Encori API

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:

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/encori_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/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:

1. miRNATarget: miRNA-target interactions supported by Ago CLIP-seq.
2. degradomeRNA: miRNA cleavage events supported by degradome-seq.
3. RNARNA: ncRNA-RNA interaction networks.
4. ceRNA: ceRNA networks.
5. RBPTarget: RBP-RNA interactions supported by CLIP-seq.
6. RBPDisease: RBP-gene interactions and somatic mutations in diseases.
7. RBPMotifScan: Binding motifs of RBPs.
8. 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.