Start, structure, and grow a persistent research wiki indexed in pro-workflow's SQLite knowledge base. Each wiki is a folder of markdown pages with provenance, plus a shadow FTS5 index so any session can recall it. Use when the user says "start a wiki", "add to wiki", "compile a page", "wiki on X", or wants a long-lived knowledge base on a topic, paper, product, person, project, or codebase.
npx skills add https://github.com/rohitg00/pro-workflow --skill wiki-builder
Persistent knowledge base for any topic. Markdown on disk + SQLite FTS5 shadow index.
~/.pro-workflow/wikis/<slug>/ — default, never committed<project>/.claude/wikis/<slug>/ — pass --scope project, committableBoth register in the same ~/.pro-workflow/data.db.
| Flavor | Use for |
|--------|---------|
| research | ongoing topic exploration |
| paper | one-paper deep dive |
| domain | broad subject area |
| product | product/tool KB |
| person | researcher/founder dossier |
| organization | company/lab profile |
| project | internal project KB |
| codebase | symbol/file-aware KB tied to a repo |
| incident | post-mortem KB |
<slug>/
├── wiki.config.md # purpose, audience, page types, style, auto_research block
├── raw/ # untouched source material (PDFs, scrapes, transcripts)
├── wiki/
│ └── index.md # entry point, hand-curated TOC
├── derived/ # generated artifacts (surveys, charts, summaries)
├── prompts/ # per-task prompts (compile-page, lint, query)
├── logs/maintenance-log.md
└── sources.md # one row per source: id | url | title | hash | fetched_at
Flavor adds folders: wiki/papers, wiki/concepts, wiki/people, wiki/products, wiki/timelines, wiki/questions.
node $SKILL_ROOT/scripts/wiki-cli.js init <slug> --title "X" --flavor research [--scope project] [--root <path>]
node $SKILL_ROOT/scripts/wiki-cli.js list
node $SKILL_ROOT/scripts/wiki-cli.js page <slug> <rel-path> --title "X" [--type concept|paper|person|...] [--from-file path]
node $SKILL_ROOT/scripts/wiki-cli.js reindex <slug>
node $SKILL_ROOT/scripts/wiki-cli.js info <slug>
init runs init_wiki.sh (mirrors dair layout) AND registers the wiki in SQLite. page writes markdown + upserts FTS row.
wiki.config.md of the target wiki before any compile.wiki/ must cite a row in sources.md (one citation = one source row).wiki-cli.js page so FTS index stays in sync.logs/maintenance-log.md per change.wiki/index.md if new top-level page.tool-use-benchmarks.md, not 2026-05-08-notes.md).> SPECULATION: block.Wikis with private: true in config never get fetched from web sources by wiki-research-loop. Local raw/ only.
Phase 3.3.0 ships builder + query only. Loop arrives in 3.3.1. To prep, wiki.config.md may include:
auto_research:
enabled: false # flip in 3.3.1
max_pages_per_run: 5
max_depth: 3
budget_usd: 0.50
fetchers: [web, arxiv, github]
See templates/ for wiki.config.md, index.md, prompt files. init_wiki.sh copies these into the new wiki root.
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
Take rohitg00/wiki-builder from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.