k-dense-ai/scientific-agent-skills · skills/ontology-term-resolution/SKILL.md

ontology-term-resolution skillA

ontology-term-resolution is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). 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ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or map.

Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.

How to install

Latest version
mdr add k-dense-ai/scientific-agent-skills/ontology-term-resolution@v1.1
Exact content
mdr add k-dense-ai/scientific-agent-skills/ontology-term-resolution@sha256:25e59f0c8fe4b8ec

Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_jfvx56qdlriagche.svg)](https://markdownregistry.com/a/art_jfvx56qdlriagche)

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Versions

versioncommittedcommitsizeaudit
v1.1 latest2026-09-02 1e5eeff 8,617 BA view · diff
v1.02026-07-26 87b598a 7,659 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (8617 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

GitHub

k-dense-ai/scientific-agent-skills · 43,331 stars · license MIT · pushed 2026-09-02 · 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/25e59f0c8fe4b8ec8ef605e54c0d7d6c57f4c2e29b93295653fddbdb2c6cdaa9