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      {
        "title": "Literature Review",
        "body": "Help write academic literature reviews using a multi-engine search integration (S2, OA, CR, PM)."
      },
      {
        "title": "Capabilities",
        "body": "Multi-Source Search: Find relevant academic papers using Semantic Scholar (S2), OpenAlex (OA), Crossref (CR), and PubMed (PM).\nFull Abstracts: All sources now return complete abstracts (PubMed uses efetch for full XML records).\nDOI Extraction: DOIs are extracted from all sources for cross-referencing and deduplication.\nAutomatic Deduplication: When searching multiple sources (--source all or --source both), results are automatically deduplicated by DOI.\nPolite Access: Automatic email identification for OpenAlex/Crossref \"Polite Pool\" (via USER_EMAIL env var).\nAbstract Reconstruction: Reconstructs abstracts from OpenAlex inverted index format.\nSynthesis: Group papers by theme and draft review sections based on metadata."
      },
      {
        "title": "Environment Variables",
        "body": "VariablePurposeDefaultUSER_EMAILEmail for polite API accessanonymous@example.orgCLAWDBOT_EMAILFallback if USER_EMAIL not set—SEMANTIC_SCHOLAR_API_KEYOptional S2 API key for higher rate limits—OPENALEX_API_KEYOptional OpenAlex API key—"
      },
      {
        "title": "1. Broad Search (All Bases)",
        "body": "Get a comprehensive overview from all major academic databases. Results are automatically deduplicated by DOI.\n\npython3 scripts/lit_search.py search \"impact of glycyrrhiza on bifidobacterium\" --limit 5 --source all"
      },
      {
        "title": "2. Targeted Search",
        "body": "OpenAlex (oa): Fast and comprehensive, good abstracts.\nSemantic Scholar (s2): High-quality citation data and TL;DRs.\nCrossref (cr): Precise DOI-based metadata (no abstracts).\nPubMed (pm): Gold standard for biomedical research, full abstracts and PMIDs.\n\npython3 scripts/lit_search.py search \"prebiotic effects of liquorice\" --source pm"
      },
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        "title": "3. Comparing Sources",
        "body": "Search both S2 and OA simultaneously to ensure nothing is missed. Deduplicated by default.\n\npython3 scripts/lit_search.py search \"Bifidobacterium infantis growth\" --source both"
      },
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        "title": "4. Getting Full Details (S2)",
        "body": "Retrieve detailed metadata including TL;DR summaries.\n\npython3 scripts/lit_search.py details \"DOI:10.1016/j.foodchem.2023.136000\""
      },
      {
        "title": "5. Writing the Review",
        "body": "Extract: Pull key findings from the abstracts found.\nOrganize: Group findings into a logical structure (e.g., chronological or thematic).\nDraft: Use the \"Think step-by-step\" approach to synthesize multiple sources into a coherent narrative."
      },
      {
        "title": "Output Format",
        "body": "Each result includes:\n\nid: Source-specific identifier (PMID for PubMed, OpenAlex ID, S2 paper ID, DOI for Crossref)\ndoi: DOI when available (used for deduplication)\ntitle: Paper title\nyear: Publication year\nauthors: List of author names\nabstract: Full abstract text (when available)\nvenue: Journal or conference name\ncitationCount: Citation count (S2, OA)\nsource: Which database the result came from"
      },
      {
        "title": "Tips for Success",
        "body": "Citations: Always cross-reference the DOI or PMID for accuracy in bibliography.\nFiltering: Focus on papers with higher citationCount or recent years for a more modern review.\nPubMed for Medicine: Use --source pm for the most reliable biomedical literature.\nDeduplication: Multi-source searches automatically remove duplicates; use single sources if you need raw counts."
      }
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    "body": "Literature Review\n\nHelp write academic literature reviews using a multi-engine search integration (S2, OA, CR, PM).\n\nCapabilities\nMulti-Source Search: Find relevant academic papers using Semantic Scholar (S2), OpenAlex (OA), Crossref (CR), and PubMed (PM).\nFull Abstracts: All sources now return complete abstracts (PubMed uses efetch for full XML records).\nDOI Extraction: DOIs are extracted from all sources for cross-referencing and deduplication.\nAutomatic Deduplication: When searching multiple sources (--source all or --source both), results are automatically deduplicated by DOI.\nPolite Access: Automatic email identification for OpenAlex/Crossref \"Polite Pool\" (via USER_EMAIL env var).\nAbstract Reconstruction: Reconstructs abstracts from OpenAlex inverted index format.\nSynthesis: Group papers by theme and draft review sections based on metadata.\nEnvironment Variables\nVariable\tPurpose\tDefault\nUSER_EMAIL\tEmail for polite API access\tanonymous@example.org\nCLAWDBOT_EMAIL\tFallback if USER_EMAIL not set\t—\nSEMANTIC_SCHOLAR_API_KEY\tOptional S2 API key for higher rate limits\t—\nOPENALEX_API_KEY\tOptional OpenAlex API key\t—\nWorkflows\n1. Broad Search (All Bases)\n\nGet a comprehensive overview from all major academic databases. Results are automatically deduplicated by DOI.\n\npython3 scripts/lit_search.py search \"impact of glycyrrhiza on bifidobacterium\" --limit 5 --source all\n\n2. Targeted Search\nOpenAlex (oa): Fast and comprehensive, good abstracts.\nSemantic Scholar (s2): High-quality citation data and TL;DRs.\nCrossref (cr): Precise DOI-based metadata (no abstracts).\nPubMed (pm): Gold standard for biomedical research, full abstracts and PMIDs.\npython3 scripts/lit_search.py search \"prebiotic effects of liquorice\" --source pm\n\n3. Comparing Sources\n\nSearch both S2 and OA simultaneously to ensure nothing is missed. Deduplicated by default.\n\npython3 scripts/lit_search.py search \"Bifidobacterium infantis growth\" --source both\n\n4. Getting Full Details (S2)\n\nRetrieve detailed metadata including TL;DR summaries.\n\npython3 scripts/lit_search.py details \"DOI:10.1016/j.foodchem.2023.136000\"\n\n5. Writing the Review\nExtract: Pull key findings from the abstracts found.\nOrganize: Group findings into a logical structure (e.g., chronological or thematic).\nDraft: Use the \"Think step-by-step\" approach to synthesize multiple sources into a coherent narrative.\nOutput Format\n\nEach result includes:\n\nid: Source-specific identifier (PMID for PubMed, OpenAlex ID, S2 paper ID, DOI for Crossref)\ndoi: DOI when available (used for deduplication)\ntitle: Paper title\nyear: Publication year\nauthors: List of author names\nabstract: Full abstract text (when available)\nvenue: Journal or conference name\ncitationCount: Citation count (S2, OA)\nsource: Which database the result came from\nTips for Success\nCitations: Always cross-reference the DOI or PMID for accuracy in bibliography.\nFiltering: Focus on papers with higher citationCount or recent years for a more modern review.\nPubMed for Medicine: Use --source pm for the most reliable biomedical literature.\nDeduplication: Multi-source searches automatically remove duplicates; use single sources if you need raw counts."
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