What is biomedical-database?

A set of rules for designing and updating databases that store biomedical information such as genes, proteins, diseases, chemicals, pathways, and research papers.

Use it for biomedical schema design, importing source data, standardising terms, checking identifiers, mapping terms to ontologies, and linking claims to evidence.

It helps prevent made-up identifiers and lost source evidence while keeping uncertain or conflicting biomedical information visible.

How stanveer/Biomedical-Agent-DB-Karpathy configures Claude Code and C

Reuse

Borrowing it

Nothing to install: this file belongs to stanveer/Biomedical-Agent-DB-Karpathy. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/stanveer/Biomedical-Agent-DB-Karpathy/master/.agents/skills/biomedical-database/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/stanveer/Biomedical-Agent-DB-Karpathy

Made for: Claude Code, Codex.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/stanveer/biomedical-agent-db-karpathy/biomedical-database/github.svg)](https://agentmods.dev/skills/stanveer/biomedical-agent-db-karpathy/biomedical-database)

Your own site

<a href="https://agentmods.dev/skills/stanveer/biomedical-agent-db-karpathy/biomedical-database"><img src="https://agentmods.dev/badge/skills/stanveer/biomedical-agent-db-karpathy/biomedical-database/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/stanveer/biomedical-agent-db-karpathy/biomedical-database"><img src="https://agentmods.dev/badge/skills/stanveer/biomedical-agent-db-karpathy/biomedical-database.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 59 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 337 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00059	$0.00337
Opus 5	$0.00030	$0.00169
Sonnet 5	$0.00012	$0.00067
Haiku 4.5	$0.00006	$0.00034

Measured 9d ago against content hash 6fea2e73f2ee, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

biomedical-database scanned grade A with 0 findings 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 9d 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.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/biomedical-database/SKILL.md · 45 lines

What it actually says

Biomedical Database Skill

Purpose

This skill helps coding agents work safely on a biomedical knowledge database.

Core rules

Do not invent identifiers, ontology mappings, or unsupported relations.
Treat genes, proteins, variants, diseases, chemicals, pathways, and papers as distinct entity types.
Preserve source provenance for every nontrivial assertion.
Preserve disagreement across sources rather than overwriting it.
Keep observed text separate from normalized canonical values.
Preserve ambiguity when normalization is not justified.
Prefer minimal schema changes and explain them before making them.

Required reading before edits

docs/chat-context.md
docs/architecture.md
CLAUDE.md
schema/tables.sql
config/source_registry.yaml

Good implementation sequence

Read the current schema and context files.
Summarize the exact task in terms of entity types, namespaces, and provenance needs.
Identify whether the change belongs in ingestion, normalization, validation, or schema.
Prefer tests for ambiguity, conflicting evidence, and identifier handling.
Verify that canonical IDs, source releases, and ingest metadata are not dropped.

Completion checklist

Canonical identifiers preserved
Entity types not collapsed
Source provenance retained
Ambiguity surfaced instead of guessed away
No speculative schema additions

Changes

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.

9d ago First seen · 45 lines · 59 tokens per session scan A 6fea2e73f2ee

Subscribe to this mod's changes

biomedical-database is a skill published in the GitHub repository stanveer/Biomedical-Agent-DB-Karpathy (2 stars, last pushed 4mo ago), licensed MIT. It adds 59 tokens to every session and 337 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Databases Scientific

lamindb

Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.

K-Dense-AI/scientific-agent-skills · 56 tokens

tiledbvcf

Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.

K-Dense-AI/scientific-agent-skills · 46 tokens

defining-cohort-phenotypes

Authors computable phenotype and cohort definitions in the OHDSI ATLAS / CIRCE style over the OMOP CDM, combining standard concept sets with NLP-derived features that OpenMed extracts. Use when the user wants to define a patient cohort, write a computable phenotype, reuse PheKB or OHDSI Phenotype Library logic, build…

maziyarpanahi/openmed · 191 tokens

benchling-integration

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

synthetic-sciences/openscience · 44 tokens

chembl-database

Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.

google-deepmind/science-skills · 53 tokens

nvalchemi-data-storage

How to write, read, compose, and load atomic data using nvalchemi's composable Zarr-backed storage pipeline (Writer, Reader, Dataset, MultiDataset, DataLoader). Use when saving simulation outputs or trajectories to disk, converting structures (e.g. ASE / extxyz) into Zarr stores, assembling datasets for training or…

NVIDIA/nvalchemi-toolkit · 90 tokens

Biomedical-Agent-DB-Karpathy: Skill for Claude Code