bio-interaction-databases
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 for signed signaling, and per-resource rate limits.
npx skills add BioTender-max/awesome-bio-agent-skills --skill interaction-databases --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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?** - Python: `requests.get()` against REST endpoints; `pandas` for parsing; `ne
- Version Compatibility
- Required Setup
- Decision matrix: which resource for which question?
- STRING (v12, channels, confidence)
- BioGRID (physical + genetic, curated + HT)
- IntAct (PSI-MI curated physical)
- SIGNOR (signed signaling)
- Reactome (curated pathways)
- HuRI / HuMAP (human-specific interactomes)
- OmniPath (meta-database)
- License gotchas (critical for commercial use)
- Code patterns
- STRING network with confidence threshold and channel inspection
- BioGRID physical interactions, low-throughput only
What does the bio-interaction-databases skill do?
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 for signed signaling, and per-resource rate limits.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill interaction-databases --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.