protein-mcp-server: get annotations
protein_get_annotationsSequence and functional annotation for a protein: UniProt positional features (domains, binding and active sites, PTMs including cross-links and lipidation, topology, DNA binding, processing products such as chains and signal peptides, mutagenesis), natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a canonical UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to select a specific one. An accession UniProt merged into another entry answers for that successor with a notice; a demerged or deleted one fails with its replacement accessions. Use "include" to scope which annotation classes are fetched. Every response carries an "attribution" block with the upstream data licenses and citations.
Tool call template
This tool declares no required parameters. Add optional parameters from the input schema as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {},
"name": "protein_get_annotations"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chain | No | Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry distinct "A" and "a" chains). Only applies with pdb_id; ignored when uniprot is supplied directly. See polymerEntities[].authAsymIds in the pdb://{entry_id} resource for an entry's author chain IDs. | |
| limit | No | Per-class page size (1–200, default 50). Continue each class independently with features_offset, variants_offset, or domains_offset; the notice gives the next offset. | |
| pdb_id | No | PDB entry ID; resolved to a UniProt accession via cross-reference. | |
| include | No | Which annotation classes to fetch: features, domains (InterPro), variants, or all. | all |
| uniprot | No | Canonical UniProt accession (e.g. P69905). Isoform accessions (e.g. P04637-2) are rejected; UniProt annotates the canonical entry. Takes precedence over pdb_id. | |
| domains_offset | No | Zero-based offset into InterPro memberships; independent of features and variants. | |
| features_offset | No | Zero-based offset into functional features; independent of variants and domains. | |
| variants_offset | No | Zero-based offset into natural variants; independent of features and domains. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| error | No | Present when the call failed. Absent on success. | |
| notice | No | The merge when UniProt merged the requested accession into another entry, first; then per class: the next offset, advice to lower an exhausted offset, an empty class, or an InterPro walk that stopped short of its count. | |
| domains | No | InterPro domain/family memberships. | |
| features | No | Positional features other than natural variants, in UniProt order (grouped by type). Secondary structure, isoform sequences, and sequence-record notes are not included. | |
| function | No | UniProt function summary. | |
| organism | No | Source organism scientific name. | |
| variants | No | Natural sequence variants. | |
| accession | No | UniProt accession the annotations describe — the successor when UniProt merged the requested accession, which the notice names. | |
| ambiguity | No | Alternative UniProt mappings when a PDB ID resolved ambiguously (no chain given). | |
| geneNames | No | Gene names. | |
| truncated | No | True when at least one requested class has records past its returned page (the notice gives the next offset), or InterPro paging stopped before retrieving every membership. | |
| attribution | No | Upstream data-source licenses and citations for every source that contributed to this response. Always present — the attribution obligation travels with the data. | |
| proteinName | No | Recommended protein name. | |
| domainsTotal | No | InterPro's membership count for the protein; present only when requested. When InterPro paging stopped short of it, the notice names how many memberships domains_offset can reach. | |
| resolvedFrom | No | PDB ID the accession was resolved from, when applicable. | |
| featuresTotal | No | Total positional features in the entry; present only when requested. | |
| variantsTotal | No | Total natural variants in the entry; present only when requested. | |
| sequenceLength | No | Sequence length in residues. |