Clinical Trials Database
google-deepmind/science-skills
Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.
Call a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand clinical codes without bundling restricted vocabulary (SNOMED CT, RxNorm, LOINC…
$ npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install maziyarpanahi/openmed querying-terminology-service --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/querying-terminology-service .claude/skills/querying-terminology-service && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "querying-terminology-service" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-service into .claude/skills/querying-terminology-service/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "querying-terminology-service", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-serviceType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install maziyarpanahi/openmed querying-terminology-service --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/querying-terminology-service .agents/skills/querying-terminology-service && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "querying-terminology-service" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-service into .agents/skills/querying-terminology-service/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "querying-terminology-service", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install maziyarpanahi/openmed querying-terminology-service --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/querying-terminology-service .cursor/skills/querying-terminology-service && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "querying-terminology-service" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-service into .cursor/skills/querying-terminology-service/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "querying-terminology-service", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/maziyarpanahi/openmed.git --path skills/querying-terminology-service--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install maziyarpanahi/openmed querying-terminology-service --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/querying-terminology-service .gemini/skills/querying-terminology-service && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "querying-terminology-service" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-service into .gemini/skills/querying-terminology-service/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "querying-terminology-service", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install maziyarpanahi/openmed querying-terminology-serviceInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/querying-terminology-service .github/skills/querying-terminology-service && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "querying-terminology-service" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-service into .github/skills/querying-terminology-service/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "querying-terminology-service", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install maziyarpanahi/openmed querying-terminology-service --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/querying-terminology-service .opencode/skills/querying-terminology-service && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "querying-terminology-service" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/querying-terminology-service into .opencode/skills/querying-terminology-service/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "querying-terminology-service", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
querying-terminology-serviceCall a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand clinical codes without bundling restricted vocabulary (SNOMED CT, RxNorm, LOINC…
Querying Terminology Service is an agent skill from maziyarpanahi/openmed. Call a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand clinical codes without bundling restricted vocabulary (SNOMED CT, RxNorm, LOINC, ICD-10) into OpenMed. Covers a thin local client, ValueSet $expand with filters/ECL, CodeSystem $lookup, ConceptMap $translate, and pointing at Ontoserver / HAPI / tx.fhir.org. Use as the grounding step for OpenMed coding skills — turn an OpenMed entity span into a validated coded CodeableConcept — when the user mentions…
Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Clinical and healthcare research. The repository describes itself as: Local-first healthcare AI: clinical NER and HIPAA PII de-identification on hardware you control. 2,200+ medical models, 35 model-backed PII languages, and Python, MLX, Android… The licence is Apache-2.0.
Read from SKILL.md and the folder at commit 34d7b8c. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
curlFrom the folder's file list and the shell code blocks in SKILL.md.
Hosts in commands or code, which the agent is likely to contact:
hl7.orgsnomed.infoAlso links to:
confluence.ihtsdotools.orgontoserver.csiro.auFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Querying Terminology Service loads about 1.9k tokens when it runs. Until then it costs about 168 tokens; SKILL.md has 499 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from maziyarpanahi/openmed at commit 34d7b8c, republished under its Apache-2.0 licence (© maziyarpanahi). 499 words, ~1,933 tokens.
.claude/skills/querying-terminology-service/SKILL.md (or your agent's skills folder).OpenMed deliberately bundles no restricted vocabulary — no SNOMED CT,
RxNorm, LOINC, ICD-10, UMLS. So when an OpenMed entity span needs a validated
code (the grounding step exporting-to-fhir references), you call a FHIR
terminology server the user already operates, with their own license. This
skill is the thin client the coding skills lean on.
Use it whenever a span must become a coded CodeableConcept, when you need to
confirm a code is valid in a system, expand a ValueSet for a picklist, look up a
display, or map between vocabularies. Triggers: "terminology server",
"$validate-code", "$expand", "ValueSet", "ECL", "is this a valid SNOMED/LOINC/
RxNorm code", "translate ICD-10 to SNOMED". It sits between OpenMed NER and
exporting-to-fhir.
The four operations are standard FHIR; point the client at whichever server the user is licensed for:
OpenMed never ships or proxies these — the credentials and content are the user's.
POST [tx]/CodeSystem/$validate-code -> is this code valid in this system?
POST [tx]/ValueSet/$expand -> enumerate the codes in a value set
POST [tx]/CodeSystem/$lookup -> display + properties for a code
POST [tx]/ConceptMap/$translate -> map a code from one system to another$validate-code — confirm before you emitcurl -s -X POST 'https://tx.example/fhir/CodeSystem/$validate-code' \
-H 'Content-Type: application/fhir+json' -d '{
"resourceType": "Parameters",
"parameter": [
{"name": "url", "valueUri": "http://snomed.info/sct"},
{"name": "code", "valueCode": "44054006"},
{"name": "display", "valueString": "Diabetes mellitus type 2"}
]}'
# -> Parameters: { result: true, display: "Diabetes mellitus type 2" }$expand — enumerate a ValueSet (with ECL for SNOMED)# Expand "disorders of the lung" via an implicit SNOMED ECL value set
curl -s -X POST 'https://tx.example/fhir/ValueSet/$expand' \
-H 'Content-Type: application/fhir+json' -d '{
"resourceType": "Parameters",
"parameter": [
{"name": "url", "valueUri":
"http://snomed.info/sct?fhir_vs=ecl/<<19829001"},
{"name": "filter", "valueString": "pneumonia"},
{"name": "count", "valueInteger": 20}
]}'<<19829001 is ECL for "19829001 (Disorder of lung) or any subtype". Use
$expand + filter to power autocomplete and to constrain which codes a span
may map to.
$lookup and $translate# Display + properties for a LOINC code
POST [tx]/CodeSystem/$lookup { url=http://loinc.org, code=4548-4 }
# Map an ICD-10-CM code to SNOMED via a ConceptMap
POST [tx]/ConceptMap/$translate {
url=<conceptmap-url>, system=http://hl7.org/fhir/sid/icd-10-cm,
code=E11.9, targetsystem=http://snomed.info/sct }import requests
class TxClient:
def __init__(self, base, token=None):
self.base = base.rstrip("/")
self.h = {"Content-Type": "application/fhir+json"}
if token:
self.h["Authorization"] = f"Bearer {token}"
def _params(self, **kv):
return {"resourceType": "Parameters",
"parameter": [{"name": k, **v} for k, v in kv.items()]}
def validate_code(self, system, code, display=None):
body = self._params(url={"valueUri": system}, code={"valueCode": code},
**({"display": {"valueString": display}} if display else {}))
out = requests.post(f"{self.base}/CodeSystem/$validate-code",
json=body, headers=self.h, timeout=15).json()
params = {p["name"]: p for p in out.get("parameter", [])}
return bool(params.get("result", {}).get("valueBoolean"))
# Ground an OpenMed span only if the code validates:
tx = TxClient("https://tx.example/fhir", token="...")
if tx.validate_code("http://snomed.info/sct", "44054006", "Diabetes mellitus type 2"):
from openmed.clinical.exporters.codeable_concept_simple import coding, codeable_concept
cc = codeable_concept([coding("snomed", "44054006",
"Diabetes mellitus type 2")], text=span.text)The system URIs here line up with OpenMed's system_uri
(snomed/loinc/rxnorm/icd-10-cm/hpo/mesh), so a validated code drops
straight into coding(...).
EntityPrediction.text (the span surface form) plus your
candidate code(s) are the input to $validate-code/$translate.coding(...) → codeable_concept(...) (exporting-to-fhir). If a span fails
validation, emit CodeableConcept with only text and flag it via
OperationOutcomeIssue(severity="warning", code="code-invalid", ...).tx.fhir.org only serves open content. Do not route
licensed lookups through a public server.$expand can be enormous. Always pass count (paginate with offset)
and filter; an unfiltered expand of a large hierarchy can time out.http://snomed.info/sct?fhir_vs=ecl/<expression>; other systems use
$expand with filter/property.version matters. SNOMED/LOINC editions change; pin the version
parameter for reproducible validation in CI.tx.fhir.org. It is a public service — only synthetic/coded
data.$validate-code: https://hl7.org/fhir/R4/valueset-operation-validate-code.html$expand: https://hl7.org/fhir/R4/valueset-operation-expand.html$lookup: https://hl7.org/fhir/R4/codesystem-operation-lookup.html$translate: https://hl7.org/fhir/R4/conceptmap-operation-translate.html© maziyarpanahi, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in skills/querying-terminology-service of maziyarpanahi/openmed.
Open the folder on GitHubat commit 34d7b8c
Querying Terminology Service next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Querying Terminology Service this skillmaziyarpanahi/openmed | 5.5k | — | ~1.9k | Automated safety check: Pass | Apache-2.0 | |
| Clinical Trials Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.2k | Automated safety check: Pass | Apache-2.0 | |
| CHARLS Paper Reproduction Guidexjtulyc/MedgeClaw | 617 | 1 repos | ~1.8k | Automated safety check: Pass | None | |
| Biomedical Analysis Dispatchxjtulyc/MedgeClaw | 617 | 1 repos | ~2k | Automated safety check: Pass | None | |
| Research Paperluwill/research-skills | 862 | — | ~1.9k | Automated safety check: Pass | None | |
| Research Proposalluwill/research-skills | 862 | — | ~4.5k | Automated safety check: Notes | None |
google-deepmind/science-skills
Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.
xjtulyc/MedgeClaw
Guides an agent through reproducing papers built on the CHARLS health and retirement survey, from variable mapping to cognition, depression and isolation scores.
xjtulyc/MedgeClaw
Routes bioinformatics, drug discovery, clinical and multi-omics tasks from a chat interface to Claude Code sessions running K-Dense scientific skills, with a live dashboard per task.
luwill/research-skills
A skill your agent uses when the user asks to write or draft an ORIGINAL RESEARCH ARTICLE — IMRaD paper, conference paper, short/workshop paper, 研究论文/期刊论文/会议论文 — reporting their own completed…
luwill/research-skills
A skill your agent uses when the user asks to write or draft a PhD / doctoral research proposal, research plan, 研究计划书, or 开题报告 — a forward-looking plan of background, gap, research questions…
LeonChaoX/qinyan-academic-skills
Write comprehensive literature reviews for medical imaging AI research.
maziyarpanahi/openmed
Checks OpenMed de-identified clinical text against the 18 HIPAA Safe Harbor identifier categories and reports gaps and residual re-identification risk.
maziyarpanahi/openmed
Fills in a model card for an OpenMed clinical NER or de-identification model from its evaluation reports: intended use, metrics, subgroups and limitations.
maziyarpanahi/openmed
Walks a data pipeline against the HIPAA Privacy and Security Rule checklist and produces a gap report before it processes patient data.
maziyarpanahi/openmed
Suggests candidate ICD-10-CM diagnosis and ICD-10-PCS procedure codes for clinical text extracted by OpenMed, with rationale for a certified coder to review.
maziyarpanahi/openmed
Maps OpenMed-extracted, terminology-coded conditions, drugs and measurements into OMOP CDM v5.4 tables for OHDSI and ATLAS analytics.
maziyarpanahi/openmed
Finds social risks such as housing instability or food insecurity in clinical notes and proposes matching ICD-10-CM Z-codes for a coder to confirm.
Categories
Call a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand clinical codes without bundling restricted vocabulary (SNOMED CT, RxNorm, LOINC…. Querying Terminology Service is an agent skill from maziyarpanahi/openmed. Call a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand clinical codes without bundling restricted vocabulary (SNOMED CT, RxNorm, LOINC, ICD-10) into OpenMed.
Querying Terminology Service fits situations like: mentions terminology server; SNOMED/RxNorm/LOINC lookups; code validation.
Run `npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a claude-code`. Or copy the skill folder (skills/querying-terminology-service in maziyarpanahi/openmed) into .claude/skills/querying-terminology-service in your project. Claude Code loads it when a task matches its description.
Run `npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a codex`. Or copy the skill folder (skills/querying-terminology-service in maziyarpanahi/openmed) into .agents/skills/querying-terminology-service in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add maziyarpanahi/openmed --skill querying-terminology-service -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/querying-terminology-service, .gemini/skills/querying-terminology-service, .github/skills/querying-terminology-service and .opencode/skills/querying-terminology-service in your project.
Going by SKILL.md and its folder, Querying Terminology Service needs the command-line tools its instructions call (curl). Our summary lists: Python 3.
SKILL.md names 4 domains. In commands or code: hl7.org and snomed.info; the agent is likely to contact these when it follows the instructions. As links in the text: confluence.ihtsdotools.org and ontoserver.csiro.au. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
Querying Terminology Service is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.9k tokens (SKILL.md is roughly 7.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Querying Terminology Service: Clinical Trials Database (google-deepmind/science-skills, 3.2k stars), CHARLS Paper Reproduction Guide (xjtulyc/MedgeClaw, 617 stars), Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars) and Research Paper (luwill/research-skills, 862 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
maziyarpanahi (a GitHub user) maintains it in maziyarpanahi/openmed, which has 5,506 GitHub stars. The repository holds 74 skills in this directory. The repository was last updated on October 11, 2026.
Source: maziyarpanahi/openmed on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.