| name | ebi-proteins-entry-summary |
| description | Use this skill to fetch a compact accession summary from the EBI Proteins API. Do not use it for bulk downloads, unsupported endpoints, or full protein annotation export. |
Purpose
Resolve a protein accession through the EBI Proteins API and return a compact protein summary with names, organism, sequence size, keywords, and a small subset of comments and features.
When to use
- You already know a protein accession such as
P38398.
- You want a quick official protein summary before deeper proteomics or protein-biology work.
When not to use
- You need bulk UniProt-scale exports.
- You need peptide evidence tables or full annotation payloads.
- You need offline execution.
Inputs
- Protein accession
- Optional output path
Outputs
- JSON payload containing a compact protein-entry summary
Requirements
- Python 3.10+
- Network access to
www.ebi.ac.uk
Procedure
- Run
python3 skills/proteomics/ebi-proteins-entry-summary/scripts/fetch_protein_summary.py --accession P38398 --out skills/proteomics/ebi-proteins-entry-summary/assets/brca1_protein_summary.json.
- Inspect
recommended_name, gene_names, organism_scientific_name, sequence_length, keywords, comments, and features.
- Use the compact summary as a lookup layer before downstream structural or proteomics workflows.
Validation
- Command exits successfully.
- Output contains the requested accession and a non-empty recommended protein name.
- Known human accessions report the correct organism and a positive sequence length.
Failure modes and fixes
- HTTP 404: confirm the accession exists and is public.
- Empty optional fields: some accessions have sparse comments or features; use the stable core fields first.
- Need bulk access: build a separate batch-oriented skill instead of overloading this single-entry helper.
Safety and limits
- Metadata lookup only.
- This skill does not perform protein design, therapeutic recommendation, or wet-lab planning.
Example
python3 skills/proteomics/ebi-proteins-entry-summary/scripts/fetch_protein_summary.py --accession P38398
Provenance
Related skills
pride-project-searchrcsb-pdb-entry-summary
