uniprot-mcp-server: map IDs
uniprot_map_idsTranslate identifiers across databases via UniProt's ID-mapping service — gene names to accessions, accession to PDB / Ensembl / RefSeq / ChEMBL / GeneID, and back. The job runs asynchronously; this tool submits it and polls within a budget. A running job returns status "running" with a ticket; pass that ticket alone to poll the same job. A completed call returns status "finished" with one results page; when continuation is present, pass it alone to fetch the next completed page without re-submitting or polling the job. A gene name often maps to one reviewed Swiss-Prot accession plus dozens of unreviewed TrEMBL ones, so target UniProtKB-Swiss-Prot (reviewed only) for the usual intent, or UniProtKB to include TrEMBL. Pair a gene-symbol from_db with tax_id to disambiguate species. A row whose UniProtKB target is inactive (merged, demerged, or deleted) carries an inactive marker naming its replacements. Chain the resulting active accessions into uniprot_get_entry.
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": "uniprot_map_ids"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| ids | No | Identifiers to translate. Required only when submitting a new mapping job; omitted when resuming with a ticket or continuation. | |
| to_db | No | Target database. UniProtKB-Swiss-Prot = reviewed accessions only (the usual intent); UniProtKB also includes unreviewed TrEMBL. Required only when submitting a new mapping job; omitted when resuming with a ticket or continuation. | |
| tax_id | No | Exact NCBI taxon node for submission, e.g. 9606 for human. Unlike protein search taxonomy filters, this excludes descendant strains and subspecies. Resolve the strain taxon with uniprot_get_taxonomy when needed; no descendant filtering is applied to mapped results. | |
| ticket | No | 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 | No | Source database. Gene_Name = gene symbol (e.g. TP53; 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 | No | Completed-page continuation from a prior status "finished" response. Pass it alone to fetch the next page without polling or re-submitting. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| error | No | Present when the call failed. Absent on success. | |
| notice | No | Status guidance — e.g. that the job is still running, that no IDs mapped, that target identity is unavailable, or that inactive targets could not be marked on this page. | |
| status | No | Job state: "finished" (one completed results page included) or "running" (poll with ticket). | |
| ticket | No | Running-job ticket (present only when status is "running"). Pass it alone to poll the same job. | |
| results | No | Resolved mappings on this completed page (present only when status is "finished"). Failed source IDs are reported in unmappedIds. | |
| mappedCount | No | Number of resolved mappings on this page (finished jobs only). | |
| unmappedIds | No | Job-wide source IDs UniProt reported as failed, repeated on every completed page. Absent when none failed. | |
| continuation | No | Next completed-page continuation (finished jobs only). Pass it alone to fetch the next page; absent on the terminal page. | |
| totalMappings | No | Job-wide total mappings reported by UniProt; absent when unavailable. |