# Pp Clinical Trials > A multi-source clinical-trials intelligence system — aggregates, normalizes, and analyzes trials across ClinicalTrials.gov, EU CTIS, and biomedical sources, with an offline SQLite engine no single-registry tool has. Trigger phrases: `what clinical trials are running for`, `recruiting trials for`, `phase 3 trials for`, `compare these two drugs trials`, `emerging therapies in`, `is this trial risky`, `watch trials for`, `clinical trials intelligence`, `use clinical-trials`, `run clinical-trials`. - Skill: `mvanhorn-printing-press-libra/pp-clinical-trials` (Agent Skill) - Install (CLI): `npx skillmds add mvanhorn-printing-press-libra/pp-clinical-trials` - Raw SKILL.md: https://api.skillmd.com/api/skills/mvanhorn-printing-press-libra/pp-clinical-trials/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - License: Apache-2.0 - Author: mvanhorn (https://skillmd.com/u/mvanhorn-printing-press-libra) - Updated: 2026-09-09 - Page: https://skillmd.com/skills/mvanhorn-printing-press-libra/pp-clinical-trials --- # ClinicalTrials.gov — Printing Press CLI ## Prerequisites: Install the CLI This skill drives the `clinical-trials-pp-cli` binary. **You must verify the CLI is installed before invoking any command from this skill.** If it is missing, install it first: 1. Install via the Printing Press installer. It defaults binaries to `$HOME/.local/bin` on macOS/Linux and `%LOCALAPPDATA%\Programs\PrintingPress\bin` on Windows: ```bash npx -y @mvanhorn/printing-press-library install clinical-trials --cli-only ``` 2. Verify: `clinical-trials-pp-cli --version` 3. Ensure the reported install directory is on `$PATH` for the agent/runtime that will invoke this skill. If the `npx` install fails (no Node, offline, etc.), fall back to a direct Go install (requires Go 1.26.6 or newer). This installs into `$GOPATH/bin` (default `$HOME/go/bin`), so add that directory to `$PATH` instead: ```bash go install github.com/mvanhorn/printing-press-library/library/health/clinical-trials/cmd/clinical-trials-pp-cli@latest ``` If `--version` reports "command not found" after install, the runtime cannot see the binary directory on `$PATH`. Do not proceed with skill commands until verification succeeds. Every other ClinicalTrials.gov tool is a single-source pass-through. This one merges registries into one normalized trial model, dedups across NCT/EUCTR/WHO IDs, and computes intelligence: emerging therapies, recruitment velocity, drug comparisons, abandonment risk, geographic hotspots, and sponsor dominance. It degrades gracefully down a fallback chain and never crashes, caching everything locally for offline, agent-native analysis. ## When to Use This CLI Reach for this CLI when the task is understanding the clinical-trials landscape — what is running, what is emerging, how two drugs compare, whether a trial is risky, or where recruitment is concentrated — across more than one registry. It is the right tool for evidence synthesis, competitive trial analysis, and weekly landscape reports. ## Anti-triggers Do not use this CLI for: - Do not use it to enroll patients or submit trial registrations — it is read-only. - Do not use it for full EHR or patient-record data — it covers public trial registries only. - Do not use --source who expecting live data — WHO ICTRP has no public API. ## Unique Capabilities These capabilities aren't available in any other tool for this API. ### Intelligence engine - **`emerging`** — See the fastest-growing trial categories for a disease area, with percent change. _Pick this when the user asks where research is heading, not about one specific trial._ ```bash clinical-trials-pp-cli emerging cancer --json ``` - **`velocity`** — Measure how fast a disease area's trials and enrollment are growing over time. _Use to quantify momentum in a field; buckets a sampled set of trials by start year and reports a recent-vs-prior growth rate (no prior snapshot needed)._ ```bash clinical-trials-pp-cli velocity "alzheimer" --json ``` - **`compare`** — Compare two drugs head-to-head across trial counts, phases, sponsors, and recruiting status. _Use to weigh two interventions by real trial activity, not marketing._ ```bash clinical-trials-pp-cli compare "Keytruda" "Opdivo" --json ``` - **`risk`** — Get an explainable risk read on a single trial from termination, enrollment, site count, sponsor track record, and phase factor (earlier phases = higher risk). _Use to triage whether a trial is likely to complete and report._ ```bash clinical-trials-pp-cli risk NCT07011732 --json ``` - **`forecast`** — Forward-looking completion outlook for a trial, derived from the same deterministic signals as `risk`. _Use to get a plain-language outlook band and the primary concerns behind it. **Caveat:** heuristic only — a read of registry signals, not a clinical prediction._ ```bash clinical-trials-pp-cli forecast NCT07011732 --json ``` - **`sponsors`** — Rank who runs the most trials in an area, classified as industry, academic, or government. _Use to see who controls research in a field._ ```bash clinical-trials-pp-cli sponsors "diabetes" --json ``` - **`digest`** — Compact "what's notable" snapshot for a condition or search term: total matched, recruiting count, newest trials, and recently-stopped ones. _Use for a fast read on a topic's current state; a read-only point-in-time snapshot (use `watch` for a persistent change feed). `--limit` bounds the newest and recently-stopped lists._ ```bash clinical-trials-pp-cli digest "type 2 diabetes" --limit 5 --json ``` ### Single-trial analysis - **`similar`** — Find trials similar to a given NCT ID by shared condition, phase, and intervention profile. _Use to surface comparable trials from registry signals only (no ML matching); `--limit` caps how many matches are returned._ ```bash clinical-trials-pp-cli similar NCT04280705 --limit 5 --json ``` - **`timeline`** — Show a trial's key dates in chronological order: start, primary completion, completion, and last-update posted. _Use to see a single trial's schedule at a glance; dates with no posted value are omitted._ ```bash clinical-trials-pp-cli timeline NCT04280705 --json ``` - **`enrollment-check`** — Heuristic plausibility check on a trial's posted enrollment target relative to its phase. _Reuses the `risk` command's enrollment signal. **Caveat:** this is a heuristic from observable registry signals only — not a clinical judgment or a prediction of whether the trial will enroll._ ```bash clinical-trials-pp-cli enrollment-check NCT04280705 --json ``` ### Interoperability - **`export-fhir`** — Export a trial's registry metadata as a minimal FHIR R4 ResearchStudy resource (JSON) or a flat CSV row. _Use to hand a trial's core metadata to a FHIR-aware system or a spreadsheet. `--format fhir` (default) emits the ResearchStudy JSON; `--format csv` emits one flat row. **Caveat:** this is a lightweight metadata export, not a full FHIR-conformant clinical dataset, and is not validated against a FHIR profile._ ```bash clinical-trials-pp-cli export-fhir NCT04280705 clinical-trials-pp-cli export-fhir NCT04280705 --format csv ``` ### Local state that compounds - **`watch`** — Track a term and report new, changed, and terminated trials since the last run. _Use to monitor a topic over time instead of re-reading full result sets._ ```bash clinical-trials-pp-cli watch "vitamin d" --json ``` ### Multi-source aggregation - **`search`** — Search a single normalized trial model aggregated and deduplicated across ClinicalTrials.gov, EU CTIS, and OpenAlex. _Use as the default entry point; it queries the merged multi-source mirror, so it sees more than any single registry._ ```bash clinical-trials-pp-cli search "glioblastoma" --json ``` ### Enrichment - **`evidence`** — Link a trial to its publications and citation context via PubMed and OpenAlex. _Use to check whether a trial actually published results._ ```bash clinical-trials-pp-cli evidence NCT07011732 --json ``` - **`safety`** — Surface FDA adverse-event signals for a trial's intervention drug. _Use to add a real-world safety lens to a trial's drug._ ```bash clinical-trials-pp-cli safety "pembrolizumab" --json ``` ### Output for humans - **`report`** — Compose search, emerging, hotspots, and sponsors into one markdown or CSV briefing for a topic. _Use for a weekly landscape summary a clinician can read at a glance._ ```bash clinical-trials-pp-cli report "long covid" --format md ``` ### Reliability - **`health`** — Show live status, latency, and failure rate for every data source in the fallback chain. _Use to know which sources are degraded before trusting a result._ ```bash clinical-trials-pp-cli health --json ``` ## Command Reference **clinicaltrials-gov-version** — Manage clinicaltrials gov version - `clinical-trials-pp-cli clinicaltrials-gov-version` — API and data versions. API version follows [Semantic Versioning 2.0.0 Schema](https://semver.org/spec/v2.0.0.html). **stats** — Data statistics - `clinical-trials-pp-cli stats field-values` — Value statistics of the study leaf fields. - `clinical-trials-pp-cli stats list-field-sizes` — Sizes of list/array fields. To search studies by a list field size, use `AREA[FieldName:size]` search operator. - `clinical-trials-pp-cli stats size` — Statistics of study JSON sizes. **studies** — Related to clinical trial studies - `clinical-trials-pp-cli studies enums` — Returns enumeration types and their values. - `clinical-trials-pp-cli studies fetch-study` — Returns data of a single study. - `clinical-trials-pp-cli studies list` — Returns data of studies matching query and filter parameters. The studies are returned page by page. - `clinical-trials-pp-cli studies metadata` — Returns study data model fields. - `clinical-trials-pp-cli studies search-areas` — Search Docs and their Search Areas. ### Finding the right command When you know what you want to do but not which command does it, ask the CLI directly: ```bash clinical-trials-pp-cli which "" ``` `which` resolves a natural-language capability query to the best matching command from this CLI's curated feature index. Exit code `0` means at least one match; exit code `2` means no confident match — fall back to `--help` or use a narrower query. ## Recipes ### Bounded agent-friendly search ```bash clinical-trials-pp-cli search "glioblastoma" --json --limit 20 ``` Searches the merged multi-source mirror and returns a bounded result set an agent can parse. ### Emerging oncology ```bash clinical-trials-pp-cli emerging cancer --json ``` Ranks the fastest-growing oncology trial categories with percent change. ### Head-to-head drug activity ```bash clinical-trials-pp-cli compare "pembrolizumab" "nivolumab" --json ``` Compares two drugs by trial counts, phases, and sponsors with RxNorm synonym resolution. ### Triage a single trial ```bash clinical-trials-pp-cli risk NCT07011732 --json ``` Returns an explainable risk score with each contributing factor. ### Weekly clinician report ```bash clinical-trials-pp-cli report "long covid" --format md ``` Composes search, emerging, hotspots, and sponsors into one markdown briefing. ## Auth Setup No credentials required for the core. ClinicalTrials.gov, EU CTIS, OpenAlex, RxNorm, and MeSH need no key. OpenFDA and PubMed accept an optional key purely for higher rate limits. Run `clinical-trials-pp-cli doctor` to verify setup. ## Agent Mode Add `--agent` to any command. Expands to: `--json --compact --no-input --no-color --yes`. - **Pipeable** — JSON on stdout, errors on stderr - **Filterable** — `--select` keeps a subset of fields. Dotted paths descend into nested structures; arrays traverse element-wise. Critical for keeping context small on verbose APIs: ```bash clinical-trials-pp-cli studies list --agent --select id,name,status ``` - **Previewable** — `--dry-run` shows the request without sending - **Offline-friendly** — sync/search commands can use the local SQLite store when available - **Non-interactive** — never prompts, every input is a flag - **Read-only** — do not use this CLI for create, update, delete, publish, comment, upvote, invite, order, send, or other mutating requests ### Response envelope Commands that read from the local store or the API wrap output in a provenance envelope: ```json { "meta": {"source": "live" | "local", "synced_at": "...", "reason": "..."}, "results": } ``` Parse `.results` for data and `.meta.source` to know whether it's live or local. A human-readable `N results (live)` summary is printed to stderr only when stdout is a terminal AND no machine-format flag (`--json`, `--csv`, `--compact`, `--quiet`, `--plain`, `--select`) is set — piped/agent consumers and explicit-format runs get pure JSON on stdout. ## Paths and state Agents should treat the CLI's path resolver as part of the runtime contract: - Use `--home ` for one invocation, or set `CLINICAL_TRIALS_HOME=` to relocate all four path kinds under one root. - Use per-kind env vars only when a specific kind must diverge: `CLINICAL_TRIALS_CONFIG_DIR`, `CLINICAL_TRIALS_DATA_DIR`, `CLINICAL_TRIALS_STATE_DIR`, `CLINICAL_TRIALS_CACHE_DIR`. - Resolution order is per-kind env var, `--home`, `CLINICAL_TRIALS_HOME`, XDG (`XDG_CONFIG_HOME`, `XDG_DATA_HOME`, `XDG_STATE_HOME`, `XDG_CACHE_HOME`), then platform defaults. - `config` contains settings like `config.toml` and profiles. `data` contains `credentials.toml`, `data.db`, cookies, and auth sidecars. `state` contains persisted queries, jobs, and `teach.log`. `cache` contains regenerable HTTP/cache files. - Stored secrets live in `credentials.toml` under the data dir. Existing legacy `config.toml` secrets are read for compatibility and leave `config.toml` on the first auth write. - Run `clinical-trials-pp-cli doctor --fail-on warn` to surface path and credential-location warnings. `agent-context` exposes a schema v4 `paths` block for agents that need the resolved dirs. - For MCP, pass relocation through the MCP host config. The MCP binary does not inherit CLI flags: ```json { "mcpServers": { "clinical-trials": { "command": "clinical-trials-pp-mcp", "env": { "CLINICAL_TRIALS_HOME": "/srv/clinical-trials" } } } } ``` Fleet precedence: an inherited per-kind env var overrides an explicit `--home` for that kind. Use `CLINICAL_TRIALS_HOME` or per-kind vars as durable fleet levers, and use `--home` only for a single invocation. Relocation is not reversible by unsetting env vars; move files manually before clearing `CLINICAL_TRIALS_HOME`, or `doctor` will not find credentials left under the former root. ## Agent Feedback When you (or the agent) notice something off about this CLI, record it: ``` clinical-trials-pp-cli feedback "the --since flag is inclusive but docs say exclusive" clinical-trials-pp-cli feedback --stdin < notes.txt clinical-trials-pp-cli feedback list --json --limit 10 ``` Entries are stored locally as `feedback.jsonl` under the resolved data dir. They are never POSTed unless `CLINICAL_TRIALS_FEEDBACK_ENDPOINT` is set AND either `--send` is passed or `CLINICAL_TRIALS_FEEDBACK_AUTO_SEND=true`. Default behavior is local-only. Write what *surprised* you, not a bug report. Short, specific, one line: that is the part that compounds. ## Output Delivery Every command accepts `--deliver `. The output goes to the named sink in addition to (or instead of) stdout, so agents can route command results without hand-piping. Three sinks are supported: | Sink | Effect | |------|--------| | `stdout` | Default; write to stdout only | | `file:` | Atomically write output to `` (tmp + rename) | | `webhook:` | POST the output body to the URL (`application/json` or `application/x-ndjson` when `--compact`) | Unknown schemes are refused with a structured error naming the supported set. Webhook failures return non-zero and log the URL + HTTP status on stderr. ## Named Profiles A profile is a saved set of flag values, reused across invocations. Use it when a scheduled agent calls the same command every run with the same configuration - HeyGen's "Beacon" pattern. ``` clinical-trials-pp-cli profile save briefing --json clinical-trials-pp-cli --profile briefing studies list clinical-trials-pp-cli profile list --json clinical-trials-pp-cli profile show briefing clinical-trials-pp-cli profile delete briefing --yes ``` Explicit flags always win over profile values; profile values win over defaults. `agent-context` lists all available profiles under `available_profiles` so introspecting agents discover them at runtime. ## Exit Codes | Code | Meaning | |------|---------| | 0 | Success | | 2 | Usage error (wrong arguments) | | 3 | Resource not found | | 5 | API error (upstream issue) | | 7 | Rate limited (wait and retry) | | 10 | Config error | ## Argument Parsing Parse `$ARGUMENTS`: 1. **Empty, `help`, or `--help`** → show `clinical-trials-pp-cli --help` output 2. **Starts with `install`** → ends with `mcp` → MCP installation; otherwise → see Prerequisites above 3. **Anything else** → Direct Use (execute as CLI command with `--agent`) ## MCP Server Installation 1. Install the MCP server: ```bash go install github.com/mvanhorn/printing-press-library/library/health/clinical-trials/cmd/clinical-trials-pp-mcp@latest ``` 2. Register with Claude Code: ```bash claude mcp add clinical-trials-pp-mcp -- clinical-trials-pp-mcp ``` 3. Verify: `claude mcp list` ## Direct Use 1. Check if installed: `which clinical-trials-pp-cli` If not found, offer to install (see Prerequisites at the top of this skill). 2. Match the user query to the best command from the Unique Capabilities and Command Reference above. 3. Execute with the `--agent` flag: ```bash clinical-trials-pp-cli [subcommand] [args] --agent ``` 4. If ambiguous, drill into subcommand help: `clinical-trials-pp-cli --help`.