firecrawl-research-index

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name: firecrawl-research-index
description: Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.
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# Firecrawl Research Index

Find the research papers that answer a research query. Some questions have a single answer; many have several — and when in doubt, lean toward returning the fuller relevant set (most relevant first) rather than narrowing to one. A reader is better served seeing the neighboring methods and papers than having them silently dropped.

## What is in the index

Paper abstracts, with full text reachable per paper. The largest share of the corpus is **biomedical and life-science** literature — **PubMed** journal articles plus **bioRxiv** and **medRxiv** preprints — so clinical, drug, gene, disease, epidemiology, and public-health questions are in scope. **arXiv** preprints cover computer science, physics, and mathematics. Coverage outside those sources is thinner: a paper that exists only behind a publisher paywall or in a niche venue may not be indexed, and the general web tools below are the fallback when it isn't.

There is **no fixed recipe**. Read the query, decide what kind it is, and choose the approach below. Some queries need a single search; others need heavy structural/semantic expansion. Don't run machinery a query doesn't call for.

## The tools, and what each is uniquely good at

- MCP: **`firecrawl_research_search_papers(query, k?)`**
  CLI: **`firecrawl research search-papers <query> [--k <number>]`**
  Semantic (HyDE) search over **abstracts**. The natural first move for almost any query.
  If results look thin or all-alike, re-run with a different framing (sibling domain, rival method, dataset/benchmark name) rather than giving up.

- MCP: **`firecrawl_research_related_papers(seed_ids, intent, mode?, k?)`**
  CLI: **`firecrawl research related-papers <seedIds...> --intent <intent> [--mode <similar|citers|references>] [--k <number>]`**
  Semantic and structural expansion, ranked to your `intent`.
  This reaches papers semantic search _cannot_, and it's how you turn one good hit into the rest of a set.
  `mode=similar` → niche siblings; `citers` → who uses/builds on the seeds; `references` → what they build on / compare against.

- MCP: **`firecrawl_research_inspect_paper(id)`**
  CLI: **`firecrawl research inspect-paper <id>`**
  Canonical metadata for **one** paper: title, abstract, authors, categories, source ids, and dates.
  Use it after `search_papers` or `related_papers` when you need the complete citation/metadata for a candidate, or when you have an id from elsewhere and need to confirm what paper it resolves to.
  This does **not** read the paper body; use `read_paper` for specific full-text questions.

- MCP: **`firecrawl_research_read_paper(id, question)`**
  CLI: **`firecrawl research read-paper <id> --question <question>`**
  In-body passages of **one** paper, to verify a load-bearing constraint (a method actually used, a score actually reported, an affiliation, what a paper compares to).
  Use it to settle a specific doubt, not on everyt