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.

Framing

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}".

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.

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.

Phase 2 — Epidemiology research

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.

Phase 3 — Biology & standard-of-care research

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.

Phase 4 — Regulatory & trials research

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.

Phase 5 — Synthesis

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.

Resuming

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.