ontology-term-resolution SKILL.md skillA
ontology-term-resolution from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/ontology-term-resolution@v1.4Pins v1.4 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/ontology-term-resolution/SKILL.md- Versions recorded
- 5
- Latest version
- v1.4, committed Oct 1, 2026
- First version recorded
- Jul 26, 2026
- Size
- 14,593 bytes
- Repository stars
- 56,497
- License
- MIT
Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA…
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
# Ontology Term Resolution ## When to use Any time an ontology identifier is about to be written down or trusted: annotating a metadata column, filling a submission template, auditing a table someone else produced, or checking whether an ID in an old file is still current. ## The rule **Never write an ontology ID from memory, and never accept one without checking it.** Ontology IDs are memorable in form and arbitrary in detail. A plausible-looking `UBERON:0002108` is a real term (small intestine) that is not the liver, and nothing downstream will catch the substitution — the ID is well-formed, the ontology is right, and the metadata is silently wrong. Reviewers cannot spot it either, which is why these errors persist into published datasets. OLS search and ZOOMA emit **candidates**. Validate each selected ID with OLS term detail, then check its definition against the sample and the target schema before accepting it. Bioregistry, Identifiers.org, ZOOMA, and Ontobee answer prefix, landing-page, and shorthand questions — they do not replace that OLS check. ## Which service | Question | Script | Authority | | --- | --- | --- | …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/ontology-term-resolution@sha256:db310515a230a470The line at the top of this page pins the label v1.4, 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_jfvx56qdlriagche)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Jul 26, 2026 and Oct 1, 2026, about one every 17 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.4 latest | 2026-10-01 | a92663a | 14,593 B | A | view · diff |
| v1.3 | 2026-09-30 | ce9e6e9 | 12,231 B | A | view · diff |
| v1.2 | 2026-09-12 | c1ed16d | 11,807 B | A | view · diff |
| v1.1 | 2026-09-02 | 1e5eeff | 8,617 B | A | view · diff |
| v1.0 | 2026-07-26 | 87b598a | 7,659 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 (14593 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
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_jfvx56qdlriagche GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/ontology-term-resolution GET https://markdownregistry.com/api/v1/blob/db310515a230a47023169be207f654458789377c98b30fa593ee420738e4eefb
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.