Deep Research

Deep Research

This skill orchestrates a multi-phase academic research workflow. It is citation-disciplined: every claim in the final output must resolve to a real source reachable through one of the configured paper MCP servers. Hallucinated DOIs are a failure mode, not a typo -- they get caught and rejected here, not after the fact.

When to use which mode

If the user did not specify, infer from their phrasing. Default to socratic when the question is too broad to research without scoping. See references/mode_selection.md.

How to invoke

User can pass --mode {name} and a topic via slash command (/research --mode lit-review "ion-gated transistors for reservoir computing") or by free text. Read the args; if none, infer from the prompt.

Iron Rules (apply to every mode)

1. No claim without a citation that resolves through Semantic Scholar, OpenAlex, arXiv, or a publisher DOI. If a claim cannot be cited, mark it as [UNVERIFIED] and either drop it or escalate it to the user -- never invent a citation.
2. The devils-advocate agent runs at three checkpoints: after scoping, after synthesis, after composition. It can block progression if claims are weak or sources gray-zone. See agents/devils-advocate.md.
3. The ethics agent can halt delivery when the topic crosses into harm-enablement territory (weapons synthesis, targeted harassment, etc.). See agents/ethics.md.
4. Socratic mode never gives direct answers -- only guiding questions. If the user demands an answer, exit Socratic mode explicitly and re-enter via a different mode.
5. Vault writes go to 00_Inbox/, not 30_Literature/. The user curates and promotes. This matches the user's feedback_obsidian_writes.md rule.
6. Capture every paper you actually read. Whenever an agent fetches and reads a paper's full text (not just the abstract), call the paper-capture skill so it lands in 30_Literature/. Do not skip this -- the whole point of the pack is that papers consumed during research are reusable on the next project.

Phases (every mode runs through these in order)

1. Scoping -- sharpen the research question, choose the mode, write a methodology blueprint.
2. Scope confirmation (mandatory pause; see Scope Confirmation Protocol below). Skip ONLY in quick and fact-check modes.
3. Investigation -- search the MCP servers in priority order (see below), download and read promising papers. Spawn the parallel investigator sub-agents listed under "Spawning sub-agents".
4. Analysis -- synthesize across sources, run risk-of-bias on each, build a claim/evidence table.
5. Composition -- draft the deliverable in the mode-appropriate format.
6. Review -- editorial pass + ethics check + devil's advocate final pass.
7. Citation pre-flight (mandatory; see Citation Pre-flight Protocol below).
8. Hand-off -- write to vault 00_Inbox/research-{slug}-{YYYY-MM-DD}.md via the obsidian MCP.

Skip phases that don't apply (e.g. fact-check skips composition).

Scope Confirmation Protocol (mandatory pause after Phase 1)

In every mode EXCEPT quick and fact-check, after Phase 1 (Scoping) you MUST present the scope back to the user and wait for confirmation. Do not start Phase 3 (Investigation) until the user replies.

Format:

=== SCOPE CONFIRMATION ===

Before I search, here's how I'm reading your request:
- Topic:        {one sentence}
- Year range:   {YYYY-YYYY or "open"}
- Languages:    {English / multilingual / etc.}
- Inclusions:   {peer-reviewed lab, preprints OK, ...}
- Exclusions:   {blog posts, retracted papers, ...}
- Depth:        {quick / lit-review / full / systematic-review / review}
- Time budget:  {e.g. 5-15 min for a quick run}

Reply 'go' to proceed, or correct any of the above. I'll wait.

If the user's original request was genuinely vague (no topic, no scope at all), don't synthesize a scope -- drop into socratic mode instead.

Citation Pre-flight Protocol (mandatory before Phase 8 Hand-off)

After Composition (Phase 5) and the Review pass (Phase 6), and before writing the final note to the vault:

1. Walk every in-text citation in the draft. Extract the DOI / arXiv id / Semantic Scholar paperId for each.
2. For each citation, call mcp__semantic-scholar__get_semantic_scholar_paper_details (or mcp__paper-mcp__paper_get_metadata as fallback).
3. Compare the returned title/authors against what the draft claims:
   • Confirmed: title + first-author both match -> mark [verified] internally.
   • Mismatch: title doesn't match -- the draft cited the wrong DOI. Either fix the DOI (re-search Semantic Scholar) or replace the in-text reference with [UNVERIFIED -- DOI mismatch].
   • 404 / not-found: re-resolve via title-author-year search; if that also fails, replace with [UNVERIFIED -- could not re-confirm].
4. Surface the count of unverified to the user in the final delivery line: Captured N citations; M re-verified, K flagged unverified.
5. If K > 0, list each unverified citation in a ## Unverified Citations section at the bottom of the draft, with what was attempted.

Pre-flight is the integrity gate that catches the rare case where a sub-step of the pipeline (or the model itself) introduced a fabricated or mistyped DOI.

MCP server priority order

The investigator MUST try these in the order below. The order is biased toward broad-source coverage and institutional full-text access -- arXiv is only authoritative for preprints and is missing most journal-published work (Nature, Science, ACS Nano, Adv. Materials, Applied Physics Letters, most of EE/MatSci, biology, chemistry). Do NOT default to arXiv-only searches.

For SEARCH (broad coverage):

1. semantic-scholar -- best for metadata, paper resolution, citation graphs, abstract preview. Spans all journals + preprints.
2. paper-search -- multi-source unified search (arXiv, bioRxiv, medRxiv, PubMed, Google Scholar). Casts the widest net for preprints AND PMC open-access journal papers.
3. paper-mcp -- secondary metadata + DOI resolution path. Useful when a venue isn't well-indexed by Semantic Scholar.
4. arxiv -- only when the topic is explicitly preprint-relevant (recent CS / physics / quant-bio that hasn't been formally published yet, OR seminal preprints from those fields). Don't make arxiv the primary source for an applied-physics or experimental-biology topic -- you'll miss the journal corpus.

For FULL-TEXT DOWNLOAD (after a paper has been chosen):

5. university-paper-access -- institutional download path via Unpaywall + on-campus IP. First choice for full-text PDF of any journal paper. Often returns a legal full-text where the user has institutional access.
6. arxiv (download_paper) -- for arXiv ids only. Free, reliable, but only covers what's posted to arXiv.
7. paper-search (download_*) -- per-source download from bioRxiv/medRxiv/PubMed/PMC.
8. scihub -- last-resort PDF when institutional access fails. Note legal/network limitations.

Always prefer abstract-level reasoning before downloading PDFs. Only download a paper when an agent has decided it actually needs the full text. Then capture it via the paper-capture skill (Iron Rule 6).

Spawning sub-agents

Use the Agent tool with subagent_type=Explore for searches and subagent_type=general-purpose for synthesis/composition. Cap at 3 parallel agents. Each agent prompt lives in agents/ -- load the file with Read and pass its body as the agent prompt, prepended with the specific topic.

For a full run, the recommended spawn pattern is:

• Phase 1: 1x scoping agent (sequential).
• Phase 2: 3x investigator agents in parallel -- one per top-level subtopic. Each may make several MCP calls.
• Phase 3: 1x synthesizer + 1x bias-auditor in parallel, sharing the Phase 2 output.
• Phase 3.5: 1x devils-advocate (checkpoint 1).
• Phase 4: 1x composer (sequential, large context).
• Phase 5: 1x editor + 1x ethics + 1x devils-advocate (checkpoint 2 & 3) in parallel.

For quick, run scoping -> 1x investigator -> 1x composer -> 1x devils-advocate. Skip bias auditor.

For socratic, never spawn agents. Stay in the main loop and ask questions until the user has a researchable question, then propose a mode.

Mode-specific instructions

Read the mode file before starting:

• modes/full.md
• modes/quick.md
• modes/lit-review.md
• modes/fact-check.md
• modes/socratic.md
• modes/systematic-review.md
• modes/review.md

Templates

Use these as the skeleton for the deliverable:

• templates/report_full.md
• templates/report_lit_review.md
• templates/prisma_flow.md
• templates/claim_evidence_table.md

Citation format

APA 7.0 in-text and reference list. For each cited source:

• DOI mandatory if it exists; arXiv id otherwise; URL only if neither.
• Mark provenance: [SS] Semantic Scholar / [XV] arXiv / [UPA] university-access / [SH] Sci-Hub. This trail is what makes the integrity gate falsifiable.

Hand-off note format

The vault note dropped in 00_Inbox/ MUST include:

---
type: research-output
mode: {mode}
topic: {topic}
date: {YYYY-MM-DD}
status: draft           # draft -> reviewed -> promoted
papers_captured: [{citekey1}, {citekey2}, ...]
---

followed by the body and a final ## Provenance section listing every MCP call made and every paper downloaded. Reviewers (you in three months, or a collaborator) should be able to reproduce the search.

Iron Rule reference

Read references/iron_rules.md at the start of every run. If you're not sure whether something violates a rule, stop and ask the user.