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Agent skill

Biogrid Orcs

by aipoch in aipoch/medical-research-skills

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores).

MITAuto-check passedResearch & Science

Install Biogrid Orcs

skills CLI
$ npx skills add aipoch/medical-research-skills --skill biogrid-orcs -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills biogrid-orcs --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/biogrid-orcs' .claude/skills/biogrid-orcs && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
biogrid-orcs
GitHub stars
1.9k
Token cost
~1.7k tokens
SKILL.md length
728 words
Files
4 (incl. scripts, references)
Skills in repo
578
Repo updated
First seen
Licence
MIT

At a glance

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores).

  • Works in 4 steps: Confirm the user input, output path, and… → Edit the in-file CONFIG block or… → Run python scripts/biogrid_client.py… → …
  • Needs to search CRISPR screens
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 11 more sections
  • Runs Python scripts from its folder; calls python

What it does

Biogrid Orcs is an agent skill from aipoch/medical-research-skills. Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.

Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `biogrid-orcs_audit_result_v2.json`, `references/api_docs.md` and `scripts/biogrid_client.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Needs to search CRISPR screens
  • Retrieve gene scores

Example prompts

  • “Use the biogrid-orcs skill to access BioGRID ORCS CRISPR screen data (organisms, screens, scores)”
  • “/biogrid-orcs”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/biogrid_client.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Biogrid Orcs loads about 1.7k tokens when it runs, and up to ~2.1k if it reads all its reference files. Until then it costs about 43 tokens; SKILL.md has 728 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~43
When it runs · the whole SKILL.md, loaded when a task matches
~1.7k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~2.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 728 words, ~1,680 tokens.

Download SKILL.mdSave it as .claude/skills/biogrid-orcs/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
biogrid-orcs
description
Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

BioGRID ORCS Skill

This skill allows querying the BioGRID ORCS (Open Repository of CRISPR Screens) REST API.

When to Use

  • Use this skill when the request matches its documented task boundary.
  • Use it when the user can provide the required inputs and expects a structured deliverable.
  • Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

  • Scope-focused workflow aligned to: "Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.".
  • Packaged executable path(s): scripts/biogrid_client.py.
  • Reference material available in references/ for task-specific guidance.
  • Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

See ## Prerequisites above for related details.

  • Python: 3.10+. Repository baseline for current packaged skills.
  • Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

See ## Usage above for related details.

bash
cd "20260316/scientific-skills/Evidence Insight/biogrid-orcs"
python -m py_compile scripts/biogrid_client.py
python scripts/biogrid_client.py --help

Example run plan:

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/biogrid_client.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

  • Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
  • Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
  • Primary implementation surface: scripts/biogrid_client.py.
  • Reference guidance: references/ contains supporting rules, prompts, or checklists.
  • Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
  • Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Prerequisites

  • Access Key: You must provide a valid BioGRID Access Key (32-character string).

Usage

The skill provides a Python script scripts/biogrid_client.py that maps to the API endpoints.

Basic Command Structure
bash
python .trae/skills/biogrid-orcs/scripts/biogrid_client.py <COMMAND> --accesskey <KEY> [OPTIONS]
Commands

  1. List Organisms

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py organisms --accesskey <KEY>

  2. List Vocabulary Categories

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py vocabs --accesskey <KEY>

  3. Get Vocabulary Terms

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py vocab <CATEGORY_ID> --accesskey <KEY>

  4. Search Screens

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py screens --accesskey <KEY> --organismID 9606 --cellLine hela

  5. Get Screen Scores

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py screen <SCREEN_ID> --accesskey <KEY> --hit yes

  6. Get Gene Scores

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py gene <GENE_ID> --accesskey <KEY>

  7. Search Genes

    bash
    python .trae/skills/biogrid-orcs/scripts/biogrid_client.py genes --accesskey <KEY> --name "BRCA1|TP53"

References

See references/api_docs.md for full API documentation and parameter lists.

When Not to Use

  • Do not use this skill when the required source data, identifiers, files, or credentials are missing.
  • Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
  • Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.
Show full SKILL.md (276 more words)Show less

Required Inputs

  • A clearly specified task goal aligned with the documented scope.
  • All required files, identifiers, parameters, or environment variables before execution.
  • Any domain constraints, formatting requirements, and expected output destination if applicable.
  1. Validate the request against the skill boundary and confirm all required inputs are present.
  2. Select the documented execution path and prefer the simplest supported command or procedure.
  3. Produce the expected output using the documented file format, schema, or narrative structure.
  4. Run a final validation pass for completeness, consistency, and safety before returning the result.

Output Contract

  • Return a structured deliverable that is directly usable without reformatting.
  • If a file is produced, prefer a deterministic output name such as biogrid_orcs_result.md unless the skill documentation defines a better convention.
  • Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

  • Validate required inputs before execution and stop early when mandatory fields or files are missing.
  • Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
  • Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
  • Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

  • If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
  • If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
  • If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

bash
python scripts/biogrid_client.py --help

Expected output format:

text
Result file: biogrid_orcs_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts, references) in scientific-skills/Evidence Insight/biogrid-orcs of aipoch/medical-research-skills.

  • SKILL.md
  • biogrid-orcs_audit_result_v2.json
  • references/api_docs.md
  • scripts/biogrid_client.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Biogrid Orcs next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Biogrid Orcs compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Biogrid Orcs this skillaipoch/medical-research-skills1.9k—~1.7kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Biogrid Orcs

What does Biogrid Orcs do?

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Biogrid Orcs is an agent skill from aipoch/medical-research-skills. Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores).

When should I use Biogrid Orcs?

Biogrid Orcs fits situations like: needs to search CRISPR screens; retrieve gene scores.

How do I install Biogrid Orcs in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill biogrid-orcs -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/biogrid-orcs in aipoch/medical-research-skills) into .claude/skills/biogrid-orcs in your project. Claude Code loads it when a task matches its description.

How do I install Biogrid Orcs in Codex?

Run `npx skills add aipoch/medical-research-skills --skill biogrid-orcs -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/biogrid-orcs in aipoch/medical-research-skills) into .agents/skills/biogrid-orcs in your project. Codex loads it when a task matches its description.

Can I use Biogrid Orcs in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill biogrid-orcs -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/biogrid-orcs, .gemini/skills/biogrid-orcs, .github/skills/biogrid-orcs and .opencode/skills/biogrid-orcs in your project.

What does Biogrid Orcs need to run?

Going by SKILL.md and its folder, Biogrid Orcs needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Biogrid Orcs access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Biogrid Orcs safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Biogrid Orcs use?

Biogrid Orcs is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Biogrid Orcs use?

About 1.7k tokens (SKILL.md is roughly 6.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 390 tokens, read only when the agent opens those files.

What are the alternatives to Biogrid Orcs?

Skills that share tags, products or a category with Biogrid Orcs: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Biogrid Orcs?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.