bio-annotation SKILL.md skillA
bio-annotation from fmschulz/omics-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fmschulz/omics-skills/bio-annotation@git:20261001.bf5afd6Pins git:20261001.bf5afd6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fmschulz/omics-skills
- Path
skills/bio-annotation/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- May 29, 2026
- Size
- 10,460 bytes
- Repository stars
- 11
- License
- MIT
Annotate proteins with functions, domains, and homology-based taxonomy. Use when assigning functional or taxonomic labels to proteins from genomes, contigs, or MAGs.
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
# Bio Annotation
Functional annotation and taxonomy inference from sequence homology.
## Instructions
1. Read `docs/README.md` and the relevant tool guides before running anything.
2. Normalize tool outputs and generate the complete comparison bundle with the schema-backed driver:
```bash
uv run --script skills/bio-annotation/scripts/build_annotation_artifacts.py \
raw_annotations.tsv --genomes genomes.tsv --markers marker_catalog.tsv \
--out results/bio-annotation
```
`raw_annotations.tsv` is one row per protein and family hit with columns `genome, protein_id, family_id, family_name, category, e_value, annotation, taxonomy, confidence`, merged by you from the tool outputs below. `genomes.tsv` has `genome, role (query|reference), domain, route`; `marker_catalog.tsv` has `category, family_id, family_name, expected`. `fixtures/` holds a runnable example. The driver refuses a non-empty destination, enforces globally unique protein identifiers, writes normalized Parquet tables, adds explicit absent-marker rows, and computes query-specific/missing/expanded/contracted families against the reference median. The artifact contract is in…
…Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-annotation@sha256:2a2df445ec445383The line at the top of this page pins the label git:20261001.bf5afd6, 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_77y2nryacqrzx6ai)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between May 29, 2026 and Oct 1, 2026, about one every 25 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261001.bf5afd6 latest | 2026-10-01 | bf5afd6 | 10,460 B | A | view · diff |
| git:20260905.3e49039 | 2026-09-05 | 3e49039 | 9,506 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 9,065 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 9,593 B | A | view · diff |
| git:20260711.5ae6f6f | 2026-07-11 | 5ae6f6f | 8,814 B | A | view · diff |
| git:20260529.7fc0335 | 2026-05-29 | 7fc0335 | 8,678 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (10460 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fmschulz/omics-skills · 11 stars · license MIT · pushed 2026-10-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_77y2nryacqrzx6ai GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-annotation GET https://markdownregistry.com/api/v1/blob/2a2df445ec445383bd18b9cf223600dd310530de3dcfc300a25c2c01d6e42722
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.