---
name: docxology/template-deep-research
source: https://app.decimal.ai/s/docxology-template-deep-research@1/SKILL.md
source_sha256: 4e06f2959d19
---

# Deep research

Template-native research workflow. This skill routes to existing repository
systems instead of running an autonomous external agent suite.

## Natural invoke

- "Research this topic and build the source corpus"
- "Do a literature review with citation keys"
- "Fact-check these manuscript claims"
- "Guide me from vague research interest to answerable question"
- "Plan a systematic review with inclusion and exclusion criteria"

## Inputs to confirm

- **Research goal** - question, audience, and expected deliverable.
- **Mode** - full, quick, lit-review, fact-check, guided, or systematic-review.
- **Corpus source** - arXiv, Crossref, local JSON corpus, provided papers, or project artifacts.
- **Project target** - if results feed a manuscript, use `docs/_generated/active_projects.md`.

## Workflow

1. **Question framing** - turn vague topics into scoped research questions, explicit in/out boundaries, and search terms. Guided mode asks before converging.
2. **Source discovery** - use `infrastructure.search.literature` and project-local corpora; record query, backend, date, DOI/arXiv IDs, and failures.
3. **Source verification** - resolve every candidate reference against Crossref / OpenAlex / arXiv with the deterministic reference-existence gate before it enters the corpus; reject `fabricated`/`mismatch` records, surface `unverifiable`/`unchecked` honestly, and never invent unavailable bibliographic fields. This is the tier-0 anti-leakage step: flag the gap, do not hallucinate the citation.
4. **Synthesis** - hand off to [literature-synthesis](../literature-synthesis/SKILL.md) for per-paper notes, thematic clusters, contradictions, and gap analysis.
5. **Claim bridge** - when research supports manuscript prose, create citekey-linked notes that [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md) can audit later.

## Deliverables

- Research brief: question, scope, search strategy, corpus table, and evidence gaps.
- Literature synthesis with bracket-key citations and source-tier notes.
- Fact-check report: claim, source, verdict, uncertainty, action.
- For systematic review mode: protocol draft, inclusion/exclusion criteria, screening counts, and limitations.

## Verification commands

```bash
uv run python -m infrastructure.search.literature search "QUERY" --max-results 20
uv run python -m infrastructure.reference.citation validate projects/<project>/manuscript/references.bib
uv run python -m infrastructure.reference.verification verify projects/<project>/manuscript/references.bib --live --json
uv run python -m infrastructure.validation.cli evidence projects/<project> --fail-on-issues
```

## References

- [MODE_REGISTRY.md](../MODE_REGISTRY.md)
- [literature-synthesis](../literature-synthesis/SKILL.md)
- [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md)