{
"openapi" : "3.0.1",
"info" : {
"title" : "OpenAPI definition",
"version" : "v0"
},
"servers" : [ {
"url" : "https://rest.uniprot.org/",
"description" : "UniProt REST API Server"
} ],
"tags" : [ {
"name" : "UniRef",
"description" : "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records. This hides redundant sequences and obtains complete coverage of the sequence space at three resolutions: UniRef100, UniRef90 and UniRef50."
} ],
"paths" : {
"/uniref/{id}" : {
"get" : {
"tags" : [ "UniRef" ],
"summary" : "Get UniRef cluster entry by a single cluster id.",
"description" : "Search UniRef entry by id to return all data associated with that entry. Specify fields to return only data for specific sections of that entry that are of interest to you",
"operationId" : "getById",
"parameters" : [ {
"name" : "id",
"in" : "query",
"description" : "Unique identifier for the UniRef cluster",
"required" : false,
"schema" : {
"pattern" : "(UniRef100|UniRef90|UniRef50)_\\w+(-[0-9]+)?",
"type" : "string"
},
"example" : "UniRef100_P05067"
}, {
"name" : "fields",
"in" : "query",
"description" : "List of entry sections (fields) to be returned, separated by commas. List of valid fields",
"required" : false,
"schema" : {
"type" : "string"
},
"example" : "id,name,types,organism,identity"
} ],
"responses" : {
"default" : {
"description" : "default response",
"content" : {
"application/json" : {
"schema" : {
"$ref" : "#/components/schemas/UniRefEntry"
}
},
"application/xml" : {
"schema" : {
"$ref" : "#/components/schemas/Entry"
}
},
"text/plain;format=tsv" : { },
"text/plain;format=list" : { },
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" : { },
"text/plain;format=fasta" : { },
"application/rdf+xml" : { },
"text/turtle" : { },
"application/n-triples" : { }
}
}
}
}
},
"/uniref/{id}/members" : {
"get" : {
"tags" : [ "UniRef" ],
"summary" : "Retrieve UniRef cluster members by a single cluster id.",
"description" : "Search UniRef entry by id to return all member data associated with that entry. Specify fields to return only data for specific sections of that entry that are of interest to you",
"operationId" : "search",
"parameters" : [ {
"name" : "id",
"in" : "query",
"description" : "Unique identifier for the UniRef cluster",
"required" : true,
"schema" : {
"pattern" : "(UniRef100|UniRef90|UniRef50)_\\w+(-[0-9]+)?",
"type" : "string"
},
"example" : "UniRef100_P05067"
}, {
"name" : "facetFilter",
"in" : "query",
"description" : "Facet filter query for UniRef Cluster Members",
"required" : false,
"schema" : {
"type" : "string"
},
"example" : "member_id_type:uniprotkb_id"
}, {
"name" : "size",
"in" : "query",
"description" : "Specify the number of entries per page of results (Pagination size). Default is 25, max is 500",
"required" : false,
"schema" : {
"maximum" : 500,
"minimum" : 0,
"type" : "integer",
"format" : "int32"
},
"example" : 50
} ],
"responses" : {
"default" : {
"description" : "default response",
"content" : {
"application/json" : {
"schema" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/UniRefMember"
}
}
},
"text/plain;format=list" : { }
}
}
}
}
},
"/uniref/{id}/members/stream" : {
"get" : {
"tags" : [ "UniRef" ],
"summary" : "Download UniRef cluster members by a single cluster id.",
"description" : "Search UniRef entry by id to return all member data associated with that entry. ",
"operationId" : "stream",
"parameters" : [ {
"name" : "id",
"in" : "query",
"description" : "Unique identifier for the UniRef cluster",
"required" : true,
"schema" : {
"pattern" : "(UniRef100|UniRef90|UniRef50)_\\w+(-[0-9]+)?",
"type" : "string"
},
"example" : "UniRef100_P05067"
}, {
"name" : "download",
"in" : "query",
"description" : "Specify true to download as file, default is false.",
"required" : false,
"schema" : {
"pattern" : "^true$|^false$",
"type" : "boolean"
}
} ],
"responses" : {
"default" : {
"description" : "default response",
"content" : {
"application/json" : {
"schema" : {
"$ref" : "#/components/schemas/StreamResult"
}
},
"application/xml" : {
"schema" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Entry"
}
}
},
"text/plain;format=tsv" : { },
"text/plain;format=list" : { },
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" : { },
"text/plain;format=fasta" : { }
}
}
}
}
},
"/uniref/{id}/light" : {
"get" : {
"tags" : [ "UniRef" ],
"summary" : "Get a light UniRef cluster entry by a single cluster id.",
"description" : "Search light UniRef entry by id to return all data associated with that entry. Specify fields to return only data for specific sections of that entry that are of interest to you",
"operationId" : "getById_1",
"parameters" : [ {
"name" : "id",
"in" : "path",
"description" : "Unique identifier for the UniRef cluster",
"required" : true,
"schema" : {
"pattern" : "(UniRef100|UniRef90|UniRef50)_\\w+(-[0-9]+)?",
"type" : "string"
},
"example" : "UniRef100_P05067"
}, {
"name" : "fields",
"in" : "query",
"description" : "List of entry sections (fields) to be returned, separated by commas. List of valid fields",
"required" : false,
"schema" : {
"type" : "string"
},
"example" : "id,name,types,organism,identity"
} ],
"responses" : {
"default" : {
"description" : "default response",
"content" : {
"application/json" : {
"schema" : {
"$ref" : "#/components/schemas/UniRefEntry"
}
},
"application/xml" : {
"schema" : {
"$ref" : "#/components/schemas/Entry"
}
},
"text/plain;format=tsv" : { },
"text/plain;format=list" : { },
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" : { },
"text/plain;format=fasta" : { },
"application/rdf+xml" : { }
}
}
}
}
},
"/uniref/stream" : {
"get" : {
"tags" : [ "UniRef" ],
"summary" : "Download light UniRef cluster entries retrieved by a search query. (Max. 10 million entries)",
"description" : "The stream endpoint uses a request query to return all entries associated with the search term in a single download. Specify fields to return only data for specific sections of that entry that are of interest to you The stream endpoint has a maximum limit of 10 million entries. For larger requests, please use the 'UniRef asynchronous download job' requests described below. The 'UniRef asynchronous download job' requests can be used for any size -- the asynchronous download jobs can be paused and resumed at your convenience, unlike the stream endpoint.",
"operationId" : "stream_1",
"parameters" : [ {
"name" : "query",
"in" : "query",
"description" : "Criteria to search UniRef. Advanced queries can be built with parentheses and conditionals such as AND, OR and NOT. List of valid search fields",
"required" : true,
"schema" : {
"type" : "string"
},
"example" : "Transcription factors"
}, {
"name" : "sort",
"in" : "query",
"description" : "Specify field by which to sort results. List of valid sort fields",
"required" : false,
"schema" : {
"type" : "string"
}
}, {
"name" : "fields",
"in" : "query",
"description" : "List of entry sections (fields) to be returned, separated by commas. List of valid fields",
"required" : false,
"schema" : {
"type" : "string"
},
"example" : "id,name,types,organism,identity"
}, {
"name" : "complete",
"in" : "query",
"description" : "Flag to include all member ids and organisms, or not. By default, it returns a maximum of 10 member ids and organisms",
"required" : false,
"schema" : {
"pattern" : "true|false",
"type" : "boolean"
}
}, {
"name" : "download",
"in" : "query",
"description" : "Specify true to download as file, default is false.",
"required" : false,
"schema" : {
"pattern" : "^true$|^false$",
"type" : "boolean"
}
} ],
"responses" : {
"default" : {
"description" : "default response",
"content" : {
"application/json" : {
"schema" : {
"$ref" : "#/components/schemas/StreamResult"
}
},
"application/xml" : {
"schema" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Entry"
}
}
},
"text/plain;format=tsv" : { },
"text/plain;format=list" : { },
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" : { },
"text/plain;format=fasta" : { }
}
}
}
}
},
"/uniref/search" : {
"get" : {
"tags" : [ "UniRef" ],
"summary" : "Retrieve light UniRef cluster entries by a search query.",
"description" : "The search endpoint uses a request query to return all entries associated with the search term in a paginated list of entries. Use ‘size’ to specify the number of entries per page of results. Specify fields to return only data for specific sections of that entry that are of interest to you",
"operationId" : "search_1",
"parameters" : [ {
"name" : "query",
"in" : "query",
"description" : "Criteria to search UniRef. Advanced queries can be built with parentheses and conditionals such as AND, OR and NOT. List of valid search fields",
"required" : true,
"schema" : {
"type" : "string"
},
"example" : "Transcription factors"
}, {
"name" : "sort",
"in" : "query",
"description" : "Specify field by which to sort results. List of valid sort fields",
"required" : false,
"schema" : {
"type" : "string"
}
}, {
"name" : "fields",
"in" : "query",
"description" : "List of entry sections (fields) to be returned, separated by commas. List of valid fields",
"required" : false,
"schema" : {
"type" : "string"
},
"example" : "id,name,types,organism,identity"
}, {
"name" : "complete",
"in" : "query",
"description" : "Flag to include all member ids and organisms, or not. By default, it returns a maximum of 10 member ids and organisms",
"required" : false,
"schema" : {
"pattern" : "true|false",
"type" : "boolean"
}
}, {
"name" : "size",
"in" : "query",
"description" : "Specify the number of entries per page of results (Pagination size). Default is 25, max is 500",
"required" : false,
"schema" : {
"maximum" : 500,
"minimum" : 0,
"type" : "integer",
"format" : "int32"
},
"example" : 50
} ],
"responses" : {
"default" : {
"description" : "UniRefEntry",
"content" : {
"application/json" : {
"schema" : {
"$ref" : "#/components/schemas/SearchResult"
}
},
"application/xml" : {
"schema" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Entry"
}
}
},
"text/plain;format=tsv" : { },
"text/plain;format=list" : { },
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" : { },
"text/plain;format=fasta" : { }
}
}
}
}
}
},
"components" : {
"schemas" : {
"CrossReferenceEvidenceDatabase" : {
"type" : "object",
"properties" : {
"database" : {
"$ref" : "#/components/schemas/EvidenceDatabase"
},
"properties" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Property"
}
},
"id" : {
"type" : "string"
}
}
},
"Evidence" : {
"type" : "object",
"properties" : {
"evidenceCode" : {
"type" : "string"
},
"id" : {
"type" : "string"
},
"source" : {
"type" : "string"
}
}
},
"EvidenceDatabase" : {
"type" : "object",
"properties" : {
"name" : {
"type" : "string"
},
"reference" : {
"type" : "boolean"
},
"evidenceDatabaseDetail" : {
"$ref" : "#/components/schemas/EvidenceDatabaseDetail"
}
}
},
"EvidenceDatabaseDetail" : {
"type" : "object",
"properties" : {
"name" : {
"type" : "string"
},
"displayName" : {
"type" : "string"
},
"category" : {
"type" : "string",
"enum" : [ "I", "C", "A" ]
},
"uriLink" : {
"type" : "string"
}
}
},
"GeneOntologyEntry" : {
"type" : "object",
"properties" : {
"aspect" : {
"type" : "string",
"enum" : [ "GO Molecular Function", "GO Biological Process", "GO Cellular Component" ]
},
"ancestors" : {
"uniqueItems" : true,
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/GeneOntologyEntry"
}
},
"name" : {
"type" : "string"
},
"id" : {
"type" : "string"
}
}
},
"Organism" : {
"type" : "object",
"properties" : {
"taxonId" : {
"type" : "integer",
"format" : "int64"
},
"lineages" : {
"type" : "array",
"items" : {
"type" : "string"
}
},
"commonName" : {
"type" : "string"
},
"scientificName" : {
"type" : "string"
},
"synonyms" : {
"type" : "array",
"items" : {
"type" : "string"
}
},
"evidences" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Evidence"
}
}
}
},
"OverlapRegion" : {
"type" : "object",
"properties" : {
"end" : {
"type" : "integer",
"format" : "int32"
},
"start" : {
"type" : "integer",
"format" : "int32"
}
}
},
"Property" : {
"type" : "object",
"properties" : {
"key" : {
"type" : "string"
},
"value" : {
"type" : "string"
}
}
},
"RepresentativeMember" : {
"type" : "object",
"properties" : {
"sequence" : {
"$ref" : "#/components/schemas/Sequence"
},
"memberId" : {
"type" : "string"
},
"uniProtAccessions" : {
"type" : "array",
"items" : {
"type" : "string"
}
},
"memberIdType" : {
"type" : "string",
"enum" : [ "UniProtKB Reviewed (Swiss-Prot)", "UniProtKB Unreviewed (TrEMBL)", "UniProtKB ID", "UniParc" ]
},
"seed" : {
"type" : "boolean"
},
"overlapRegion" : {
"$ref" : "#/components/schemas/OverlapRegion"
},
"organismName" : {
"type" : "string"
},
"organismTaxId" : {
"type" : "integer",
"format" : "int64"
},
"sequenceLength" : {
"type" : "integer",
"format" : "int32"
},
"proteinName" : {
"type" : "string"
},
"uniRef50Id" : {
"type" : "string"
},
"uniRef90Id" : {
"type" : "string"
},
"uniRef100Id" : {
"type" : "string"
},
"uniParcId" : {
"type" : "string"
}
}
},
"Sequence" : {
"type" : "object",
"properties" : {
"value" : {
"type" : "string"
},
"length" : {
"type" : "integer",
"format" : "int32",
"xml" : {
"attribute" : true
}
},
"checksum" : {
"type" : "string",
"xml" : {
"attribute" : true
}
}
}
},
"UniRefEntry" : {
"type" : "object",
"properties" : {
"entryType" : {
"type" : "string",
"enum" : [ "UniRef100", "UniRef90", "UniRef50" ]
},
"updated" : {
"type" : "string",
"format" : "date"
},
"memberCount" : {
"type" : "integer",
"format" : "int32"
},
"commonTaxon" : {
"$ref" : "#/components/schemas/Organism"
},
"representativeMember" : {
"$ref" : "#/components/schemas/RepresentativeMember"
},
"goTerms" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/GeneOntologyEntry"
}
},
"seedId" : {
"type" : "string"
},
"name" : {
"type" : "string"
},
"id" : {
"type" : "string"
},
"members" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/UniRefMember"
}
}
}
},
"UniRefMember" : {
"type" : "object",
"properties" : {
"memberId" : {
"type" : "string"
},
"uniProtAccessions" : {
"type" : "array",
"items" : {
"type" : "string"
}
},
"memberIdType" : {
"type" : "string",
"enum" : [ "UniProtKB Reviewed (Swiss-Prot)", "UniProtKB Unreviewed (TrEMBL)", "UniProtKB ID", "UniParc" ]
},
"seed" : {
"type" : "boolean"
},
"overlapRegion" : {
"$ref" : "#/components/schemas/OverlapRegion"
},
"organismName" : {
"type" : "string"
},
"organismTaxId" : {
"type" : "integer",
"format" : "int64"
},
"sequenceLength" : {
"type" : "integer",
"format" : "int32"
},
"proteinName" : {
"type" : "string"
},
"uniRef50Id" : {
"type" : "string"
},
"uniRef90Id" : {
"type" : "string"
},
"uniRef100Id" : {
"type" : "string"
},
"uniParcId" : {
"type" : "string"
}
}
},
"DbReferenceType" : {
"type" : "object",
"properties" : {
"property" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/PropertyType"
}
},
"type" : {
"type" : "string",
"xml" : {
"attribute" : true
}
},
"id" : {
"type" : "string",
"xml" : {
"attribute" : true
}
}
}
},
"Entry" : {
"required" : [ "name", "representativeMember" ],
"type" : "object",
"properties" : {
"name" : {
"type" : "string"
},
"property" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/PropertyType"
}
},
"representativeMember" : {
"$ref" : "#/components/schemas/MemberType"
},
"member" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/MemberType"
}
},
"id" : {
"type" : "string",
"xml" : {
"attribute" : true
}
},
"updated" : {
"type" : "string",
"format" : "date-time",
"xml" : {
"attribute" : true
}
}
},
"xml" : {
"name" : "entry",
"namespace" : "http://uniprot.org/uniref"
}
},
"MemberType" : {
"required" : [ "dbReference" ],
"type" : "object",
"properties" : {
"dbReference" : {
"$ref" : "#/components/schemas/DbReferenceType"
},
"sequence" : {
"$ref" : "#/components/schemas/Sequence"
}
}
},
"PropertyType" : {
"type" : "object",
"properties" : {
"type" : {
"type" : "string",
"xml" : {
"attribute" : true
}
},
"value" : {
"type" : "string",
"xml" : {
"attribute" : true
}
}
}
},
"StreamResult" : {
"type" : "object",
"properties" : {
"results" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/UniRefEntry"
}
},
"error" : {
"type" : "string"
}
}
},
"Facet" : {
"type" : "object",
"properties" : {
"label" : {
"type" : "string"
},
"name" : {
"type" : "string"
},
"allowMultipleSelection" : {
"type" : "boolean"
},
"values" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/FacetItem"
}
}
}
},
"FacetItem" : {
"type" : "object",
"properties" : {
"label" : {
"type" : "string"
},
"value" : {
"type" : "string"
},
"count" : {
"type" : "integer",
"format" : "int64"
}
}
},
"ProblemPair" : {
"type" : "object",
"properties" : {
"code" : {
"type" : "integer",
"format" : "int32"
},
"message" : {
"type" : "string"
}
}
},
"SearchResult" : {
"type" : "object",
"properties" : {
"results" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/UniRefEntry"
}
},
"facets" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Facet"
}
},
"matchedFields" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/TermInfo"
}
},
"suggestions" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/Suggestion"
}
},
"warnings" : {
"type" : "array",
"items" : {
"$ref" : "#/components/schemas/ProblemPair"
}
}
}
},
"Suggestion" : {
"type" : "object",
"properties" : {
"query" : {
"type" : "string"
},
"hits" : {
"type" : "integer",
"format" : "int64"
}
}
},
"TermInfo" : {
"type" : "object",
"properties" : {
"name" : {
"type" : "string"
},
"hits" : {
"type" : "integer",
"format" : "int64"
}
}
}
}
}
}