uniprot-mcp-server

uniprot-mcp-server: get proteome

uniprot_get_proteome

Read-onlyIdempotent

Fetch the reference proteome for an organism by UPID (e.g. "UP000005640") or NCBI taxon ID (e.g. 9606) — provide exactly one. Returns metadata inline: proteome type, total protein count, BUSCO completeness (score, complete/fragmented/missing counts, lineage dataset), and the genome assembly accession. The protein set is opt-in via include_proteins (it is large — human is ~147,506) and returns a capped page with a forward cursor; narrow it with the query filter (UniProtKB Lucene syntax) for a subset. Resolve an organism name to a taxon ID first with uniprot_get_taxonomy.

Input Schema

TableJSON Schema

Name	Required	Description
`size`	No	Proteins per page when include_proteins is true (max 500). Omit for the server default.
`upid`	No	Proteome UPID. Provide this OR taxon_id, not both.
`query`	No	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`	No	Opaque cursor from this tool for the same resolved UPID and exact query. Identifier aliases resolving to that UPID and size changes are allowed. Older raw cursors are rejected; restart without cursor. Only meaningful with include_proteins.
`taxon_id`	No	NCBI taxon ID, e.g. 9606 for human. Resolves to the reference proteome. Provide this OR upid, not both.
`include_proteins`	No	When true, also return a capped, cursor-paginated page of the proteome's proteins. Defaults to false — metadata alone is the common case.

Output Schema

TableJSON Schema

Name	Required	Description
`cap`	No	The page-size cap that was applied.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	Number of proteins returned in this page.
`cursor`	No	Forward cursor for the next protein page. Absent on the last page.
`notice`	No	Truncation guidance when the protein page was capped — how to reach the rest (walk the cursor or narrow with the query filter).
`proteins`	No	A capped page of the proteome's proteins. Present only when include_proteins is true.
`proteome`	No	Proteome metadata.
`truncated`	No	True when the protein page hit the size cap — more remain via cursor.
`totalProteinsMatched`	No	Total proteins matching the (optionally filtered) proteome query.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 22, 2026

changedInput schema / properties / cursor / description

Previous value: -"Forward-pagination cursor from a prior protein page. Only meaningful with include_proteins."New value: +"Opaque cursor from this tool for the same resolved UPID and exact query. Identifier aliases resolving to that UPID and size changes are allowed. Older raw cursors are rejected; restart without cursor. Only meaningful with include_proteins."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"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. `invalid_query`: The query filter has unbalanced parentheses (rejected before any request), or UniProtKB rejected it — the message names the rejected field or syntax. `invalid_cursor`: UniProt could not continue from the protein cursor (it answered HTTP 500) — the cursor is malformed or truncated. Other values are possible when a failure originates below the handler."New value: +"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. `invalid_query`: The query filter has unbalanced parentheses (rejected before any request), or UniProtKB rejected it — the message names the rejected field or syntax. `invalid_cursor`: The protein cursor is malformed, from an older version, belongs to another tool, resolved UPID or query, or UniProt could not continue from it (HTTP 500). Other values are possible when a failure originates below the handler."

Changed2 schema fields changedOct 14, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"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."New value: +"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. `invalid_query`: The query filter has unbalanced parentheses (rejected before any request), or UniProtKB rejected it — the message names the rejected field or syntax. `invalid_cursor`: UniProt could not continue from the protein cursor (it answered HTTP 500) — the cursor is malformed or truncated. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "missing_identifier",
-  "conflicting_identifier",
-  "not_found"
-]New value: +[
+  "missing_identifier",
+  "conflicting_identifier",
+  "not_found",
+  "invalid_query",
+  "invalid_cursor"
+]

First observedAug 22, 2026

TDQS

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