uniprot-mcp-server

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['accessions'], 'properties': {'fields': {'type': 'string', 'description': 'Comma-separated UniProtKB field names to project, e.g. "accession,gene_names,cc_function,ft_variant". Omit for the full curated default set. Use this on the initial call to trim payload.'}, 'sections': {'type': 'array', 'items': {'type': 'string', 'description': 'A section key from a prior outline response, e.g. "disease", "variants", "function", "xrefs".'}, 'description': 'Only used to re-call after a kind: "outline" response â\x80\x94 pass a subset of the outlined section keys to fetch just those sections. Do not pass on the initial call.'}, 'accessions': {'type': 'array', 'items': {'type': 'string', 'pattern': '^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$', 'description': 'A UniProtKB primary accession, e.g. "P04637". Canonical form only â\x80\x94 strip any "-N" isoform suffix.'}, 'maxItems': 20, 'minItems': 1, 'description': 'Accessions to fetch (1â\x80\x9320). From uniprot_search_proteins or uniprot_map_ids.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['kind']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'kind': {'enum': ['full', 'outline'], 'type': 'string', 'description': 'Result kind. "full": the batch resolved â\x80\x94 read succeeded[] and failed[]. "outline": a single record exceeded the context budget and is returned as a section listing â\x80\x94 re-call the same accession with sections:[...] to pull specific sections.'}, 'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['all_not_found'], 'description': 'Machine-readable failure mode. Declared by this tool: `all_not_found`: Every accession in the batch was well-formed but unknown to UniProtKB. Other values are possible when a failure originates below the handler.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'failed': {'type': 'array', 'items': {'type': 'object', 'required': ['accession', 'error'], 'properties': {'error': {'type': 'string', 'description': 'Why it failed and how to recover.'}, 'accession': {'type': 'string', 'description': 'The requested accession that did not resolve.'}}, 'description': 'A per-accession failure.', 'additionalProperties': False}, 'description': 'Accessions that were well-formed but not found in UniProtKB. Present when kind is "full".'}, 'notice': {'type': 'string', 'description': 'Re-call guidance when kind is "outline" â\x80\x94 re-call the same accession with sections:[...] to pull specific sections.'}, 'sections': {'type': 'array', 'items': {'type': 'object', 'required': ['name', 'bytes'], 'properties': {'name': {'type': 'string', 'description': 'Section identifier â\x80\x94 pass a subset in sections:[...] to retrieve it.'}, 'bytes': {'type': 'number', 'description': 'Serialized byte size of the section.'}}, 'description': 'An outlined section with its serialized size.', 'additionalProperties': False}, 'description': 'Section outline returned when a single record exceeds the context budget. Present when kind is "outline".'}, 'succeeded': {'type': 'array', 'items': {'type': 'object', 'required': ['accession', 'entryName', 'genes', 'organism', 'length', 'reviewed', 'annotationScore', 'proteinExistence'], 'properties': {'ptms': {'type': 'array', 'items': {'type': 'object', 'required': ['type', 'location'], 'properties': {'type': {'type': 'string', 'description': 'Feature type, e.g. "Modified residue" or "Domain".'}, 'location': {'type': 'object', 'properties': {'end': {'type': 'number', 'description': 'End residue position. Omitted when not exact.'}, 'start': {'type': 'number', 'description': 'Start residue position. Omitted when not exact.'}}, 'description': 'Residue range of the feature.', 'additionalProperties': False}, 'featureId': {'type': 'string', 'description': 'Stable feature identifier, e.g. "VAR_066493". Omitted when none.'}, 'description': {'type': 'string', 'description': 'Free-text description of the feature. Omitted when absent.'}}, 'description': 'A sequence feature.', 'additionalProperties': False}, 'description': 'Post-translational modification features (modified residues, glycosylation, etc.). Absent when none.'}, 'genes': {'type': 'array', 'items': {'type': 'string', 'description': 'A gene name or synonym.'}, 'description': 'Gene names and synonyms.'}, 'xrefs': {'type': 'object', 'description': 'Cross-references grouped by database (PDB, Ensembl, RefSeq, ChEMBL, AlphaFoldDB). Chain a PDB id into protein-mcp-server, a ChEMBL id into chembl. Absent when none.', 'propertyNames': {'type': 'string'}, 'additionalProperties': {'type': 'array', 'items': {'type': 'string', 'description': 'A cross-reference identifier in that database.'}}}, 'length': {'type': 'number', 'description': 'Canonical sequence length in residues.'}, 'disease': {'type': 'array', 'items': {'type': 'object', 'required': ['name'], 'properties': {'name': {'type': 'string', 'description': 'Disease name.'}, 'omimId': {'type': 'string', 'description': 'OMIM identifier. Omitted when none.'}, 'acronym': {'type': 'string', 'description': 'Disease acronym. Omitted when none.'}, 'diseaseId': {'type': 'string', 'description': 'UniProt disease accession, e.g. "DI-01537". Omitted when none.'}, 'description': {'type': 'string', 'description': 'Disease description. Omitted when none.'}}, 'description': 'A disease association.', 'additionalProperties': False}, 'description': 'Disease involvements (DISEASE comments). Absent when none.'}, 'domains': {'type': 'array', 'items': {'type': 'object', 'required': ['type', 'location'], 'properties': {'type': {'type': 'string', 'description': 'Feature type, e.g. "Modified residue" or "Domain".'}, 'location': {'type': 'object', 'properties': {'end': {'type': 'number', 'description': 'End residue position. Omitted when not exact.'}, 'start': {'type': 'number', 'description': 'Start residue position. Omitted when not exact.'}}, 'description': 'Residue range of the feature.', 'additionalProperties': False}, 'featureId': {'type': 'string', 'description': 'Stable feature identifier, e.g. "VAR_066493". Omitted when none.'}, 'description': {'type': 'string', 'description': 'Free-text description of the feature. Omitted when absent.'}}, 'description': 'A sequence feature.', 'additionalProperties': False}, 'description': 'Domain and region features. Absent when none.'}, 'goTerms': {'type': 'array', 'items': {'type': 'object', 'required': ['id', 'term', 'aspect'], 'properties': {'id': {'type': 'string', 'description': 'GO identifier, e.g. "GO:0006915".'}, 'term': {'type': 'string', 'description': 'GO term label, e.g. "apoptotic process".'}, 'aspect': {'type': 'string', 'description': 'GO aspect: P (process), F (function), or C (component).'}}, 'description': 'A Gene Ontology annotation.', 'additionalProperties': False}, 'description': 'GO annotations. Absent when none.'}, 'function': {'type': 'array', 'items': {'type': 'object', 'required': ['value'], 'properties': {'value': {'type': 'string', 'description': 'The annotated text.'}, 'evidence': {'type': 'array', 'items': {'type': 'string', 'description': 'A PubMed/source evidence reference, e.g. "PubMed:11025664".'}, 'description': 'Source evidence codes. Omitted when none are attached.'}}, 'description': 'An annotation with its source evidence preserved.', 'additionalProperties': False}, 'description': 'FUNCTION annotations. Absent on most TrEMBL entries.'}, 'isoforms': {'type': 'array', 'items': {'type': 'object', 'required': ['isoformId'], 'properties': {'name': {'type': 'string', 'description': 'Isoform name. Omitted when none.'}, 'isoformId': {'type': 'string', 'description': 'Isoform accession, e.g. "P04637-2".'}, 'sequenceStatus': {'type': 'string', 'description': 'Sequence status, e.g. "Displayed" or "Described". Omitted when none.'}}, 'description': 'An alternatively-spliced isoform.', 'additionalProperties': False}, 'description': 'Isoforms (ALTERNATIVE PRODUCTS). Absent when only one product.'}, 'keywords': {'type': 'array', 'items': {'type': 'object', 'required': ['id', 'name'], 'properties': {'id': {'type': 'string', 'description': 'Keyword identifier, e.g. "KW-0053".'}, 'name': {'type': 'string', 'description': 'Keyword name, e.g. "Apoptosis".'}, 'category': {'type': 'string', 'description': 'Keyword category. Omitted when none.'}}, 'description': 'A UniProt keyword.', 'additionalProperties': False}, 'description': 'UniProt keywords. Absent when none.'}, 'organism': {'type': 'object', 'required': ['scientificName', 'taxonId'], 'properties': {'taxonId': {'type': 'number', 'description': 'NCBI taxonomy ID.'}, 'mnemonic': {'type': 'string', 'description': 'Organism mnemonic, e.g. "HUMAN". Omitted when none.'}, 'commonName': {'type': 'string', 'description': 'Organism common name. Omitted when none.'}, 'scientificName': {'type': 'string', 'description': 'Organism scientific name.'}}, 'description': 'Source organism.', 'additionalProperties': False}, 'reviewed': {'type': 'boolean', 'description': 'True for reviewed Swiss-Prot, false for unreviewed TrEMBL.'}, 'variants': {'type': 'array', 'items': {'type': 'object', 'required': ['location'], 'properties': {'location': {'type': 'object', 'properties': {'end': {'type': 'number', 'description': 'End residue position. Omitted when not exact.'}, 'start': {'type': 'number', 'description': 'Start residue position. Omitted when not exact.'}}, 'description': 'Residue range of the variant.', 'additionalProperties': False}, 'original': {'type': 'string', 'description': 'Original residue(s). Omitted when not a substitution.'}, 'featureId': {'type': 'string', 'description': 'Variant identifier, e.g. "VAR_066493". Omitted when none.'}, 'variation': {'type': 'string', 'description': 'Variant residue(s). Omitted when not a substitution.'}, 'description': {'type': 'string', 'description': 'Variant description. Omitted when none.'}}, 'description': 'A natural variant.', 'additionalProperties': False}, 'description': 'Natural variants (dbSNP/ClinVar-linked). Absent when none.'}, 'accession': {'type': 'string', 'description': 'UniProtKB primary accession.'}, 'cofactors': {'type': 'array', 'items': {'type': 'object', 'required': ['name'], 'properties': {'name': {'type': 'string', 'description': 'Cofactor name, e.g. "Zn(2+)".'}, 'chebiId': {'type': 'string', 'description': 'ChEBI identifier. Omitted when none.'}}, 'description': 'A required cofactor.', 'additionalProperties': False}, 'description': 'Cofactors. Absent when none are annotated.'}, 'entryName': {'type': 'string', 'description': 'UniProtKB mnemonic ID, e.g. "P53_HUMAN".'}, 'proteinName': {'type': 'string', 'description': 'Recommended full protein name. Omitted when none.'}, 'annotationScore': {'type': 'number', 'description': 'Annotation confidence on a 1â\x80\x935 scale.'}, 'proteinExistence': {'type': 'string', 'description': 'Protein-existence evidence level.'}, 'catalyticActivity': {'type': 'array', 'items': {'type': 'object', 'required': ['name'], 'properties': {'name': {'type': 'string', 'description': 'Reaction equation, e.g. "ATP + L-tyrosyl-[protein] = ...".'}, 'rheaId': {'type': 'string', 'description': 'Rhea reaction ID, e.g. "RHEA:10596". Omitted when none.'}, 'ecNumber': {'type': 'string', 'description': 'Enzyme Commission number. Omitted when none.'}}, 'description': 'A catalyzed reaction.', 'additionalProperties': False}, 'description': 'Catalytic-activity reactions (Rhea-cross-referenced). Absent when not an enzyme.'}, 'subcellularLocation': {'type': 'array', 'items': {'type': 'object', 'required': ['location'], 'properties': {'location': {'type': 'string', 'description': 'Subcellular location, e.g. "Nucleus".'}, 'topology': {'type': 'string', 'description': 'Membrane topology. Omitted when not applicable.'}}, 'description': 'A subcellular location.', 'additionalProperties': False}, 'description': 'Subcellular locations. Absent when none are annotated.'}}, 'description': 'A full curated UniProtKB entry.', 'additionalProperties': False}, 'description': 'Entries that resolved successfully. Present when kind is "full".'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'size': {'type': 'integer', 'maximum': 500, 'description': 'Proteins per page when include_proteins is true (max 500). Omit for the server default.', 'exclusiveMinimum': 0}, 'upid': {'anyOf': [{'type': 'string', 'const': ''}, {'type': 'string', 'pattern': '^UP[0-9]{9}$', 'description': 'Proteome identifier, e.g. "UP000005640".'}], 'description': 'Proteome UPID. Provide this OR taxon_id, not both.'}, 'query': {'type': 'string', 'description': 'Optional UniProtKB Lucene filter to narrow the protein list, e.g. "reviewed:true AND keyword:KW-0067". Only applies when include_proteins is true.'}, 'cursor': {'type': 'string', 'description': 'Forward-pagination cursor from a prior protein page. Only meaningful with include_proteins.'}, 'taxon_id': {'type': 'integer', 'maximum': 9007199254740991, 'description': 'NCBI taxon ID, e.g. 9606 for human. Resolves to the reference proteome. Provide this OR upid, not both.', 'exclusiveMinimum': 0}, 'include_proteins': {'type': 'boolean', 'default': False, 'description': "When true, also return a capped, cursor-paginated page of the proteome's proteins. Defaults to false â\x80\x94 metadata alone is the common case."}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['proteome']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'cap': {'type': 'number', 'description': 'The page-size cap that was applied.'}, 'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['missing_identifier', 'conflicting_identifier', 'not_found'], 'description': 'Machine-readable failure mode. Declared by this tool: `missing_identifier`: Neither upid nor taxon_id was provided. `conflicting_identifier`: Both upid and taxon_id were provided. `not_found`: The UPID or taxon has no reference proteome. Other values are possible when a failure originates below the handler.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'shown': {'type': 'number', 'description': 'Number of proteins returned in this page.'}, 'cursor': {'type': 'string', 'description': 'Forward cursor for the next protein page. Absent on the last page.'}, 'notice': {'type': 'string', 'description': 'Truncation guidance when the protein page was capped â\x80\x94 how to reach the rest (walk the cursor or narrow with the query filter).'}, 'proteins': {'type': 'array', 'items': {'type': 'object', 'required': ['accession', 'entryName', 'geneNames', 'organism', 'length', 'reviewed', 'annotationScore', 'proteinExistence'], 'properties': {'length': {'type': 'number', 'description': 'Canonical sequence length in residues.'}, 'organism': {'type': 'object', 'required': ['scientificName', 'taxonId'], 'properties': {'taxonId': {'type': 'number', 'description': 'NCBI taxonomy ID.'}, 'commonName': {'type': 'string', 'description': 'Organism common name. Omitted when none.'}, 'scientificName': {'type': 'string', 'description': 'Organism scientific name.'}}, 'description': 'Source organism.', 'additionalProperties': False}, 'reviewed': {'type': 'boolean', 'description': 'True for reviewed Swiss-Prot, false for unreviewed TrEMBL.'}, 'accession': {'type': 'string', 'description': 'UniProtKB primary accession.'}, 'entryName': {'type': 'string', 'description': 'UniProtKB mnemonic ID.'}, 'geneNames': {'type': 'array', 'items': {'type': 'string', 'description': 'A gene name or synonym.'}, 'description': 'Gene names and synonyms.'}, 'proteinName': {'type': 'string', 'description': 'Recommended protein name. Omitted when none.'}, 'annotationScore': {'type': 'number', 'description': 'Annotation confidence on a 1â\x80\x935 scale.'}, 'functionSnippet': {'type': 'string', 'description': 'First function sentence(s), evidence stripped. Omitted when none.'}, 'proteinExistence': {'type': 'string', 'description': 'Protein-existence evidence level.'}}, 'description': 'A protein in the proteome.', 'additionalProperties': False}, 'description': "A capped page of the proteome's proteins. Present only when include_proteins is true."}, 'proteome': {'type': 'object', 'required': ['upid', 'proteomeType', 'organism', 'proteinCount'], 'properties': {'upid': {'type': 'string', 'description': 'Proteome identifier, e.g. "UP000005640".'}, 'busco': {'type': 'object', 'required': ['complete', 'completeSingle', 'completeDuplicated', 'fragmented', 'missing', 'total'], 'properties': {'score': {'type': 'number', 'description': 'Completeness percentage (0â\x80\x93100). Omitted when none.'}, 'total': {'type': 'number', 'description': 'Total BUSCO genes searched.'}, 'missing': {'type': 'number', 'description': 'Missing BUSCOs.'}, 'complete': {'type': 'number', 'description': 'Complete BUSCO genes.'}, 'lineageDb': {'type': 'string', 'description': 'BUSCO lineage dataset, e.g. "primates_odb10". Omitted when none.'}, 'fragmented': {'type': 'number', 'description': 'Fragmented BUSCOs.'}, 'completeSingle': {'type': 'number', 'description': 'Complete and single-copy BUSCOs.'}, 'completeDuplicated': {'type': 'number', 'description': 'Complete and duplicated BUSCOs.'}}, 'description': 'BUSCO completeness report. Absent for proteomes without one.', 'additionalProperties': False}, 'organism': {'type': 'object', 'required': ['scientificName', 'taxonId'], 'properties': {'taxonId': {'type': 'number', 'description': 'NCBI taxonomy ID.'}, 'mnemonic': {'type': 'string', 'description': 'Organism mnemonic, e.g. "HUMAN". Omitted when none.'}, 'commonName': {'type': 'string', 'description': 'Organism common name. Omitted when none.'}, 'scientificName': {'type': 'string', 'description': 'Organism scientific name.'}}, 'description': 'Source organism.', 'additionalProperties': False}, 'proteinCount': {'type': 'number', 'description': 'Total number of proteins in the proteome.'}, 'proteomeType': {'type': 'string', 'description': 'Proteome type, e.g. "Reference proteome".'}, 'genomeAssembly': {'type': 'string', 'description': 'Genome assembly accession, e.g. "GCA_000001405.29". Omitted when none.'}}, 'description': 'Proteome metadata.', 'additionalProperties': False}, 'truncated': {'type': 'boolean', 'description': 'True when the protein page hit the size cap â\x80\x94 more remain via cursor.'}, 'totalProteinsMatched': {'type': 'number', 'description': 'Total proteins matching the (optionally filtered) proteome query.'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'required': ['accession'], 'properties': {'accession': {'type': 'string', 'pattern': '^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$', 'description': 'UniProtKB primary accession, e.g. "P04637". Canonical form only â\x80\x94 strip any "-N" isoform suffix.'}, 'include_isoforms': {'type': 'boolean', 'default': False, 'description': 'When true, also return the isoform sequences. Defaults to false (canonical only).'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['accession', 'canonical']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['not_found'], 'description': 'Machine-readable failure mode. Declared by this tool: `not_found`: The accession has no sequence in UniProtKB. Other values are possible when a failure originates below the handler.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'isoforms': {'type': 'array', 'items': {'type': 'object', 'required': ['header', 'sequence', 'length', 'isoformId'], 'properties': {'header': {'type': 'string', 'description': 'The FASTA header line (without the leading ">"), e.g. "sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens OX=9606 GN=TP53 PE=1 SV=4".'}, 'length': {'type': 'number', 'description': 'Sequence length in residues.'}, 'sequence': {'type': 'string', 'description': 'The amino-acid sequence as a single string (newlines removed).'}, 'isoformId': {'type': 'string', 'description': 'Isoform accession, e.g. "P04637-2".'}}, 'description': 'An isoform sequence record.', 'additionalProperties': False}, 'description': 'Isoform sequence records. Present only when include_isoforms is true and isoforms exist.'}, 'accession': {'type': 'string', 'description': 'The accession that was fetched.'}, 'canonical': {'type': 'object', 'required': ['header', 'sequence', 'length'], 'properties': {'header': {'type': 'string', 'description': 'The FASTA header line (without the leading ">"), e.g. "sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens OX=9606 GN=TP53 PE=1 SV=4".'}, 'length': {'type': 'number', 'description': 'Sequence length in residues.'}, 'sequence': {'type': 'string', 'description': 'The amino-acid sequence as a single string (newlines removed).'}}, 'description': 'The canonical sequence record.', 'additionalProperties': False}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'name': {'type': 'string', 'description': 'Organism scientific name, e.g. "Homo sapiens". Provide this OR taxon_id, not both. Matched against the scientific name.'}, 'taxon_id': {'type': 'integer', 'maximum': 9007199254740991, 'description': 'NCBI taxonomy ID, e.g. 9606. Provide this OR name, not both.', 'exclusiveMinimum': 0}, 'include_children': {'type': 'boolean', 'default': False, 'description': 'When true, also fetch the immediate child taxa via a follow-up search. Defaults to false.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['taxon', 'lineage']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['missing_identifier', 'conflicting_identifier', 'not_found'], 'description': 'Machine-readable failure mode. Declared by this tool: `missing_identifier`: Neither taxon_id nor name was provided. `conflicting_identifier`: Both taxon_id and name were provided. `not_found`: The taxon ID or name did not resolve to a record. Other values are possible when a failure originates below the handler.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'taxon': {'type': 'object', 'required': ['taxonId', 'scientificName', 'rank'], 'properties': {'rank': {'type': 'string', 'description': 'Taxonomic rank, e.g. "species".'}, 'parent': {'type': 'object', 'required': ['taxonId', 'scientificName'], 'properties': {'taxonId': {'type': 'number', 'description': 'Parent taxon ID.'}, 'scientificName': {'type': 'string', 'description': 'Parent scientific name.'}}, 'description': 'Immediate parent taxon. Omitted at the root.', 'additionalProperties': False}, 'taxonId': {'type': 'number', 'description': 'NCBI taxonomy ID.'}, 'mnemonic': {'type': 'string', 'description': 'UniProt organism mnemonic, e.g. "HUMAN". Omitted when none.'}, 'commonName': {'type': 'string', 'description': 'Common name. Omitted when none.'}, 'otherNames': {'type': 'array', 'items': {'type': 'string', 'description': 'An alternative name or synonym.'}, 'description': 'Synonyms and alternative spellings. Omitted when none.'}, 'scientificName': {'type': 'string', 'description': 'Scientific name.'}}, 'description': 'The taxonomy record.', 'additionalProperties': False}, 'lineage': {'type': 'array', 'items': {'type': 'object', 'required': ['taxonId', 'scientificName', 'rank'], 'properties': {'rank': {'type': 'string', 'description': 'Taxonomic rank, e.g. "phylum", "clade", "no rank".'}, 'taxonId': {'type': 'number', 'description': 'NCBI taxonomy ID of the lineage node.'}, 'commonName': {'type': 'string', 'description': 'Common name of the node. Omitted when none.'}, 'scientificName': {'type': 'string', 'description': 'Scientific name of the lineage node.'}}, 'description': 'A node in the lineage, ordered root â\x86\x92 near.', 'additionalProperties': False}, 'description': "Full lineage from root to the taxon's near ancestor."}, 'children': {'type': 'array', 'items': {'type': 'object', 'required': ['taxonId', 'scientificName', 'rank'], 'properties': {'rank': {'type': 'string', 'description': 'Child rank.'}, 'taxonId': {'type': 'number', 'description': 'Child taxon ID.'}, 'scientificName': {'type': 'string', 'description': 'Child scientific name.'}}, 'description': 'An immediate child taxon.', 'additionalProperties': False}, 'description': 'Immediate children. Present only when include_children is true.'}, 'childCount': {'type': 'number', 'description': 'Number of immediate children returned (when include_children is true).'}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'ids': {'type': 'array', 'items': {'type': 'string', 'description': 'A source identifier in the from_db namespace, e.g. "TP53" for Gene_Name.'}, 'maxItems': 100000, 'description': 'Identifiers to translate. Required only when submitting a new mapping job; omitted when resuming with a ticket or continuation.'}, 'to_db': {'enum': ['UniProtKB', 'UniProtKB-Swiss-Prot', 'UniProtKB_AC-ID', 'Gene_Name', 'GeneID', 'Ensembl', 'Ensembl_Protein', 'PDB', 'RefSeq_Nucleotide', 'RefSeq_Protein', 'ChEMBL', 'PomBase', 'WormBase_Protein'], 'type': 'string', 'description': 'Target database. UniProtKB-Swiss-Prot = reviewed accessions only (the usual intent); UniProtKB / UniProtKB_AC-ID also include unreviewed TrEMBL. Required only when submitting a new mapping job; omitted when resuming with a ticket or continuation.'}, 'tax_id': {'type': 'integer', 'maximum': 9007199254740991, 'description': 'NCBI taxon ID to disambiguate ambiguous source IDs (e.g. a gene symbol across species). Recommended with Gene_Name; e.g. 9606 for human.', 'exclusiveMinimum': 0}, 'ticket': {'type': 'string', 'minLength': 1, 'description': 'Running-job ticket from a prior status "running" response. Pass it alone to poll that job; do not combine it with continuation or submission inputs.'}, 'from_db': {'enum': ['UniProtKB_AC-ID', 'Gene_Name', 'GeneID', 'Ensembl', 'Ensembl_Protein', 'PDB', 'RefSeq_Nucleotide', 'RefSeq_Protein', 'ChEMBL', 'PomBase', 'WormBase_Protein'], 'type': 'string', 'description': 'Source database. Gene_Name = HGNC symbol (pair with tax_id); UniProtKB_AC-ID = accession or entry name; Ensembl/Ensembl_Protein = ENSG/ENSP; PDB; RefSeq_Nucleotide/RefSeq_Protein = NM_/NP_; ChEMBL; GeneID = NCBI Gene. Required only when submitting a new mapping job; omitted when resuming with a ticket or continuation.'}, 'continuation': {'type': 'object', 'required': ['jobId', 'cursor'], 'properties': {'jobId': {'type': 'string', 'minLength': 1, 'description': 'UniProt ID-mapping job identifier for the completed job.'}, 'cursor': {'type': 'string', 'minLength': 1, 'description': 'Opaque cursor for the next completed results page.'}}, 'description': 'Completed-page continuation from a prior status "finished" response. Pass it alone to fetch the next page without polling or re-submitting.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['status']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['missing_inputs', 'conflicting_inputs', 'unsupported_db_pair', 'invalid_ticket', 'invalid_continuation'], 'description': 'Machine-readable failure mode. Declared by this tool: `missing_inputs`: No complete submission, running-job ticket, or completed-page continuation was provided. `conflicting_inputs`: Submission inputs, a running-job ticket, or a completed-page continuation were combined. `unsupported_db_pair`: The from_db/to_db combination is not supported by the ID-mapping service. `invalid_ticket`: The resume ticket is unknown or has expired server-side (UniProt holds jobs only temporarily). `invalid_continuation`: The completed-page continuation refers to a result page that is unknown or expired. Other values are possible when a failure originates below the handler.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'notice': {'type': 'string', 'description': 'Status guidance â\x80\x94 e.g. that the job is still running, or that no IDs mapped.'}, 'status': {'enum': ['finished', 'running'], 'type': 'string', 'description': 'Job state: "finished" (one completed results page included) or "running" (poll with ticket).'}, 'ticket': {'type': 'string', 'description': 'Running-job ticket (present only when status is "running"). Pass it alone to poll the same job.'}, 'results': {'type': 'array', 'items': {'type': 'object', 'required': ['from', 'to'], 'properties': {'to': {'type': 'string', 'description': 'The resolved target identifier (e.g. a UniProtKB accession).'}, 'from': {'type': 'string', 'description': 'The source identifier that was mapped.'}}, 'description': 'A single fromâ\x86\x92to mapping.', 'additionalProperties': False}, 'description': 'Resolved mappings on this completed page (present only when status is "finished"). Failed source IDs are reported in unmappedIds.'}, 'mappedCount': {'type': 'number', 'description': 'Number of resolved mappings (finished jobs only).'}, 'unmappedIds': {'type': 'array', 'items': {'type': 'string', 'description': 'A source ID that resolved to nothing.'}, 'description': 'Source IDs UniProt reported as failed on this completed page. Absent when none failed.'}, 'continuation': {'type': 'object', 'required': ['jobId', 'cursor'], 'properties': {'jobId': {'type': 'string', 'minLength': 1, 'description': 'UniProt ID-mapping job identifier for the completed job.'}, 'cursor': {'type': 'string', 'minLength': 1, 'description': 'Opaque cursor for the next completed results page.'}}, 'description': 'Next completed-page continuation (finished jobs only). Pass it alone to fetch the next page; absent on the terminal page.', 'additionalProperties': False}}, 'additionalProperties': False}

{'type': 'object', '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'size': {'type': 'integer', 'maximum': 500, 'description': 'Number of hits per page (max 500). Omit for the server default.', 'exclusiveMinimum': 0}, 'query': {'type': 'string', 'description': 'UniProtKB Lucene query with field prefixes â\x80\x94 gene, organism_id, keyword (KW-xxxx), go (GO id), reviewed, protein_name, family, length, existence, accession. Example: "gene:BRCA1 AND organism_id:9606 AND reviewed:true". Provide this OR text_search, not both.'}, 'cursor': {'type': 'string', 'description': 'Opaque forward-pagination cursor from a prior response. Walk pages with this; random access to page N is not supported.'}, 'facets': {'type': 'string', 'description': 'Comma-separated upstream facet names for count breakdowns, e.g. "reviewed,model_organism,proteins_with". Returns a facets array alongside the hits.'}, 'fields': {'type': 'string', 'description': 'Comma-separated UniProtKB field names to project, e.g. "accession,gene_names,cc_function". Omit for a sensible default set covering name, gene, organism, length, reviewed, score, and a function snippet.'}, 'reviewed': {'type': 'boolean', 'default': True, 'description': 'Restrict to reviewed Swiss-Prot entries. Defaults to true (curated only); set false to include unreviewed TrEMBL. Ignored when query already pins a reviewed: clause.'}, 'organism_id': {'type': 'integer', 'maximum': 9007199254740991, 'description': 'Restrict to an NCBI taxon ID, e.g. 9606 for human. A convenience filter ANDed onto the query; resolve names with uniprot_get_taxonomy.', 'exclusiveMinimum': 0}, 'text_search': {'type': 'string', 'description': 'Plain-language search across protein names, gene names, and function, e.g. "kinase apoptosis". Provide this OR query, not both.'}}, 'additionalProperties': False}

{'type': 'object', 'anyOf': [{'not': {'required': ['error']}, 'required': ['results', 'totalResults', 'effectiveQuery']}, {'required': ['error']}], '$schema': 'https://json-schema.org/draft/2020-12/schema', 'properties': {'error': {'type': 'object', 'required': ['code', 'message'], 'properties': {'code': {'type': 'integer', 'maximum': 9007199254740991, 'minimum': -9007199254740991, 'description': 'JSON-RPC error code for this failure.'}, 'data': {'type': 'object', 'properties': {'reason': {'type': 'string', 'examples': ['missing_query', 'conflicting_query'], 'description': 'Machine-readable failure mode. Declared by this tool: `missing_query`: Neither text_search nor query was provided. `conflicting_query`: Both text_search and query were provided. Other values are possible when a failure originates below the handler.'}, 'recovery': {'type': 'object', 'required': ['hint'], 'properties': {'hint': {'type': 'string'}}, 'description': 'Actionable next step for the caller.', 'additionalProperties': {}}, 'retryable': {'type': 'boolean', 'description': 'Whether retrying may succeed.'}}, 'additionalProperties': {}}, 'message': {'type': 'string', 'description': 'Human-readable description of what went wrong.'}}, 'description': 'Present when the call failed. Absent on success.', 'additionalProperties': {}}, 'cursor': {'type': 'string', 'description': 'Forward cursor for the next page. Absent on the last page.'}, 'facets': {'type': 'array', 'items': {'type': 'object', 'required': ['name', 'label', 'values'], 'properties': {'name': {'type': 'string', 'description': 'Facet identifier, e.g. "reviewed".'}, 'label': {'type': 'string', 'description': 'Human-readable facet label, e.g. "Status".'}, 'values': {'type': 'array', 'items': {'type': 'object', 'required': ['value', 'label', 'count'], 'properties': {'count': {'type': 'number', 'description': 'Number of matches in this bucket.'}, 'label': {'type': 'string', 'description': 'Human-readable value label, e.g. "Reviewed (Swiss-Prot)".'}, 'value': {'type': 'string', 'description': 'Facet value, e.g. "true".'}}, 'description': 'A single facet bucket.', 'additionalProperties': False}, 'description': 'Count buckets for this facet.'}}, 'description': 'A server-side facet breakdown.', 'additionalProperties': False}, 'description': 'Upstream facet count breakdowns. Present only when facets were requested.'}, 'notice': {'type': 'string', 'description': 'Guidance when nothing matched â\x80\x94 echoes the query and suggests how to broaden.'}, 'results': {'type': 'array', 'items': {'type': 'object', 'required': ['accession', 'entryName', 'geneNames', 'organism', 'length', 'reviewed', 'annotationScore', 'proteinExistence'], 'properties': {'length': {'type': 'number', 'description': 'Canonical sequence length in residues.'}, 'organism': {'type': 'object', 'required': ['scientificName', 'taxonId'], 'properties': {'taxonId': {'type': 'number', 'description': 'NCBI taxonomy ID, e.g. 9606.'}, 'commonName': {'type': 'string', 'description': 'Organism common name, e.g. "Human". Omitted when none.'}, 'scientificName': {'type': 'string', 'description': 'Organism scientific name, e.g. "Homo sapiens".'}}, 'description': 'Source organism.', 'additionalProperties': False}, 'reviewed': {'type': 'boolean', 'description': 'True for reviewed Swiss-Prot (manually curated), false for unreviewed TrEMBL (computationally predicted).'}, 'accession': {'type': 'string', 'description': 'UniProtKB primary accession, e.g. "P04637". The lookup key for uniprot_get_entry and uniprot_get_sequence.'}, 'entryName': {'type': 'string', 'description': 'UniProtKB mnemonic ID, e.g. "P53_HUMAN". Not an input key â\x80\x94 use accession.'}, 'geneNames': {'type': 'array', 'items': {'type': 'string', 'description': 'A gene name or synonym.'}, 'description': 'Gene names and synonyms for the protein.'}, 'proteinName': {'type': 'string', 'description': 'Recommended full protein name. Omitted when the entry has none.'}, 'annotationScore': {'type': 'number', 'description': 'Annotation confidence on a 1â\x80\x935 scale; higher means more curation evidence.'}, 'functionSnippet': {'type': 'string', 'description': 'First sentence(s) of the FUNCTION annotation, evidence references stripped. Omitted when no function is annotated.'}, 'proteinExistence': {'type': 'string', 'description': 'Evidence level for the protein\'s existence, e.g. "1: Evidence at protein level".'}}, 'description': 'A UniProtKB search hit.', 'additionalProperties': False}, 'description': 'Matching protein hits for this page.'}, 'totalResults': {'type': 'number', 'description': 'Total matches for the query before pagination (from the upstream result count).'}, 'effectiveQuery': {'type': 'string', 'description': 'The query as the server assembled and sent it to UniProtKB.'}}, 'additionalProperties': False}