Clinical Trials Database
google-deepmind/science-skills
Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.
Condensed working reference for writing FHIRPath expressions — syntax, function signatures, operator precedence, date/time arithmetic, and common patterns.
$ npx skills add aehrc/pathling --skill fhirpath -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aehrc/pathling fhirpath --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/aehrc/pathling.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/fhirpath .claude/skills/fhirpath && 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 "fhirpath" agent skill from https://github.com/aehrc/pathling/tree/main/.claude/skills/fhirpath into .claude/skills/fhirpath/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fhirpath", 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/aehrc/pathling/tree/main/.claude/skills/fhirpathType 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 aehrc/pathling --skill fhirpath -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aehrc/pathling fhirpath --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aehrc/pathling.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/fhirpath .agents/skills/fhirpath && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "fhirpath" agent skill from https://github.com/aehrc/pathling/tree/main/.claude/skills/fhirpath into .agents/skills/fhirpath/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fhirpath", 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 aehrc/pathling --skill fhirpath -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aehrc/pathling fhirpath --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aehrc/pathling.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/fhirpath .cursor/skills/fhirpath && 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 "fhirpath" agent skill from https://github.com/aehrc/pathling/tree/main/.claude/skills/fhirpath into .cursor/skills/fhirpath/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fhirpath", 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/aehrc/pathling.git --path .claude/skills/fhirpath--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 aehrc/pathling --skill fhirpath -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aehrc/pathling fhirpath --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aehrc/pathling.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/fhirpath .gemini/skills/fhirpath && 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 "fhirpath" agent skill from https://github.com/aehrc/pathling/tree/main/.claude/skills/fhirpath into .gemini/skills/fhirpath/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fhirpath", 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 aehrc/pathling fhirpathInstalls 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 aehrc/pathling --skill fhirpath -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aehrc/pathling.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/fhirpath .github/skills/fhirpath && 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 "fhirpath" agent skill from https://github.com/aehrc/pathling/tree/main/.claude/skills/fhirpath into .github/skills/fhirpath/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fhirpath", 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 aehrc/pathling --skill fhirpath -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aehrc/pathling fhirpath --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aehrc/pathling.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/fhirpath .opencode/skills/fhirpath && 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 "fhirpath" agent skill from https://github.com/aehrc/pathling/tree/main/.claude/skills/fhirpath into .opencode/skills/fhirpath/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fhirpath", 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.
fhirpathCondensed working reference for writing FHIRPath expressions — syntax, function signatures, operator precedence, date/time arithmetic, and common patterns.
Fhirpath is an agent skill from aehrc/pathling. Condensed working reference for writing FHIRPath expressions — syntax, function signatures, operator precedence, date/time arithmetic, and common patterns. Use this skill when writing or reading a FHIRPath expression, navigating FHIR resource trees, filtering collections, or writing FHIR invariants. Trigger keywords include "FHIRPath", "path expression", "FHIR navigation", "where()", "select()", "exists()", "ofType()", "resolve()", "FHIR invariant", "collection filtering". For questions about what the…
Its SKILL.md is about 2.8k 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: Tools that make it easier to use FHIR and clinical terminology within data analytics, built on Apache Spark. The licence is Apache-2.0.
11 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 56a3b4a. 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.
No scripts in the folder and no shell commands in SKILL.md.
From 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:
unitsofmeasure.orgsnomed.infoloinc.orgFrom 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.
Fhirpath loads about 2.8k tokens when it runs. Until then it costs about 164 tokens; SKILL.md has 396 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 aehrc/pathling at commit 56a3b4a, republished under its Apache-2.0 licence (© aehrc). 396 words, ~2,825 tokens.
.claude/skills/fhirpath/SKILL.md (or your agent's skills folder).A condensed reference for writing FHIRPath expressions. Use it to orient quickly or to recall a signature.
It is a summary, not a source of truth. When exact semantics matter — empty propagation, coercion,
precision, error conditions — use the fhirpath-spec skill, which reads the normative spec text and
the fhirpath.js reference implementation. Where this file and the spec disagree, the spec wins.
FHIRPath is a path-based navigation and extraction language for hierarchical data models, used extensively in FHIR and CQL. All operations return collections.
Patient.name.given // Navigate to given names
Patient.name[0].given // First name's given (0-based indexing)
Patient.name.first().given // Equivalent using first()
Observation.value.ofType(Quantity).unit // Filter by type then navigatePrefix with type name to restrict context: Patient.name.given only works on Patient resources.
| Type | Examples |
|---|---|
| Boolean | true, false |
| Integer | 42, -5 |
| Decimal | 3.14159 |
| String | 'hello', 'urn:oid:1.2.3' (single quotes, use \' to escape) |
| Date | @2024-01-15, @2024-01, @2024 (partial dates allowed) |
| DateTime | @2024-01-15T14:30:00Z, @2024-01-15T14:30:00+10:00, @2024T |
| Time | @T14:30:00, @T14:30 |
| Quantity | 10 'mg', 4 days, 100 '[degF]' (UCUM units in quotes) |
{ }name.exists() // true if any names
name.exists(use = 'official') // true if any official names
name.all(given.exists()) // true if all names have given
telecom.where(system='phone').empty() // true if no phone telecoms
name.count() // number of namesname.where(use = 'official') // Filter by criteria
entry.select(resource as Patient) // Project/transform
name.select(given.first() + ' ' + family) // Combine fields
telecom.distinct() // Remove duplicates
item.repeat(item) // Recursive traversal (unique)
expansion.repeat(contains) // Navigate tree structuresname[0] // First item (0-based)
name.first() // First item
name.last() // Last item
name.tail() // All but first
name.skip(2) // Skip first 2
name.take(3) // Take first 3
name.single() // Error if not exactly onename.given | name.family // Union (removes duplicates)
a.union(b) // Same as |
a.combine(b) // Merge without removing duplicates
a.intersect(b) // Items in both
a.exclude(b) // Items in a but not bvalue is Quantity // Type check (returns Boolean)
value as Quantity // Cast (empty if wrong type)
entry.resource.ofType(Patient) // Filter collection by type'hello'.length() // 5
'hello'.substring(1, 3) // 'ell'
'hello'.startsWith('he') // true
'hello'.endsWith('lo') // true
'hello'.contains('ell') // true (different from contains operator)
'hello'.indexOf('l') // 2
'HELLO'.lower() // 'hello'
'hello'.upper() // 'HELLO'
'a-b-c'.replace('-', '_') // 'a_b_c'
'abc'.matches('[a-z]+') // true (partial match)
'abc'.matchesFull('[a-z]+') // true (full match)
'a,b,c'.split(',') // {'a', 'b', 'c'}
('a' | 'b' | 'c').join(',') // 'a,b,c'
' hello '.trim() // 'hello'(-5).abs() // 5
1.5.ceiling() // 2
1.5.floor() // 1
1.5.round() // 2
1.5.truncate() // 1
2.power(3) // 8.0
9.sqrt() // 3.0
2.718.ln() // ~1.0
100.log(10) // 2.0
0.exp() // 1.0'42'.toInteger() // 42
42.toString() // '42'
'3.14'.toDecimal() // 3.14
'true'.toBoolean() // true (also 't', 'yes', 'y', '1')
'2024-01-15'.toDate() // @2024-01-15
'10:30:00'.toTime() // @T10:30:00
'5 mg'.toQuantity() // 5 'mg'
value.convertsToInteger() // true if conversion would succeed@2024-03-15.yearOf() // 2024
@2024-03-15.monthOf() // 3
@2024-03-15.dayOf() // 15
@2024-03-15T10:30:45.123.hourOf() // 10
@2024-03-15T10:30:45.123.minuteOf() // 30
@2024-03-15T10:30:45.123.secondOf() // 45
@2024-03-15T10:30:45.123.millisecondOf() // 123
@2024-03-15T10:30:00+10:00.timezoneOffsetOf() // 10.0
@2024-03-15T10:30:00.dateOf() // @2024-03-15
@2024-03-15T10:30:00.timeOf() // @T10:30:00now() // Current DateTime
today() // Current Date
timeOfDay() // Current Time
iif(condition, true-result, else) // Conditional (short-circuit)
coalesce(a, b, c) // First non-empty (STU)
trace('label', projection) // Debug logging
defineVariable('name', expr) // Define variable for later use (STU)(1 | 2 | 3).sum() // 6
(1 | 2 | 3).min() // 1
(1 | 2 | 3).max() // 3
(1 | 2 | 3).avg() // 2.0
values.aggregate($this + $total, 0) // Custom aggregationa = b // Equal (empty if either empty)
a ~ b // Equivalent (false if precisions differ, case-insensitive for strings)
a != b // Not equal
a !~ b // Not equivalenta > b // Greater than
a < b // Less than
a >= b // Greater or equal
a <= b // Less or equalComparison with different date/time precisions returns empty: @2024-01 > @2024-01-15 → { }
a and b // Three-valued AND
a or b // Three-valued OR
a xor b // Exclusive OR
a implies b // Implication
not() // Negation (function, not operator)Three-valued logic: true and { } → { }, false and { } → false
5 + 3 // Addition (also string concatenation)
5 - 3 // Subtraction
5 * 3 // Multiplication
5 / 3 // Division (always Decimal)
5 div 3 // Integer division
5 mod 3 // Modulo
'a' & 'b' // String concat (empty → empty string)item in collection // Membership
collection contains item // Containership (converse of in)
a | b // Union. (path), [] (indexer)+, -*, /, div, mod+, -, &is, as|>, <, >=, <==, ~, !=, !~in, containsandxor, orimpliesAdd/subtract time-valued quantities from dates/times:
@2024-01-15 + 1 month // @2024-02-15
@2024-01-31 + 1 month // @2024-02-29 (last day of month)
@2024-03-15 - 10 days // @2024-03-05
now() - 1 year // One year agoCalendar duration keywords: year(s), month(s), week(s), day(s), hour(s), minute(s), second(s), millisecond(s)
UCUM definite durations ('a', 'mo', 'd') are NOT equivalent for arithmetic above seconds.
%ucum // UCUM URL (http://unitsofmeasure.org)
%context // Original evaluation context
%`custom` // Custom variables (backtick-delimited)When a function expects a single item but receives a collection:
name.where(use = 'official').exists() implies name.where(use = 'official').given.exists()iif(gender = 'male', 'M', iif(gender = 'female', 'F', 'U'))coalesce(name.where(use='official'), name.where(use='usual'), name.first())subject.resolve().ofType(Patient).birthDate
generalPractitioner.all(resolve() is Practitioner)code.coding.where(system = 'http://snomed.info/sct').code
code.coding.exists(system = 'http://loinc.org' and code = '12345-6')Questionnaire.repeat(item) // All nested items
ValueSet.expansion.repeat(contains) // All expansion conceptsObservation.value.ofType(Quantity).value > 100
(Observation.value as Quantity).value > 100FHIRPath is used to define constraints in FHIR profiles:
// Name must have family or given
name.family.exists() or name.given.exists()
// If dosage exists, it must have timing or asNeeded
dosage.exists() implies (dosage.timing.exists() or dosage.asNeeded.exists())
// All references must be resolvable as Practitioner
performer.all(resolve() is Practitioner)Patient.name.given + ' ' + Patient.name.family fails if multiple names{ } = { } returns { }, not true@2024 = @2024-01 returns { } (unknown).contains('x') is string function; contains x is operator[0])© aehrc, 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 .claude/skills/fhirpath of aehrc/pathling.
Open the folder on GitHubat commit 56a3b4a
Fhirpath 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 |
|---|---|---|---|---|---|---|
| Fhirpath this skillaehrc/pathling | 137 | — | ~2.8k | 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 | |
| Model AssessmentAperivue/medsci-skills | 329 | 1 repos | ~4.5k | Automated safety check: Pass | MIT | |
| Biomedical Analysis Dispatchxjtulyc/MedgeClaw | 617 | 1 repos | ~2k | Automated safety check: Pass | None | |
| Research Proposalluwill/research-skills | 857 | — | ~4.4k | 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.
Aperivue/medsci-skills
A skill your agent uses when validating or evaluating a trained medical-imaging model.
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 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.
aehrc/pathling
Expert guidance for implementing FHIR RESTful API servers and clients following the HL7 FHIR specification.
aehrc/pathling
Expert guidance for implementing FHIR Bulk Data Access (Flat FHIR) following the HL7 specification.
aehrc/pathling
Expert guidance for using the Databricks CLI to manage Databricks workspaces, clusters, jobs, pipelines, Unity Catalog, SQL warehouses, serving endpoints, secrets, bundles, and all other Databricks…
aehrc/pathling
FHIR RESTful search specification expert with access to the official HL7 search specification text and the formal SearchParameter registry.
aehrc/pathling
Design and generate comprehensive FHIRPath test suites using input domain partitioning and Pathling's DSL test framework.
aehrc/pathling
Expert guidance for implementing FHIR servers using HAPI FHIR Plain Server framework.
Categories
Condensed working reference for writing FHIRPath expressions — syntax, function signatures, operator precedence, date/time arithmetic, and common patterns. Fhirpath is an agent skill from aehrc/pathling. Condensed working reference for writing FHIRPath expressions — syntax, function signatures, operator precedence, date/time arithmetic, and common patterns.
Fhirpath fits situations like: reading a FHIRPath expression; navigating FHIR resource trees; filtering collections; writing FHIR invariants.
Run `npx skills add aehrc/pathling --skill fhirpath -a claude-code`. Or copy the skill folder (.claude/skills/fhirpath in aehrc/pathling) into .claude/skills/fhirpath in your project. Claude Code loads it when a task matches its description.
Run `npx skills add aehrc/pathling --skill fhirpath -a codex`. Or copy the skill folder (.claude/skills/fhirpath in aehrc/pathling) into .agents/skills/fhirpath 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 aehrc/pathling --skill fhirpath -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/fhirpath, .gemini/skills/fhirpath, .github/skills/fhirpath and .opencode/skills/fhirpath in your project.
SKILL.md names no scripts, command-line tools or credentials: Fhirpath is instructions for the agent only.
SKILL.md names 3 domains. In commands or code: unitsofmeasure.org, snomed.info and loinc.org; the agent is likely to contact these when it follows the instructions. 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.
Fhirpath is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.8k tokens (SKILL.md is roughly 11k 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 Fhirpath: Clinical Trials Database (google-deepmind/science-skills, 3.2k stars), CHARLS Paper Reproduction Guide (xjtulyc/MedgeClaw, 617 stars), Model Assessment (Aperivue/medsci-skills, 329 stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
aehrc (a GitHub organization) maintains it in aehrc/pathling, which has 137 GitHub stars. The repository holds 25 skills in this directory. The repository was last updated on October 7, 2026.
Source: aehrc/pathling on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.