What is bio-uniprot-access?

A guide to querying UniProt, a public protein database, through its REST API. It covers protein sequences, annotations, Gene Ontology terms, cross-references, identifier conversion, and proteomes.

Use it to retrieve selected protein fields, map identifiers, download annotations or sequences, and query protein sets in bulk.

It helps avoid outdated API endpoints, oversized responses, and confusion between UniProt's different database collections.

bio-uniprot-access — Skill for Claude Code and Codex by GPTomics

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add GPTomics/bioSkills --skill uniprot-access

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/uniprot-access/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/uniprot-access)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/uniprot-access"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/uniprot-access/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/uniprot-access"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/uniprot-access.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 137 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 5,046 The whole file, excluding the scripts and references it only reads on demand.

Security scan B 2 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00137	$0.05046
Opus 5	$0.00068	$0.02523
Sonnet 5	$0.00027	$0.01009
Haiku 4.5	$0.00014	$0.00505

Measured 8d ago against content hash 55409daaa0dc, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade B, and why

bio-uniprot-access scanned grade B with 2 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (examples/isoforms_and_xrefs.py, examples/uniprot_query.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Sends data to an external URLmediumData exfiltration

A POST to an outside endpoint may be telemetry or may be exfiltration; either way the mod talks to somewhere, and you should know where.

submit = requests.post('https://rest.uniprot.org/idmapping/run',

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- Python: `requests.get('https://rest.uniprot.org/uniprotkb/...')` (REST API)

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-uniprot-access — 95% identical, 12 lines differ

database-access/uniprot-access/SKILL.md · 441 lines

How it starts

The opening of the file, as written. The whole thing — 441 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: requests 2.31+, pandas 2.2+; UniProt REST API as of 2024_06 release

Before using code patterns, verify installed versions match. If versions differ:

Python: pip show requests pandas
API surface: confirm endpoint URLs match https://www.uniprot.org/help/api

The REST API JSON schema is stable within a release; major schema changes are documented at https://www.uniprot.org/release-notes. The 2022 migration broke the legacy https://www.uniprot.org/uniprot/... endpoints.

UniProt Access

"Get protein information from UniProt" -> Two facts dominate every UniProt workflow in 2026: (1) the API endpoint migrated in 2022 from https://www.uniprot.org/uniprot/... to https://rest.uniprot.org/uniprotkb/... with a substantially different JSON schema; pre-2022 code does not work as-is. (2) ?fields= is essential — default JSON returns the full entry (~20-30 KB each); for bulk pulls, request only the fields actually needed.

The major databases under the UniProt umbrella have different scopes:

UniProtKB: the curated knowledgebase — Swiss-Prot (manually reviewed, ~570K entries as of 2024) + TrEMBL (auto-annotated, ~250M). Always specify reviewed:true for high-quality reference work.
UniRef: clustered sequences at 100%, 90%, 50% identity. UniRef50 is the standard for redundancy reduction.
UniParc: archival "every unique sequence ever seen" — for provenance and historical lookup.
Proteomes: organism-level groupings; reference proteomes (one per species) are the canonical subset.
Python: requests.get('https://rest.uniprot.org/uniprotkb/...') (REST API)
Python: Bio.ExPASy.get_sprot_raw() (BioPython; legacy SwissProt format)
CLI: curl https://rest.uniprot.org/uniprotkb/P04637.json

Required Setup

import requests
import pandas as pd
import time

No API key required. Rate limit is generous (~200 req/sec tolerated empirically); ID-mapping has its own job queue.

Read the full file on GitHub · 441 lines

Files

What ships with it

3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

8d ago First seen · 441 lines · 137 tokens per session scan B 55409daaa0dc

Subscribe to this mod's changes

bio-uniprot-access is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 137 tokens to every session and 5,046 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it B with 2 findings (sends data to an external url, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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bio-uniprot-access