.org/"
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},
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"eco_code": {
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"type": "string",
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"description": "Evidence Code Ontology (ECO) code - http://www.evidenceontology.org/",
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"pattern": "^ECO_[0-9]{7}$"
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}
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},
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"required": [
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"eco_code"
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],
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"additionalProperties": false
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},
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"minItems": 1,
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"uniqueItems": true
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}
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},
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"required": [
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"data_resource",
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"pdb_id",
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"chains",
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"evidence_code_ontology",
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"sites"
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],
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"additionalProperties": false
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}
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