indication-dossier · diff
git:20260721.77e7d29 to git:20260816.42573eb
66 added, 112 removed. Audit A to A.
---
name: indication-dossier
- description: >
- Generate a therapeutic indication dossier. Covers the patient population,
- epidemiology, disease biology, standard of care, regulatory precedent, and
- landmark clinical trials.
+ description: Build a sourced research dossier for one therapeutic indication — patient population, epidemiology, disease biology, standard of care, regulatory path, and landmark trials. Use when the user asks for an indication overview, disease landscape, or trial-design background.
license: Apache-2.0
---
- # Indication Dossier
+ # Indication dossier
- Produces a structured research dossier on a single indication, framed as a
- patient population: who they are, what's wrong, how they're treated today,
- and how clinical trials can be designed to help them. Runs as five phases
- that write resumable waypoint files; after a brief identity check at the end
- of Phase 1, the remaining phases run straight through.
+ Five research phases, each writing one waypoint JSON under
+ `<workdir>/waypoints/`, ending in a cited Markdown report. Waypoints make the
+ run resumable: a later invocation reads which files exist and continues from
+ the first missing one. The only pause for user input is after Phase 1.
- ## Framing
+ ## The framing rule
- **Think of an indication as a patient population.** Frame everything
- from the patient perspective: "Who are these patients?" not "What is this
- disease?"; "How are these patients identified and managed?" not "What causes
- this condition?"; population nesting: "all patients in {child} are patients
- in {parent}".
+ Treat the indication as a *patient population*, not a disease entry. Every
+ section answers a population question — who are these patients, how are they
+ identified and managed, which trials would help them — rather than a textbook
+ question about the condition. Nesting is population nesting: everyone in the
+ child indication is in the parent.
- Some indications don't map to ICD codes or standard disease definitions:
- "immunosenescence" is a biological state, not a billable diagnosis; "ageing"
- is not an FDA-accepted indication; "GLP-1 induced sarcopenia" is an
- iatrogenic population. Note these distinctions explicitly. They matter for
- regulatory path and trial design.
+ Some inputs are not billable diagnoses at all: a biological state
+ ("immunosenescence"), a non-accepted indication ("ageing"), an iatrogenic
+ population ("GLP-1 induced sarcopenia"). Detect and label this early — it
+ changes the epidemiology evidence base, the regulatory path, and what a
+ "complete" dossier even looks like.
## Inputs
- - **`indication`** (required) — indication name (e.g., "sarcopenia",
- "idiopathic pulmonary fibrosis").
- - **`additional_context`** (optional) — areas to focus on, parent
- indication, or other framing.
- - **`workdir`** (optional) — where to write waypoints and the final report.
- Defaults to `./do_not_commit/indication-dossier-<slug>/`.
-
- ## Tools this skill expects
-
- | Purpose | Tool |
- |---|---|
- | ClinicalTrials.gov | `clinical-trials` MCP |
- | Literature | `pubmed` MCP |
- | Web | `WebSearch`, `WebFetch` — FDA guidance, treatment guidelines (NCCN, AASLD, specialty societies), CDC/WHO epidemiology data |
- | Documents | `WebFetch` for remote PDFs; `Read` for local PDFs |
- | Subagents | `Agent` for parallel evidence gathering |
-
- If a listed MCP isn't connected, say so and fall back to `WebSearch` against
- the underlying public source (clinicaltrials.gov, pubmed.ncbi.nlm.nih.gov).
-
- ## Output layout
-
- ```
- <workdir>/
- └── waypoints/
- ├── progress.json # loop control
- ├── meta.json # phase 1
- ├── epidemiology.json # phase 2
- ├── biology_soc.json # phase 3
- ├── regulatory_trials.json # phase 4
- ├── sources_evaluated.json
- ├── research_output.json # phase 5 — structured output
- └── indication_dossier_report.md # phase 5 — the deliverable
- ```
-
- Schemas for every waypoint file are in `references/waypoint-schemas.md`.
- Waypoints are the resumable state. If the workdir already has waypoints, read
- them, summarize what's done, and ask which phase to resume from.
-
- ## Before starting
-
- Read `references/00-research-standards.md`. It governs sourcing and the
- anti-fabrication rules for every phase. Then create `<workdir>/waypoints/`.
-
- ## Workflow
-
- The dossier is built in five phases. After each phase, write the waypoint
- file and emit a ≤200-word summary of what you found and what's uncertain,
- then proceed directly to the next phase. The one exception is Phase 1: after
- writing `meta.json`, show the resolved indication identity and end the turn
- with a concise request for **Proceed**, **Revise identity**, or **Stop**. Do
- not start the expensive phases until the user answers; Wisp has no separate
- interactive-question tool that can be called from the workflow.
-
- ### Phase 1 — Meta initialization
-
- Read `references/01-meta-initialization.md`. Resolve the indication identity:
- clinical definition, ICD codes, aliases, parent indication, and whether it's
- a recognized diagnostic entity. Run a quick CT.gov landscape scan. Stand up
- `waypoints/meta.json`.
+ | Input | Required | Meaning |
+ |---|---|---|
+ | `indication` | yes | e.g. "sarcopenia", "idiopathic pulmonary fibrosis" |
+ | `additional_context` | no | focus areas, parent indication, framing |
+ | `workdir` | no | waypoint/report location; default `./do_not_commit/indication-dossier-<slug>/` |
- ### Phase 2 — Epidemiology research
+ ## Tooling
- Read `references/02-epidemiology-research.md`. Characterize the population:
- diagnostic criteria, prevalence and incidence, demographics and risk factors,
- natural history. Use parallel subagents to search PubMed and the web
- simultaneously. Write `waypoints/epidemiology.json`.
+ Preferred: `clinical-trials` MCP for CT.gov, `pubmed` MCP for literature,
+ `WebSearch`/`WebFetch` for FDA guidance, specialty-society guidelines
+ (NCCN, AASLD, …), and CDC/WHO data; `WebFetch` for remote PDFs, `Read` for
+ local ones; `Agent` subagents for parallel evidence gathering. When a listed
+ MCP is not connected, say so and fall back to `WebSearch` against the public
+ site itself.
- ### Phase 3 — Biology & standard-of-care research
+ ## Run protocol
- Read `references/03-biology-soc-research.md`. Establish pathophysiology,
- biomarkers, approved therapies, treatment guidelines, and unmet need. Use
- parallel subagents: PubMed for biology, web for guidelines, FDA for
- approvals. Write `waypoints/biology_soc.json`.
+ Read `references/standards.md` first — it defines what counts as a citable
+ finding, the anti-fabrication rules, and the report style. Phase-by-phase
+ instructions live in `references/phases.md`; waypoint formats in
+ `references/waypoints.md`.
- ### Phase 4 — Regulatory & trials research
+ 1. **Identity.** Resolve definition, ICD codes, aliases, parent, diagnostic
+ status; quick CT.gov landscape count. Write `meta.json`. Then show the
+ resolved identity and end the turn asking **Proceed / Revise identity /
+ Stop** — the expensive phases wait for the answer (Wisp has no separate
+ interactive-question tool, so this is a normal turn end).
+ 2. **Epidemiology.** Case definition, prevalence/incidence, demographics,
+ natural history → `epidemiology.json`.
+ 3. **Biology & standard of care.** Mechanism, biomarkers, approved
+ therapies, guidelines, unmet need → `biology_soc.json`.
+ 4. **Regulatory & trials.** Accepted endpoints, precedents, design
+ parameters, landmark trials, failures → `regulatory_trials.json`.
+ 5. **Synthesis.** No new research threads (single targeted gap-fills only).
+ Write `indication_dossier_report.md` and `research_output.json`, then
+ mark `progress.json` complete.
- Read `references/04-regulatory-trials-research.md`. Establish FDA/EMA
- accepted endpoints, regulatory precedents, typical trial design parameters,
- landmark trials, and notable failures. Use parallel subagents: FDA for
- guidance/approvals, CT.gov for trial patterns, PubMed for trial-history
- reviews. Write `waypoints/regulatory_trials.json`.
+ After each of phases 2–5, write the waypoint, emit a ≤200-word summary of
+ findings and open uncertainties, and continue directly.
- ### Phase 5 — Synthesis
+ ## Resuming
- Read `references/05-synthesis.md` and `references/06-writing-style.md`. Read
- all four consolidated waypoint files. Write
- `waypoints/indication_dossier_report.md` — narrative sections in the order
- the synthesis reference specifies, with inline citations per the style guide
- — and `waypoints/research_output.json`. No new research threads in this
- phase. Targeted gap-fills are allowed: a single fetch to resolve a specific
- missing value in an existing waypoint field (an approval year, an NCT ID, a
- figure from a sponsor pipeline page). Anything broader than that, name as a
- gap rather than filling it.
+ When `workdir` already contains waypoints: list which phases are complete
+ (file exists and is non-empty), show the meta summary, and ask which phase to
+ run. Never overwrite an existing waypoint without confirmation.
- ## Resuming
+ ## Output layout
- If invoked with a `workdir` that already contains waypoints: list which phases
- are complete (waypoint file exists and is non-empty), show the meta summary,
- and ask the user which phase to run next. Never overwrite an existing waypoint
- without confirmation.
+ ```
+ <workdir>/waypoints/
+ ├── progress.json # loop control, flipped last
+ ├── meta.json # phase 1
+ ├── epidemiology.json # phase 2
+ ├── biology_soc.json # phase 3
+ ├── regulatory_trials.json # phase 4
+ ├── sources_evaluated.json # appended by every phase
+ ├── research_output.json # phase 5, structured
+ └── indication_dossier_report.md # phase 5, the deliverable
+ ```