ebi-proteins-entry-summary

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

1. 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.
2. Inspect recommended_name, gene_names, organism_scientific_name, sequence_length, keywords, comments, and features.
3. 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

• EBI Proteins API docs: https://www.ebi.ac.uk/proteins/api/doc/

Related skills

• pride-project-search
• rcsb-pdb-entry-summary