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 fmschulz/omics-skills --skill public-db-lookupgit clone --depth 1 https://github.com/fmschulz/omics-skillsWrote 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/fmschulz/omics-skills/public-db-lookup)<a href="https://agentmods.dev/skills/fmschulz/omics-skills/public-db-lookup"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/public-db-lookup/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/fmschulz/omics-skills/public-db-lookup"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/public-db-lookup.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 | $0.00065 | $0.01367 |
| Opus 5 | $0.00032 | $0.00683 |
| Sonnet 5 | $0.00013 | $0.00273 |
| Haiku 4.5 | $0.00006 | $0.00137 |
Grade A, and why
public-db-lookup 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 4d 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.
How it starts
The opening of the file, as written. The whole thing — 91 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Public Database Lookup
One bounded GET against a public life-science REST API. The bundled script picks the base URL, adds a User-Agent, retries on 429 and 5xx, and prints a compact JSON envelope instead of the full payload.
Instructions
- Pick the service that owns the record:
uniprot,ncbi-entrez,ncbi-datasets,mgnify,interpro,alphafold,string, orena. - Read the card for that service in references/services.md for the path, parameters, and the right
--record-path. - Run the wrapper:
- In this repository:
skills/public-db-lookup/scripts/lookup - After installation:
~/.agents/skills/public-db-lookup/scripts/lookup
- In this repository:
- Keep
--max-itemssmall (default 5). Raise it only when the user needs more rows. - When the full payload matters, add
--save-raw PATHand work from the file; the envelope still carries the compacted view. - For the two NCBI services, export
NCBI_API_KEYandNCBI_EMAIL(andNCBI_TOOLif you have one). The script adds them as request parameters and redacts the key from its output. - Requests are paced across invocations, not just within one, so calling the CLI in a loop stays inside each service's documented rate. The timestamps live under
$XDG_STATE_HOME/omics-skills/public-db-lookup; override with--state-dir. Never pass a credential in--pathor--param: the script refuses it, because it would be echoed back in the emitted URL and land in shell history. - Route PubMed and PMC literature searches to
/polars-dovmed; this skill does not cover them.
Execution behavior
- Summarize the JSON envelope in Markdown by default.
- Return raw JSON only when the user asks for machine-readable output.
- When the payload is large, use
--save-rawand report the path instead of pasting the content. - Re-run the lookup rather than trust tool output from earlier in a long conversation.
Quick Reference
| Flag | Meaning |
|---|---|
--service NAME |
One of the eight services (required) |
--path PATH |
Endpoint path relative to the service base URL, or a full URL under that base (required) |
--param KEY=VALUE |
Query parameter; repeat as needed |
--record-path a.b.c |
Dotted path to the record list; inferred from common keys when omitted |
--max-items N |
Records, list items, and dict keys kept per level (default 5) |
--max-depth N |
Nesting depth kept before containers collapse (default 3) |
--format auto|json|text |
Parse as JSON, or keep the first 800 characters of text (default auto) |
--save-raw PATH |
Write the full response body to PATH |
--timeout SEC |
Request timeout (default 30) |
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.
- 4d ago Changed · +1 lines 46f158eacac0
- 11d ago First seen · 90 lines · 65 tokens per session scan A 320715bba321
public-db-lookup is a skill published in the GitHub repository fmschulz/omics-skills (7 stars, last pushed 5d ago), licensed MIT. It adds 65 tokens to every session and 1,367 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.
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