Ebi proteins entry summary

Skill ma-compbio-lab/SkillFoundry/skills/proteomics/ebi-proteins-entry-summary

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill ebi-proteins-entry-summary

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What its author says it does

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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.

SKILL.md

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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

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

Related skills

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