| name | encori-api |
| description | Access ENCORI (StarBase) database for miRNA-target, RNA-RNA, and other regulatory data. Invoke when user asks to search ENCORI or retrieve regulatory interactions. |
| 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 ENCORI (StarBase) database for miRNA-target, RNA-RNA, and other regulatory data. Invoke when user asks to search ENCORI or retrieve regulatory interactions.".
- Packaged executable path(s):
scripts/encori_client.py plus 1 additional script(s).
- Structured execution path designed to keep outputs consistent and reviewable.
Dependencies
- Python 3
requests library
Example Usage
See ## Usage above for related details.
cd "20260316/scientific-skills/Evidence Insight/encori-api"
python -m py_compile scripts/encori_client.py
python scripts/encori_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/encori_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/encori_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
ENCORI API Skill
This skill allows you to query the ENCORI (The Encyclopedia of RNA Interactomes) database programmatically. It supports multiple endpoints for retrieving data on miRNA-target interactions, RNA-RNA networks, RBP-target interactions, and more.
Capabilities
The skill provides access to the following data modules via the encori_client.py script:
- miRNATarget: miRNA-target interactions supported by Ago CLIP-seq.
- degradomeRNA: miRNA cleavage events supported by degradome-seq.
- RNARNA: ncRNA-RNA interaction networks.
- ceRNA: ceRNA networks.
- RBPTarget: RBP-RNA interactions supported by CLIP-seq.
- RBPDisease: RBP-gene interactions and somatic mutations in diseases.
- RBPMotifScan: Binding motifs of RBPs.
- bindingSite: Binding sites of CLIP-seq.
Usage
Run the python script .trae/skills/encori-api/scripts/encori_client.py with the appropriate subcommand and arguments.
Common Arguments
Most endpoints support:
--assembly: Genome version (default: hg38)--geneType: Main gene type (default: mRNA)--cellType: Cell type (default: all)
Examples
1. miRNA-Target
Get all miRNA data for PDCD4 in HeLa cells:
python .trae/skills/encori-api/scripts/encori_client.py miRNATarget --target PDCD4 --cellType HeLa
2. Degradome-RNA
Get all miRNA cleavage data for TP53:
python .trae/skills/encori-api/scripts/encori_client.py degradomeRNA --target TP53
3. RNA-RNA
Get interaction networks of TP53-mRNA:
python .trae/skills/encori-api/scripts/encori_client.py RNARNA --RNA TP53
4. CeRNA
Get ceRNAs for a specific miRNA family:
python .trae/skills/encori-api/scripts/encori_client.py ceRNA --family "miR-10-5p"
5. RBP-Target
Get data of all RBPs that bind to TP53 in HeLa cells:
python .trae/skills/encori-api/scripts/encori_client.py RBPTarget --target TP53 --cellType HeLa
6. RBP-Disease
Get RBP-MYC interactions in breast carcinoma:
python .trae/skills/encori-api/scripts/encori_client.py RBPDisease --tissue breast --disease carcinoma --target MYC
7. RBP Motif Scan
Retrieve binding motifs containing 'UGCAUG':
python .trae/skills/encori-api/scripts/encori_client.py RBPMotifScan --motif UGCAUG
8. Binding Sites
Retrieve binding sites for a specific dataset ID:
python .trae/skills/encori-api/scripts/encori_client.py bindingSite --datasetID SBDH2131
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
encori_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/encori_client.py --help
Expected output format:
Result file: encori_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.
