| name | cellosaurus-api |
| description | Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info. |
| license | MIT |
| author | AIPOCH |
Source: https://github.com/aipoch/medical-research-skills
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: "Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.".
- Packaged executable path(s):
scripts/client.py plus 1 additional script(s).
- Structured execution path designed to keep outputs consistent and reviewable.
Dependencies
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.
cd "20260316/scientific-skills/Evidence Insight/cellosaurus-api"
python -m py_compile scripts/client.py
python scripts/client.py --help
Example run plan:
- Confirm the user input, output path, and any required config values.
- Edit the in-file
CONFIG block or documented parameters if the script uses fixed settings.
- Run
python scripts/client.py with the validated inputs.
- 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/client.py with additional helper scripts under scripts/.
- 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.
Validation Shortcut
Run this minimal command first to verify the supported execution path:
python scripts/validate_skill.py --help
Cellosaurus API Skill
This skill allows querying the Cellosaurus database for cell line information.
Capabilities
- Get Release Info: Retrieve current database version and stats.
- Get Cell Line: Fetch details for a specific cell line by Accession Number (AC).
- Search: Query cell lines using Solr syntax.
Usage
1. Get Release Information
python .trae/skills/cellosaurus-api/scripts/client.py info
2. Get Cell Line Details
Get details for HeLa (CVCL_0030):
python .trae/skills/cellosaurus-api/scripts/client.py get CVCL_0030
With specific fields:
python .trae/skills/cellosaurus-api/scripts/client.py get CVCL_0030 --fields id,ac,sy
3. Search Cell Lines
Search for 'HeLa':
python .trae/skills/cellosaurus-api/scripts/client.py search "id:HeLa"
Search with limit:
python .trae/skills/cellosaurus-api/scripts/client.py search "id:HeLa" --rows 5
References
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.
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.
Recommended Workflow
- Validate the request against the skill boundary and confirm all required inputs are present.
- Select the documented execution path and prefer the simplest supported command or procedure.
- Produce the expected output using the documented file format, schema, or narrative structure.
- 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
cellosaurus_api_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:
python scripts/client.py --help
Expected output format:
Result file: cellosaurus_api_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any
Deterministic Output Rules
- Use the same section order for every supported request of this skill.
- Keep output field names stable and do not rename documented keys across examples.
- If a value is unavailable, emit an explicit placeholder instead of omitting the field.
Completion Checklist
- Confirm all required inputs were present and valid.
- Confirm the supported execution path completed without unresolved errors.
- Confirm the final deliverable matches the documented format exactly.
- Confirm assumptions, limitations, and warnings are surfaced explicitly.
