rcsb_find_organisms
Resolve common names or clades like 'human' or 'bacteria' to NCBI taxonomy IDs, enabling precise taxonomy-based PDB structure searches instead of keyword guessing.
Instructions
Resolve a free-text organism, common name, or clade (e.g. human, mouse, baker's yeast, Escherichia coli, mammals, bacteria, primates) to NCBI Taxonomy ids, for precise taxonomy-based PDB searches instead of keyword guessing.
Use when a request restricts structures by SOURCE ORGANISM or any higher taxon — a common name you want as a canonical taxon ("human", "fruit fly"), or a CLADE, which a plain name search cannot expand. Resolve the phrase to a taxon id here, then search by it — see the resolver guidance in the server instructions for the attribute path, lineage semantics and the id-typing gotcha.
Args: query: Free-text organism / clade / common name, e.g. "human", "mammals", "E. coli". limit: Max taxa to return. with_pdb_counts: If true (default), annotate each taxon with pdb_entry_count (PDB entries from it or any organism beneath it, via taxonomy_lineage.id) — this also disambiguates a species from its strains.
Returns: {query, count, taxa:[{tax_id, scientific_name, common_name, rank, pdb_entry_count?}]}.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | ||
| query | Yes | ||
| with_pdb_counts | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||