'biomedical' 검색 결과

Search PubMed biomedical literature database

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The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to

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Screens biomedical / life-science papers for signs of data fabrication, image manipulation, and statistical anomalies, using the detection techniques distilled from the field's canonical exposure platforms (PubPeer, Data Colada, Science Integrity Digest, For Better Science) and tools (ImageTwin/Proofig, statcheck, GRIM/GRIMMER, Problematic Paper Screener, Seek & Blastn). Use when asked to check a paper/figure for image duplication, blot splicing, impossible statistics, paper-mill or tortured-phrase signals, research integrity, or "is this data faked"; or when a user shares a figure, Western blot, supplementary dataset, or DOI and asks whether it looks manipulated. Reports observable anomalies as questions for clarification — it never accuses anyone of fraud.

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Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.

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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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Use Flair for NLP annotation, embeddings, text/sequence model prediction, corpus loading, training/fine-tuning, HunFlair biomedical NER/linking, and production troubleshooting.

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Find and synthesize research papers, whitepapers, PDFs, technical reports, and academic sources with Firecrawl Research, using semantic paper search, related-paper expansion, and in-body verification over Firecrawl's paper index — largely biomedical and life-science literature from PubMed, bioRxiv, and medRxiv, plus arXiv preprints in CS, physics, and math. Use when the user wants a literature review, systematic review, survey of studies, paper summary, research landscape, or sourced synthesis from scholarly and industry publications, including clinical, drug, gene, disease, epidemiology, and public-health topics. Prefer this over a general web-research workflow whenever the evidence base is published papers rather than web pages.

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Produce an intensive, cited analytical report: executive summary, multi-angle findings, contrarian views, open questions, and full sources. Use only when the user needs rigorous synthesis of a complex topic (scientific, technical, policy, or market-analytical) that cannot be answered with a short search, and wants a formal written report, not a recommendation list. Do not use for product picks, top-N lists, quick lookups, or routine "find out about X" tasks. If the request does not clearly need this kind of report, do not use this skill. Do not use for a literature review over published papers. This skill collects evidence from the open web. A request for the literature on a biomedical, clinical, life-science, or other scientific topic — papers, studies, trials, preprints — belongs to firecrawl-research-papers, which queries Firecrawl's paper index (PubMed, bioRxiv, medRxiv, arXiv) instead of searching websites.

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Computes a numeric or categorical answer to a quantitative data-science question by cleaning and analyzing local data files (CSV, Excel, TSV, and scientific formats .npz/.fits/.h5) with pandas, numpy, and scipy. Use whenever a task ships its own dataset (in whatever local directory it provides) and asks you to derive a value via statistical, geospatial, temporal, ratio, percentage, growth-rate, correlation, signal-processing, orbital, or forecasting analysis. Spans domains including archeology (demographics, paleoclimate proxies, radiocarbon dating, historical conflicts); biomedical/bioinformatics (tumor histology, genes, proteins, peptides, genomic variants); environmental (water quality, bacterial/Enterococcus exceedance, rainfall correlations, environmental justice); legal/consumer (fraud, identity theft, consumer complaints by state/metro); wildfire (incidents, causes, suppression costs, acres burned, fatalities, geospatial intersections); and astronomy/heliophysics/space weather (satellite telemetry TLE/Swarm/SP3, indices OMNI/GOES, solar activity, atmospheric density, orbital mechanics, forecasting).

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Find and synthesize research papers, whitepapers, PDFs, technical reports, and academic sources with Firecrawl Research, using semantic paper search, related-paper expansion, and in-body verification over Firecrawl's paper index — largely biomedical and life-science literature from PubMed, bioRxiv, and medRxiv, plus arXiv preprints in CS, physics, and math. Use when the user wants a literature review, systematic review, survey of studies, paper summary, research landscape, or sourced synthesis from scholarly and industry publications, including clinical, drug, gene, disease, epidemiology, and public-health topics. Prefer this over a general web-research workflow whenever the evidence base is published papers rather than web pages.

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Produce an intensive, cited analytical report: executive summary, multi-angle findings, contrarian views, open questions, and full sources. Use only when the user needs rigorous synthesis of a complex topic (scientific, technical, policy, or market-analytical) that cannot be answered with a short search, and wants a formal written report, not a recommendation list. Do not use for product picks, top-N lists, quick lookups, or routine "find out about X" tasks. If the request does not clearly need this kind of report, do not use this skill. Do not use for a literature review over published papers. This skill collects evidence from the open web. A request for the literature on a biomedical, clinical, life-science, or other scientific topic — papers, studies, trials, preprints — belongs to firecrawl-research-papers, which queries Firecrawl's paper index (PubMed, bioRxiv, medRxiv, arXiv) instead of searching websites.

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Use this skill when reasoning about deep tech commercialization, biomedical engineering, drug delivery, material design, or overcoming institutional skepticism. Robert Langer, MIT professor and pioneer of drug delivery systems, approaches problems through first-principles engineering, interdisciplinary convergence, and relentless perseverance against consensus. Trigger this skill whenever the user is evaluating high-risk/high-reward research, deciding between incremental vs. paradigm-shifting impact, spinning out academic discoveries into startups, or designing physical/biological systems from scratch. Apply his frameworks to navigate patenting, funding, and translating lab science into real-world impact.

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Applies the operational and scientific frameworks of Stacey Gabriel (genomicist and sequencing platform leader at the Broad Institute). Use this skill whenever the user is designing large-scale biomedical research, operationalizing lab workflows, standardizing data governance, or transitioning from bespoke academic experiments to industrial-scale science. It is highly relevant for queries involving genomics, precision medicine, multiomics, cellular perturbation pipelines, or building massive datasets to fuel AI. Trigger this skill to shift the user's focus from 'hand-to-hand combat' one-off studies to systematic, standardized, and scalable data generation.

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Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological relationships across genes and proteins, drugs, diseases, phenotypes, pathways, biological processes, exposures and anatomy. Use this skill to search entities by name, pull direct neighbours and their evidence types, summarise the local network around a disease, and find direct or two-hop drug-disease connections for repurposing hypotheses. Also trigger on PrimeKG, kg.csv, Harvard Dataverse knowledge graph, disease_protein, drug_protein, indication and contraindication edges, or network pharmacology over a biomedical knowledge graph.

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Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.

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Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.

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Retrieves scientific papers from PubMed and creates plain-language research summaries. Use when users ask about medical research, scientific studies, clinical trials, disease treatments, or want to understand recent scientific literature on any biomedical topic.

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NLM PubTator3 实体级关系挖掘原子 skill — 在 PubMed 文献里检索"疾病-药物-基因-化学品-突变-物种-细胞系"的标注与关系三元组。当用户问"BTK 与肺曲霉病的关联文献"、"BTK 抑制剂(MeSH D000077180)在哪些研究被讨论"、"标注这些 PMID 中提到的所有疾病/药物/基因实体"、"ibrutinib 的 MeSH/DrugBank ID"、"voriconazole 与 CYP2C19 药物-基因相互作用"、"BRAF V600E 突变 / rs113488022 检索"、"实体共现 / co-mention / 关系挖掘 / 实体规范化 / NER / annotation / entity normalization / disease-gene association / drug-gene interaction / chemical-disease relation" 时使用。无需 API key,跨平台稳定。**实体级 + 关系级**定位 — 不做综合文献检索(走 pubmed-eutils / europepmc-search)、不做全文段落抽取(走 bioc-fulltext-fetch)、不做证据等级排序(走 medical-evidence-grading)。

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Validates predictive models on omics and biomedical data with nested cross-validation, group/batch/temporal-aware splits, the full data-leakage taxonomy, probability calibration, decision-curve net benefit, optimism correction, sample-size planning, and TRIPOD+AI reporting. Use when estimating model performance honestly, choosing a CV scheme, detecting leakage, or judging whether reported discrimination means the model is actually useful. For feature selection itself see machine-learning/biomarker-discovery; for confirmatory-trial inference see clinical-biostatistics/trial-reporting.

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