「pubmed」の検索結果

Generates academic reviews for molecules in diseases using PubMed research. Invoke when user needs biomedical literature review with Vancouver citation format.

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Extracts clinical trial baseline data (study, region, participants, etc.) from article text or PMID. Checks PubMed for metadata; always falls back to LLM extraction for full details.

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Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles.

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A multi-stage workflow for writing long-form medical reviews; used when the user needs to build an outline based on PubMed literature, write chapter by chapter, perform supplementary searches, and format citations; input is the review topic and project directory, output is a c...

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Automatically find references for academic paper Markdown files. Reads full paper text, identifies each knowledge point requiring citation (epidemiological data, mechanism descriptions, existing research conclusions, etc.), searches PubMed for 3-5 most relevant articles per kn...

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Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date filters, or adapt a query across multiple databases. Also triggers when the user says "help me search for papers on X", "build a search strategy", "what are the MeSH terms for", or "I need a systematic review search string".

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Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.

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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.

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This skill should be used when the user asks to "search for papers", "find research papers", "search arXiv", "search PubMed", "look up a DOI", "download a paper", "search IEEE", or "search Scopus".

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Benchmark LLM reference recommendation capabilities by verifying every cited paper against Crossref, PubMed, arXiv, and DBLP. Measures hallucination rate, per-field accuracy (title/author/year/DOI), discipline breakdown, and year constraint compliance. Supports tool-augmented (ReAct + web search) mode. Use when the user asks to evaluate, benchmark, or compare models on academic reference hallucination, literature recommendation quality, or citation accuracy.

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Benchmark LLM reference recommendation capabilities by verifying every cited paper against Crossref, PubMed, arXiv, and DBLP. Measures hallucination rate, per-field accuracy (title/author/year/DOI), discipline breakdown, and year constraint compliance. Supports tool-augmented (ReAct + web search) mode. Use when the user asks to evaluate, benchmark, or compare models on academic reference hallucination, literature recommendation quality, or citation accuracy.

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Agents should invoke this skill for academic or technical papers, arXiv/PubMed/IEEE/ACM links, PDFs, methodology review, limitations, practical implications, or extracting findings for engineering decisions.

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ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.

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Conducting systematic, scoping, and narrative literature reviews. Covers PRISMA/PRISMA-ScR protocols, search strategy (Boolean, MeSH), database selection (PubMed, Scopus, Web of Science, Embase), screening, data extraction, evidence synthesis (narrative, meta-analysis, thematic), and reporting. Use when planning or executing a formal literature review.

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Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search use openalex-database.

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HuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes, diseases, chemicals), relation extraction, QA, text classification, abstract summarization. Covers loading, biomedical tokenization, inference pipelines, fine-tuning. Alternatives: spaCy en_core_sci_lg (rule-based NER), Stanza (biomedical models), NLTK.

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Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.

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Use when checking whether a manuscript's references are real. Audits each citation against PubMed and CrossRef, flags fabricated or mismatched entries and writes qc/reference_audit.json. Audit-only; never edits references or refs.bib. Citation-key checks are /manage-refs.

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Use when finding papers or building a reference list. Searches PubMed, Semantic Scholar and bioRxiv/medRxiv, includes only references verified through an API, and generates BibTeX. Auditing an existing reference list is /verify-refs.

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Use when users ask to 找文献、做文献检索、查论文、查临床试验、核验引用、去重文献、设计 PubMed/MeSH 检索式、追踪上下游引文、解析 DOI/PMID/PMCID/arXiv/OpenAlex/Semantic Scholar/NCT ID， 或导出 RIS、BibTeX、NBIB、ENW；also use for multi-source academic search, citation verification, citation graphs, trial registration search, research workflows, or DeepSeek Harness academic-search MCP setup.

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Search NCBI databases using Biopython Bio.Entrez (ESearch, EInfo, EGQuery, ESpell). Use when finding records by keyword, building reproducible field-qualified queries, navigating the Entrez Query Translator, exploiting the history server for large result sets, handling retmax caps, or interpreting weekly index lag. Covers PubMed, Nucleotide, Protein, Gene, SRA, GEO, Assembly, Taxonomy, ClinVar, dbSNP.

日本語の概要は準備中です。原文の説明を表示しています。

Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

日本語の概要は準備中です。原文の説明を表示しています。