Biostudies Arrayexpress Skill for Codex

Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval. Use when a user wants concise BioStudies summaries

3k tokens

context cost

the whole folder, loaded on every use

files

ships runnable scripts

copies elsewhere

how many repositories repackaged it

4915

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/openai/plugins --skill biostudies-arrayexpress-skill

What comes with it

10 856 bytes besides the instruction

agents/openai.yaml

scripts/rest_request.py

The instruction itself

6 sections, as written by the author

Operating rules

Use scripts/rest_request.py for all BioStudies and ArrayExpress calls.
Use base_url=https://www.ebi.ac.uk/biostudies/api/v1.
Search pages are better with pageSize=10 and max_items=10; accession lookups usually do not need max_items.
Re-run requests in long conversations instead of relying on older tool output.
Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

Return concise markdown summaries from the script JSON by default.
Prefer these paths: search, ArrayExpress/search, studies/<accession>, and studies/<accession>/info.
If the user needs the full payload, set save_raw=true and report the saved file path instead of pasting large study records into chat.

Input

Read one JSON object from stdin.
Required fields: base_url, path
Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
Common BioStudies patterns:
{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"search","params":{"query":"rna","page":1,"pageSize":10},"record_path":"hits","max_items":10}
{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"ArrayExpress/search","params":{"query":"single cell","page":1,"pageSize":10},"record_path":"hits","max_items":10}
{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"studies/E-MTAB-6701"}

Output

Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
Use raw_output_path when save_raw=true.
Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://www.ebi.ac.uk/biostudies/api/v1","path":"search","params":{"query":"rna","page":1,"pageSize":10},"record_path":"hits","max_items":10}' | python scripts/rest_request.py

References

No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.

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How to use it

Copy the folder

Take openai/biostudies-arrayexpress-skill from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.