Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-database-access-interaction-databasesgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-database-access-interaction-databases)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-database-access-interaction-databases"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-database-access-interaction-databases/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-database-access-interaction-databases"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-database-access-interaction-databases.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00120 | $0.05525 |
| Opus 5 | $0.00060 | $0.02763 |
| Sonnet 5 | $0.00024 | $0.01105 |
| Haiku 4.5 | $0.00012 | $0.00553 |
Grade A, and why
bio-interaction-databases scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
- Python: `requests.get()` against REST endpoints; `pandas` for parsing; `networkx` for graphs This is a copy
94% identical to bio-interaction-databases — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 445 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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;pandasfor parsing;networkxfor graphs - R:
STRINGdb,OmnipathR(mature Bioconductor clients) - Web: STRING, BioGRID, IntAct, SIGNOR, OmniPath, ConsensusPathDB browsers
Required Setup
import requests
import pandas as pd
import networkx as nx
from io import StringIO
CALLER = 'bioskills-2026' # STRING + OmniPath accept caller_identity for usage attribution
API key requirements:
- BioGRID: free key required (
https://webservice.thebiogrid.org/) - STRING, IntAct, SIGNOR, OmniPath, Reactome: no key
Decision matrix: which resource for which question?
| Question | Best resource | Why |
|---|---|---|
| "Build a network around 10 genes" | STRING (medium confidence ~400) | Comprehensive; channels combinable; good viz integration |
| "Only physically interacting proteins" | IntAct or BioGRID physical | Curated physical interactions; PSI-MI standard |
| "Signed/directed signaling (phospho, ubiq, etc.)" | SIGNOR | Only major DB with mechanism types and direction |
| "Functional enrichment based on co-mentioned genes" | STRING functional (default) | Includes textmining channel |
| "Genetic interactions (synthetic lethality)" | BioGRID genetic | Largest curated genetic interaction set |
| "High-throughput Y2H interactome" | HuRI | Reference yeast-2-hybrid map of human |
| "Mass-spec-derived protein complexes" | HuMAP v2 or BioPlex | AP-MS complex maps |
| "Curated pathways with interactions" | Reactome | Pathway-organized; gold standard for signaling |
| "Meta-database aggregating 100+ sources" | OmniPath | The modern "one-stop"; pre-aggregated |
| "Cross-species or non-human" | STRING | Species coverage broadest |
| "Bacterial interactome" | STRING bacterial | Limited curated alternatives |
| "Phosphorylation site-specific" | PhosphoSitePlus (commercial license) or SIGNOR | PSP has best PTM coverage but requires license |
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 445 lines · 120 tokens per session scan A 7a34528f9745
bio-interaction-databases is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 120 tokens to every session and 5,525 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 94% identical to bio-interaction-databases, differing in 12 lines, and is treated as a copy.
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