linking-umls-concepts
Links entities extracted by OpenMed to UMLS Metathesaurus CUIs using the USER'S OWN UTS API key, with nothing from the Metathesaurus bundled or cached. Use when the user wants to normalize concepts across vocabularies to a single CUI, resolve synonyms via the UMLS, filter by semantic type, or cross-walk between SNOMED CT, ICD-10, RxNorm and MeSH through their shared CUI. Trigger keywords: UMLS, CUI, Metathesaurus, UTS API key, semantic type, TUI, MetaMap, QuickUMLS, concept normalization, cross-vocabulary. Pairs after OpenMed NER: consume Disease/Pharmaceutical/Chemical/Anatomy entities from o
npx skills add maziyarpanahi/openmed --skill linking-umls-concepts --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Linking OpenMed entities to UMLS CUIs Resolve concept spans that OpenMed extracts to **UMLS Metathesaurus** concepts. The atom is the **CUI** (Concept Unique Identifier, e.g. `C0011860`): one CUI unifies synonyms from many source vocabularies (SNOMED CT, ICD-10-CM, RxNorm, MeSH, LOINC), making the CUI the natural hub for cross-vocabulary normalization. Every concept also carries one or more **semantic types** (TUIs, e.g. *Disease or Syndrome* `T047`) for type-based filtering. > **Hard licensing boundary — read first.** The UMLS Metathesaurus is > **license-restricted**. OpenMed and this skill **never bundle, ship, or cache** > Metathesaurus content. Concept linking runs **out-of-process against the NLM > UTS (UMLS Terminology Services) REST API using the user's own UTS API key**. > A free UTS account + API key is required (request at uts.nlm.nih.gov and accept > the UMLS license). The Metathesaurus stays user-supplied: your code holds only > the key (from the environment) and stores only returned CUIs/strings. ## When to use - You need **one canonical id across vocabularies** — e.g. to unify a SNOMED CT disorder, an ICD-10 code, and a free-text mention onto a single CUI. - You wa
- When to use
- Quick start (user-supplied UTS API key)
- Workflow
- Hand-off from OpenMed
- Edge cases & gotchas
- Standards & references
What does the linking-umls-concepts skill do?
Links entities extracted by OpenMed to UMLS Metathesaurus CUIs using the USER'S OWN UTS API key, with nothing from the Metathesaurus bundled or cached. Use when the user wants to normalize concepts across vocabularies to a single CUI, resolve synonyms via the UMLS, filter by semantic type, or cross-walk between SNOMED CT, ICD-10, RxNorm and MeSH through their shared CUI. Trigger keywords: UMLS, CUI, Metathesaurus, UTS API key, semantic type, TUI, MetaMap, QuickUMLS, concept normalization, cross-vocabulary. Pairs after OpenMed NER: consume Disease/Pharmaceutical/Chemical/Anatomy entities from o
How do I install it?
Run `npx skills add maziyarpanahi/openmed --skill linking-umls-concepts --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From maziyarpanahi/openmed, a repository with 4,851 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.