--- name: clinical-trials-database description: > Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching. --- # Clinical Trials Database ## Prerequisites 1. **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure `uv` is installed and on PATH. 2. **User Notification**: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://clinicaltrials.gov/, then (2) create the file recording the notification text and timestamp. ## Overview Access worldwide clinical trial data from ClinicalTrials.gov via the REST API v2. The CLI script at `scripts/clinical_trials_api.py` wraps the API with dedicated flags for common filters (phase, age group, status, intervention, sponsor, etc.) so you rarely need to construct raw queries. ## Core Rules - **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully. - **Always use `--fields`** — trial JSON records can be very large; restrict to the data points you need. - **Use `--count-total` first** — check result volume before fetching all records. - **Paginate large result sets** — use `--limit` with `--page-token` to iterate. - **Trust Search Filters**: Do not manually re-filter results unless explicitly asked to verify detailed eligibility. - **Notification**: If this skill is used, ensure this is mentioned in the output. ## Context Efficiency Warning Trial JSON records can be very large. **Always** use the `--fields` parameter to restrict the response to only the data points you need. After writing to file, read only the fields you need rather than the entire file. > [!TIP] Use `references/studies_schema.md` to identify exact field paths for > `--fields`. ## Response Layout Summary API responses contain a list of studies (usually in a `studies[]` array). Each study is split into `protocolSection` and optional `resultsSection`. > [!Tip] Use the **shorthand aliases** below with the `--fields` parameter to > request specific data and keep responses small. ### Top-Level Fields - `totalCount` — Total studies matching query (integer) - `studies[]` — Array of study objects - `nextPageToken` — cursor string for pagination ### Common Study Fields (and shorthand alias) - **Identification** - `protocolSection.identificationModule.nctId` (`NCTId`) — Unique trial ID - `protocolSection.identificationModule.briefTitle` (`BriefTitle`) — Short title - **Status** - `protocolSection.statusModule.overallStatus` (`OverallStatus`) — Recruitment status - **Description** - `protocolSection.descriptionModule.briefSummary` (`BriefSummary`) — Short description - **Arms & Interventions** - `protocolSection.armsInterventionsModule.interventions` (`ArmsInterventionsModule`) - **Eligibility** - `protocolSection.eligibilityModule.eligibilityCriteria` (`EligibilityCriteria`) — Inclusion/Exclusion - `protocolSection.eligibilityModule.stdAges` (`StdAge`) — CHILD, ADULT, etc. Consult `references/studies_schema.md` for full paths (Locations, Outcomes, Results) and common `--fields` recipes. ## Commands ### Search for studies Use for: finding trials by disease, drug, phase, status, age group, or any combination of these filters. ```bash uv run scripts/clinical_trials_api.py search \ --condition "" \ --intervention "" \ --status "" \ --phase "" \ --age-group "" \ --study-type "" \ --sponsor "" \ --has-results \ --sort ":" \ --fields "" \ --limit \ --count-total \ --page-token "" \ --output /tmp/search_results.json ``` All flags are optional and combine via AND logic. **Flag reference:** - `--condition` — Disease or condition to search for (e.g. `"cystic fibrosis"`). - `--intervention` — Drug, device, or treatment name (e.g. `"pembrolizumab"`). - `--status` — Recruitment status filter. Values: RECRUITING, COMPLETED, NOT_YET_RECRUITING, ACTIVE_NOT_RECRUITING, ENROLLING_BY_INVITATION, TERMINATED, SUSPENDED, WITHDRAWN. - `--phase` — Trial phase filter. Values: PHASE1, PHASE2, PHASE3, PHASE4, EARLY_PHASE1, NA. - `--age-group` — Patient age group filter. Values: CHILD (0–17), ADULT (18–64), OLDER_ADULT (65+). - `--study-type` — Type of study. Values: INTERVENTIONAL, OBSERVATIONAL, EXPANDED_ACCESS. - `--sponsor` — Lead sponsor or institution name (e.g. `"National Cancer Institute"`). - `--has-results` — Boolean flag (no value needed). When present, filters for studies that have results available on ClinicalTrials.gov. - `--sort` — Sort order as `FieldName:asc` or `FieldName:desc`. Common fields: `LastUpdatePostDate`, `EnrollmentCount`, `StudyFirstPostDate`, `StartDate`. - `--fields` — Comma-separated list of JSON field names to include in the response. Use this to keep responses small (e.g. `"NCTId,BriefTitle,OverallStatus,Phase"`). See `references/studies_schema.md` for available field paths. - `--limit` — Maximum number of studies to return per request (1–1000, default 10). - `--count-total` — Boolean flag (no value needed). When present, the response includes a `totalCount` field showing the total number of matching studies across all pages. - `--page-token` — An opaque cursor string used to fetch the next page of results. Obtain this value from the `nextPageToken` field in a previous search response. Do not construct this string yourself; always copy it verbatim from the API response. See the Pagination section below. - `--advanced` — Raw Essie filter expression for structured queries beyond the dedicated flags (e.g. `"AREA[LocationCountry]United States"`). Combined with other flags via AND. See `references/clinical_trials_api.md` for syntax. - `--output` — **(Required)** File path where the JSON response is written. **Example — actively recruiting Phase 3 pediatric cystic fibrosis trials:** ```bash uv run scripts/clinical_trials_api.py search \ --condition "cystic fibrosis" \ --status RECRUITING \ --phase PHASE3 \ --age-group CHILD \ --fields "NCTId,BriefTitle,OverallStatus,Phase" \ --limit 10 \ --output /tmp/cf_trials.json ``` **Example — recruiting atezolizumab trials for esophageal cancer:** ```bash uv run scripts/clinical_trials_api.py search \ --condition "esophageal cancer" \ --intervention "Atezolizumab" \ --status RECRUITING \ --fields "NCTId,BriefTitle,Phase" \ --limit 10 \ --output /tmp/atezolizumab_trials.json ``` ### Retrieve a study by NCT ID Use for: fetching full details of a specific trial when you already have the NCT identifier. ```bash uv run scripts/clinical_trials_api.py get-study \ [--fields ""] \ --output /tmp/study.json ``` Returns a useful default set of fields if `--fields` is omitted: `NCTId,BriefTitle,OverallStatus,Phase,BriefSummary,` `ConditionsModule,ArmsInterventionsModule,EligibilityModule` **Structure of the default response:** ```json { "protocolSection": { "identificationModule": { "nctId": "NCT00000000", "briefTitle": "Study Title" }, "statusModule": { "overallStatus": "RECRUITING" }, "descriptionModule": { "briefSummary": "This study is about..." }, "conditionsModule": { "conditions": [ "Condition Name" ] }, "armsInterventionsModule": { "interventions": [ { "type": "DRUG", "name": "Drug Name" } ] }, "eligibilityModule": { "eligibilityCriteria": "Inclusion:\n- ...", "stdAges": [ "ADULT" ] } } } ``` ### Get eligibility / inclusion criteria Use for: pulling inclusion/exclusion rules, age ranges, and sex requirements for patient-matching tasks. ```bash uv run scripts/clinical_trials_api.py \ get-eligibility \ --output /tmp/eligibility.json ``` Shortcut that returns title and the full eligibility module (inclusion/exclusion criteria, age range, sex). **Example — inclusion criteria for NCT04886804:** ```bash uv run scripts/clinical_trials_api.py \ get-eligibility NCT04886804 \ --output /tmp/eligibility_NCT04886804.json ``` ### Count matching studies Use for: exploring the trial landscape — checking how many trials exist for a condition, phase, or status before fetching full records. ```bash uv run scripts/clinical_trials_api.py count \ --condition "" \ [--status ""] [--phase ""] ... \ --output /tmp/count.json ``` Returns only the total count of clinical trials matching the search criteria without fetching study records. Accepts the same filter flags as `search`. ### Search by location / geography Use for: narrowing trials to a specific country, state, or city. Use `--advanced` with `AREA[LocationCountry]` or `AREA[LocationCity]` to restrict results by geography: ```bash uv run scripts/clinical_trials_api.py search \ --condition "cystic fibrosis" \ --status RECRUITING \ --advanced "AREA[LocationCity]New York" \ --fields "NCTId,BriefTitle" \ --limit 20 \ --output /tmp/nyc_cf_trials.json ``` ### Search by sponsor / organization Use for: identifying a sponsor's or institution's trial portfolio. Use `--sponsor` to find trials run by a specific institution or company: ```bash uv run scripts/clinical_trials_api.py search \ --sponsor "National Cancer Institute" \ --fields "NCTId,BriefTitle,LeadSponsorName" \ --limit 20 \ --output /tmp/nci_trials.json ``` ### Combined multi-criteria search Use for: complex queries that layer multiple filters (condition and drug and phase and geography and sponsor, etc.). All flags combine via AND, so you can layer conditions, interventions, status, phase, geography, and sponsor in a single query: ```bash uv run scripts/clinical_trials_api.py search \ --condition "pancreatic cancer" \ --intervention "immunotherapy" \ --status RECRUITING \ --phase PHASE3 \ --advanced "AREA[LocationCountry]United States" \ --fields "NCTId,BriefTitle,Phase,LeadSponsorName" \ --limit 20 \ --output /tmp/panc_trials.json ``` ### Raw API query (escape hatch) Use for: uncommon endpoints or parameter combinations not covered by the dedicated flags. ```bash uv run scripts/clinical_trials_api.py raw-query \ --endpoint \ --params '' \ --output /tmp/raw_result.json ``` ## Pagination When results exceed `--limit`, the response includes a `nextPageToken`. Pass it with `--page-token` to fetch the next page: ```bash uv run scripts/clinical_trials_api.py search \ --condition "breast cancer" \ --status RECRUITING \ --limit 50 --count-total \ --output /tmp/breast_cancer_p1.json uv run scripts/clinical_trials_api.py search \ --condition "breast cancer" \ --status RECRUITING \ --limit 50 --page-token "CAo=" \ --output /tmp/breast_cancer_p2.json ``` ## Advanced Querying For complex filtering beyond the dedicated flags, use `--advanced` with an Essie expression. **What is an Essie Expression?** Essie is the search engine powering ClinicalTrials.gov. An Essie expression is a structured query that targets specific fields (e.g., country, phase) rather than doing general keyword searches. - **`AREA[Field]Value`**: Targets a specific field. - `AREA[LocationCountry]United States` - `AREA[Phase]PHASE3` - **Boolean operators**: Combine with `AND`, `OR`, `NOT`. - **`RANGE[min, max]`**: For numeric/date fields (e.g. `RANGE[500, MAX]`). See `references/clinical_trials_api.md` for syntax and available fields. It is combined with other flags via AND: ```bash uv run scripts/clinical_trials_api.py search \ --condition "diabetes" \ --advanced "AREA[LocationCountry]United States \ AND AREA[EnrollmentCount]RANGE[500, MAX]" \ --fields "NCTId,BriefTitle,EnrollmentCount" \ --output /tmp/diabetes_us_large.json ``` ## References - **API parameters, enum values, and Essie syntax:** `references/clinical_trials_api.md` - **JSON field paths and `--fields` recipes:** `references/studies_schema.md`