research-hub

Use research-hub to operate Zotero, Obsidian, and NotebookLM research workflows through CLI, MCP, REST, and dashboard. Trigger when the user asks to find papers, ingest sources, organize a literature review, build Obsidian research notes, upload sources to NotebookLM, inspect clusters, generate AI briefs, or maintain a research vault.

Turn a list of papers (Zotero collection, Obsidian cluster, manual list) into a compact comparison matrix written to .research/literature_matrix.md, instead of generic per-paper summaries. Use when the user asks to "make a literature matrix", "compare these papers by method/data/limitations", or "decide which papers are central to my review". If the user says "extract the claims from these papers": cross-paper comparison matrix → this skill; claims from their own manuscript draft → `paper-memory-builder`; per-cited-paper Key Findings → `paper-summarize`. This skill compares a KNOWN paper set; to turn a research area into a go/no-go decision on a candidate thesis/proposal topic, use `gap-to-topic`.

After research-hub ingests a cluster of cited papers, fill the per-paper Key Findings + Methodology + Relevance sections in BOTH Obsidian markdown and the Zotero child note. Use when the user says "fill the TODO Key Findings/Methodology blocks left by research-hub auto", "I just ran auto and don't know what these papers are about", or "summarize the papers in cluster X". Invokes a supported LLM CLI on each paper's abstract. NOT for summarizing the user's own manuscript draft — that's `paper-memory-builder`. NOT for cluster-level briefs — that's `research-hub notebooklm generate`. This skill is per-cited-paper only. If the user says "extract claims from these papers", disambiguate before acting: their own manuscript draft → `paper-memory-builder`; a cross-paper comparison matrix → `literature-triage-matrix`; per-cited-paper Key Findings → this skill.

Operate research-hub workflows for literature discovery, source ingest into Zotero/Obsidian/NotebookLM, dashboard inspection, and vault maintenance. Use when the user asks to find papers and organize them, build a knowledge base, ingest a folder of PDFs, upload to NotebookLM, generate research briefs, inspect clusters, or maintain a research vault. NOT for auditing or cleaning up an existing Zotero library — that's `zotero-library-curator` (read-only audit) plus `zotero-skills` (for CRUD).

Research-domain router that writes `.coord/multi_ai_plan.md` when a single round of work will need two or more delegates AND the work touches research-hub artifacts (`.research/`, `.paper/`, Zotero/Obsidian/NotebookLM pipelines). For a single delegate, use `codex-delegate` or `gemini-delegate` directly — do not invoke this skill. For generic non-research multi-agent decomposition (pure code refactor, generic translation, no research-hub artifact), use `agent-collab-workspace:agent-task-splitter` instead (different artifact `.coord/plan.yml`, different scope). The router decides task splitting, dependency ordering, and reconciliation; the leaves execute.

Audit and curate a Zotero library — find duplicate DOIs, orphan items missing required tags, propose collection rebinds, identify bloated or under-used collections, generate tag hygiene reports, emit preview-only cleanup plans. Use when the user asks to "audit Zotero", "find duplicates", "tag hygiene report", "which collections are bloated or under-used", or "propose a Zotero cleanup plan". Defers all CRUD operations to the standalone `zotero-skills` skill or `research-hub zotero` CLI. Includes a backup-first reminder before any apply/CRUD handoff suggestion.

Convert a paper draft + figures + Zotero metadata into reusable .paper/claims.yml and .paper/figures.yml files so the academic-writing-skills skill can do writing, revision, and audit passes without re-reading the manuscript every time. Use when the user asks to "build paper memory", "extract claims from this manuscript", "extract claims, supporting evidence, and figure key numbers", or "prepare this paper for AI-assisted writing". NOT for summarizing cited papers in a literature cluster — that's `paper-summarize`. This skill is for the user's own manuscript draft only.

Guide a researcher through 5 Socratic segments — research question sharpening, expected mechanism, identifiability check, validation plan, risk register — and produce `.research/design_brief.md`. Use when the user asks to "frame this research question", "design my study", "help me think through what model to build", "sharpen my hypothesis", "is my research question sharp enough to be falsifiable?", or "before I start coding, walk me through the design". Runs AFTER a topic is chosen — it designs the study for a given question; to decide whether a research gap is worth pursuing at all (open / a contribution / feasible), use `gap-to-topic`. Does NOT write the model spec; does NOT invent the research question — guides the human to articulate them.

Inspect a research repository and write a compact `.research/` workspace manifest (project_manifest.yml, experiment_matrix.yml, data_dictionary.yml) so future AI sessions can orient themselves without rescanning the whole repo. Use when the user asks to "compress this project context", "create a research manifest", or "save the project context for future agents".

Turn a research area into a go/no-go decision dossier for ONE candidate thesis/proposal topic — a 3-gate verdict (is the gap open? is it a contribution? is it feasible?) with the evidence laid out so the researcher can verify it. Use when the user asks "is this gap worth pursuing", "help me pick a thesis topic", "is this idea already taken", "find me a defensible research gap", "vet this research idea before I commit", or "should I do this". NOT a literature review (use `literature-triage-matrix` for a comparison matrix) and NOT a study design (use `research-design-helper` once a topic is chosen). Produces a `.research/topic_dossier.md`, a `.research/topic_dossier.docx` (Word, colour-coded), a `.bib`, and a `.gaps.yml`.

Read the .research/ manifest files at a project root and produce a single orientation memo (research question, datasets, current stage, key entrypoints, evidence artifacts, open questions). Use when the user asks to "orient me in this project", "what is this repo about", or "build a context map for this paper" — and the project already has .research/ manifests (or trigger research-context-compressor first).

Compare a downloaded NotebookLM brief against the source bundle research-hub uploaded, and report missed sources, unsupported claims, contradictions, and recommended follow-up prompts. Use when the user asks to "verify this NotebookLM brief", "check if the brief missed anything", or "compare downloaded notes to the cluster papers".