bio-interaction-databases SKILL.md skillA
bio-interaction-databases from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-interaction-databases@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-interaction-databases/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- 662
- License
- MIT
Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use when building PPI networks, choosing between physical vs functional vs genetic interactions, signed/directed vs undirected, high-throughput vs curated, picking confidence thresholds, aggregating across resources, or navigating license constraints. Encodes the database decision matrix, STRING v12 channel semantics, OmniPath as meta-database, SIGNOR…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: requests 2.31+, pandas 2.2+, networkx 3.2+; STRING v12.0, BioGRID 4.4+, IntAct (live), SIGNOR 3.0+, OmniPath (live) Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show requests pandas networkx` - API surface: confirm endpoint URLs match each resource's current docs STRING URL is version-pinned (`version-12-0` as of 2024); older URLs (`version-11-5`) were deprecated 2023. The Cytoscape/Cytoscape.js ecosystem uses different version semantics; check the docs for the targeted version. # Interaction Databases **"Get protein-protein interactions for these genes"** -> The choice of database matters more than the choice of API. Different resources index different evidence (physical binding, functional association, genetic interaction, signed signaling), with different curation pipelines (manually curated vs high-throughput vs text-mined), different species coverage, and different licenses. The decision matrix below is the postdoc-grade view: **what question is being asked, and which resource answers it best?** …
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How to install
mdr add pku-yuangroup/openai4s/bio-interaction-databases@sha256:7a34528f9745c311The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_v6z5rpb6rvbi44vg)
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_v6z5rpb6rvbi44vg GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-interaction-databases GET https://markdownregistry.com/api/v1/blob/7a34528f9745c3113831193ef0d899953dcb2dde56e02de0c313ad6ef76589fb
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