National Biomedical Information Services

国家生物医学信息服务

• 批准号: 10018448
• 负责人: Jerry Sheehan
• 金额: $ 32957.47万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10018448
• 关键词: Adverse event; African American; All of Us Research Program; Antibiotic-resistant organism; Antimicrobial Resistance; Archives; Area; Bibliographic Databases; Bioinformatics; Biological; Biomedical Computing; Biomedical Research; Biotechnology; Books; Breast Feeding; Catalogs; Centers for Disease Control and Prevention (U.S.); Characteristics; Clinical; Clinical Data; Clinical Practice Guideline; Clinical Research; Clinical Trials; Code; Collaborations; Collection; Combating Antibiotic Resistant Bacteria; Common Data Element; Communication; Communities; Competence; Computational Biology; DNA Sequence; Data; Data Collection; Data Quality; Data Science; Data Set; Data Sources; Databases; Development; Diagnostic; Diagnostics Research; Disasters; Drug Labeling; Education and Outreach; Educational Activities; Environment; Environmental Health; Escherichia coli; Family; Farming environment; Food; Fostering; Funding; Funding Agency; Genbank; Gene Proteins; General Population; Generations; Genetic; Genetic Sequence Databases; Genetic screening method; Genome; Genomics; Goals; Guidelines; Hazardous Chemicals; Hazardous Substances; Health; Health Professional; Health Promotion; Health Science Library; Health Sciences; Health Services Accessibility; Health Services Research; Health Technology; Healthcare; Herbal supplement; High-Throughput Nucleotide Sequencing; Hispanic Americans; History of Medicine; Hour; Human; Human Genome; Image; Imagery; Improve Access; Individual; Information Centers; Information Dissemination; Information Resources; Information Services; Information Specialists; Information Systems; Infrastructure; International; International Classification of Disease Codes; Intramural Research Program; Journals; Knowledge; Language; Librarians; Libraries; Link; Listeria; Literature; Maps; Measures; Medical; Medical Device; Medical Informatics; Medicine; MedlinePlus; Methods; Mission; Molecular Biology; Mothers; Names; Native Americans; Nuclear Accidents; Nursing infant; Package Insert; Pathogen detection; Patients; Pharmaceutical Preparations; Phenotype; Play; Policies; Policy Maker; Population; Positioning Attribute; Privatization; Process; Proteins; PubChem; PubMed; Public Health; Radiation Accidents; Readability; Readiness; Recipe; Records; Registries; Regulation; Reporting; Research; Research Personnel; Research Project Grants; Research Support; Resources; Retrieval; Role; SNOMED Clinical Terms; Salmonella; Sampling; Science; Software Tools; Solid; Source; Speed; Strategic Planning; Support System; Surveys; System; Systematized Nomenclature of Medicine; Technology; Testing; Text; Time; Toxicology; Toxicology Data Network; Training; Training Activity; Training Programs; Transcript; Travel; Trust; United States National Institutes of Health; United States National Library of Medicine; Update; Variant; Vendor; Vocabulary; Work; annotation system; authority; base; bioinformatics tool; biomedical informatics; biomedical information system; chemical decontamination; citizen science; clinical diagnostics; combat; data archive; data management; data sharing; data warehouse; database of Genotypes and Phenotypes; dietary supplements; dosage; drug resource; drug standard; environmental toxicology; exhibitions; experience; foodborne illness; foodborne pathogen; genome annotation; genome database; health data; health disparity; health information technology; health training; historical article; implantable device; improved; instrument; interoperability; journal article; language processing; liver injury; nerve agent; news; off-label drug; outreach; pathogen; patient portal; petabyte; precision medicine; preservation; programs; repository; research and development; research study; response; scientific computing; skills; text searching; tool; trend; usability

In FY19, NLM made significant progress on enhancing its National Biomedical Information Services as it: Added 1.35 million citations to the PubMed bibliographic database (now with 30 million citations to biomedical journal articles) and developed updated search technology and mobile optimization to be included in a new PubMed in late FY19. Added 600,000 articles to PubMed Central (PMC), which provides free public access to 5.5 million full text journal articles from research supported by NIH, other federal agencies, and private and international research funders. Launched the PMC Associated Data box to show data citations, availability, and supplementary materials to facilitate discovery of openly available datasets. Completed a multi-year partnership with Wellcome Trust to make thousands of articles from historical biomedical journals freely available via PMC Text Mining Collections. Partnered via the National Network of Libraries of Medicine (NNLM: more than 7,000 health science libraries and information centers) with public libraries to: educate consumers about precision medicine and the NIH All of Us Research Program in communities that are underrepresented in biomedical research; train health sciences librarians in research data management and data science; encourage citizen science; and improve access to high-quality science-based medical information online. Trained via NNLM more than 100,000 people (3,000 educational activities; 5,000 resource demonstrations); Supported 335 outreach and training activities for 200,000 users. Added 32,000 new clinical research studies and 6100 new results summaries to Clinicaltrials.gov (total of 318,000 studies and 39,000 summaries of study results and adverse events information). Contributed to implementation of regulations (42 CFR Part 11) and NIH policy for clinical trial transparency. Improved access to reference information on environmental health and toxicology by migrating information from TOXNET (e.g., TOXLINE, Hazardous Substances Data Bank, and Haz-Map) to PubMed and PubChem. Migrated MedlinePlus (information on medical tests, drugs, healthy recipes, and educational videos in 60 languages) to the cloud and doubled lab tests to 157. Via MedlinePlus Connect, linked EHRs and patient portals to consumer health information from MedlinePlus using standard codes and vocabularies. Coordinated clinical data standards for HHS and provided tools for exchanging, using, and facilitating interoperability of machine-readable clinical health data: added 240,000 implantable devices to AccessGUDID database (links FDA and SNOMED codes for medical devices) to support certified EHR requirements; Updated SNOMED CT to ICD10CM map in the Interactive Map Assisted Generation of ICD Codes (i-MAGIC) tool; Deepened support of CMS clinical quality measures in Value Set Authority Center; augmented NIH Common Data Element Repository with tools and content to facilitate data sharing, aggregation, collaboration, comparison, and usability. Enhanced drug information resources: Drug Information Portal, DailyMed (drug labeling information from package inserts for 110,000 drugs, with mobile access), Pillbox (rapid identification of unknown solid-dosage medications based on physical characteristics and images), LiverTox (clinical, diagnostic and research information and case registry on liver injury due to drugs, herbals and dietary supplements), and LactMed (effects of 1,300 drugs, dietary supplements, and diagnostic agents on breastfeeding mothers and their nursing infants; available in NCBI Books). DailyMed and Pillbox are linked to NLM's RxNorm standard drug names. Updated training classes for the Disaster Information Specialist Program that enables information professionals and librarians to be health information responders in their communities. NLM provides tools for hazardous materials and chemical, biological, radiological, and nuclear incidents (WISER, CHEMM, and REMM). Added information on fourth generation nerve agents per White House Office of Science and Technology Policy request and new chemical decontamination guidelines per HHS Office of the Assistant Secretary for Preparedness and Response request. Added new WISER features to view data sources and export/share protective distance maps. Added 380 million sequences to GenBank (the NIH genetic sequence database which contains all publicly available DNA sequences), 42 million sequence records (a 26% increase) to RefSeq (database of reference sequences including genomic, transcript, and protein) and 80,000 human genome sequence variants to ClinVar (archive of reports of the relationships among human variations and phenotypes). Via Sequence Data Delivery Project moved 5 petabytes of public SRA data to two cloud vendors (NIH STRIDES initiative) and released BLAST and prokaryotic genome annotation tools that were packaged to support use in cloud or compute center environments. Related work improved: the search experience for users seeking data and information about genomes, proteins and clinical variation; discovery and access of enormous quantities of data from high throughput sequencing; and submission processing and data quality assessment. Collaborated with CDC, FDA, and USDA to use high throughput sequencing to rapidly and accurately identify pathogens causing foodborne illnesses and combat antimicrobial resistance (AMR). Used Pathogen Detection pipeline to process genome sequence data for 100,000 food, factory, farm and other samples to identify sources of human illnesses such as Salmonella, E. coli, and Listeria; Improved turnaround time for results to the FDA in 24 hours, enabling the first real-time US foodborne pathogen surveillance system (used by FDA to support more than 370 actions intended to protect consumers from foodborne illness). Released a new version of the AMRFinderPlus tool to identify AMR genes and proteins and the new National Database of Antibiotic Resistant Organisms (NDARO) to provide access to AMR data for more than 400, 000 pathogens (part of the White House National Action Plan for Combating Antibiotic-Resistant Bacteria). Combined contemporary and historical inquiry to advance biomedical knowledge via: Circulating Now blog (6,000 subscribers and 338,000 followers); 40 NLM traveling exhibitions (260,000 visitors); and hosting seven Michael E. DeBakey Fellows in the History of Medicine who conducted research using the world-renowned NLM historical collections. Launched workforce transformation initiative, Data Science NLM Training Program, to hone NLM staff skills. More than 750 staff completed survey to assess skills in 10 data science competencies and received individual training plans linked to NLMs Data Science Course Catalog. Provided access to health services research information for researchers, practitioners, and policy makers via NICHSR ONESearch to: identify trends and gaps in funded research (HSRProj database of 36,000 active health services research projects from 380+ funding sources); locate 1800 essential datasets, data collection instruments and related literature (Health Services Research Resources database); and find current news, reports and data (PHPartners and HSR Information Central portals).

2019 财年，NLM 在加强国家生物医学信息服务方面取得了重大进展，因为： 向 PubMed 书目数据库添加了 135 万次引用（目前生物医学期刊文章的引用量为 3000 万次），并开发了更新的搜索技术和移动优化，将在 2019 财年末纳入新的 PubMed 中。 向 PubMed Central (PMC) 添加了 600,000 篇文章，公众可以免费访问 NIH、其他联邦机构以及私人和国际研究资助者支持的研究中的 550 万篇全文期刊文章。推出了 PMC 关联数据框，以显示数据引用、可用性和补充材料，以方便发现公开可用的数据集。与 Wellcome Trust 完成多年合作伙伴关系，通过 PMC 文本挖掘集合免费提供历史生物医学期刊中的数千篇文章。 通过国家医学图书馆网络（NNLM：超过 7,000 个健康科学图书馆和信息中心）与公共图书馆合作，以： 在生物医学研究代表性不足的社区中向消费者宣传精准医学和 NIH 全民研究计划；对健康科学图书馆员进行研究数据管理和数据科学方面的培训；鼓励公民科学；并改善在线获取高质量科学医疗信息的机会。通过 NNLM 培训了超过 100,000 人（3,000 项教育活动；5,000 项资源演示）；为 20 万用户支持了 335 场外展和培训活动。 向 ClinicalTrials.gov 添加了 32,000 项新的临床研究和 6100 项新结果摘要（总计 318,000 项研究以及 39,000 项研究结果和不良事件信息摘要）。为临床试验透明度法规 (42 CFR Part 11) 和 NIH 政策的实施做出了贡献。 通过将信息从 TOXNET（例如 TOXLINE、有害物质数据库和 Haz-Map）迁移到 PubMed 和 PubChem，改进了对环境健康和毒理学参考信息的访问。将 MedlinePlus（有关医疗测试、药物、健康食谱和 60 种语言的教育视频的信息）迁移到云端，并将实验室测试数量增加一倍，达到 157 项。通过 MedlinePlus Connect，使用标准代码和词汇将 EHR 和患者门户链接到来自 MedlinePlus 的消费者健康信息。 协调 HHS 的临床数据标准，并提供用于交换、使用和促进机器可读临床健康数据的互操作性的工具：在 AccessGUDID 数据库中添加了 240,000 个植入式设备（链接 FDA 和 SNOMED 医疗设备代码），以支持经过认证的 EHR 要求；在交互式地图辅助生成 ICD 代码 (i-MAGIC) 工具中将 SNOMED CT 更新为 ICD10CM 地图；深化价值集权威中心对 CMS 临床质量措施的支持；通过工具和内容增强了 NIH 通用数据元素存储库，以促进数据共享、聚合、协作、比较和可用性。 增强的药品信息资源：药品信息门户、DailyMed（110,000 种药品说明书上的药品标签信息，可通过移动设备访问）、Pillbox（根据物理特征和图像快速识别未知固体剂量药物）、LiverTox（药物、草药和膳食补充剂引起的肝损伤的临床、诊断和研究信息以及病例登记）和 LactMed（1,300 种药品、膳食补充剂、 以及针对母乳喂养的母亲及其哺乳婴儿的诊断剂；可在 NCBI 书籍中找到）。 DailyMed 和 Pillbox 与 NLM 的 RxNorm 标准药物名称相关联。 更新了灾害信息专家计划的培训课程，使信息专业人员和图书馆员能够成为其社区中的健康信息响应者。 NLM 提供针对危险材料以及化学、生物、放射性和核事故的工具（WISER、CHEMM 和 REMM）。根据白宫科技政策办公室的要求添加了有关第四代神经毒剂的信息，并根据负责准备和响应的助理部长办公室的要求添加了新的化学净化指南。添加了新的 WISER 功能来查看数据源和导出/共享保护距离地图。 向 GenBank（包含所有公开可用 DNA 序列的 NIH 基因序列数据库）添加了 3.8 亿条序列，向 RefSeq（包括基因组、转录本和蛋白质的参考序列数据库）添加了 4200 万条序列记录（增加了 26%），向 ClinVar（人类变异和表型之间关系的报告档案）添加了 80,000 个人类基因组序列变体。 Via Sequence Data Delivery Project 将 5 PB 的公共 SRA 数据转移到两家云供应商（NIH STRIDES 计划），并发布了 BLAST 和原核基因组注释工具，这些工具经过打包以支持在云或计算中心环境中使用。相关工作得到改进：用户寻找有关基因组、蛋白质和临床变异的数据和信息的搜索体验；从高通量测序中发现和访问大量数据；提交处理和数据质量评估。 与 CDC、FDA 和 USDA 合作，利用高通量测序快速准确地识别引起食源性疾病的病原体并对抗抗菌素耐药性 (AMR)。使用病原体检测管道处理 100,000 个食品、工厂、农场和其他样本的基因组序列数据，以识别沙门氏菌、大肠杆菌和李斯特菌等人类疾病的来源；将向 FDA 提交结果的周转时间缩短为 24 小时，从而实现了美国第一个实时食源性病原体监测系统（FDA 使用它来支持旨在保护消费者免受食源性疾病影响的 370 多项行动）。发布了新版本的 AMRFinderPlus 工具来识别 AMR 基因和蛋白质，并发布了新的国家抗生素耐药生物数据库 (NDARO)，以提供对超过 400, 000 种病原体的 AMR 数据的访问（白宫抗击抗生素耐药细菌国家行动计划的一部分）。 通过以下方式结合当代和历史探究来推进生物医学知识： Circulate Now 博客（6,000 名订阅者和 338,000 名关注者）； 40 个 NLM 巡回展览（260,000 名参观者）；并接待了七位医学史迈克尔·E·德贝基 (Michael E. DeBakey) 研究员，他们利用世界著名的 NLM 历史馆藏进行研究。 启动了劳动力转型计划“数据科学 NLM 培训计划”，以磨练 NLM 员工技能。超过 750 名员工完成了评估 10 项数据科学能力技能的调查，并接受了与 NLM 数据科学课程目录相关的个人培训计划。 通过 NICHSR ONESearch 为研究人员、从业者和政策制定者提供卫生服务研究信息，以： 确定受资助研究的趋势和差距（HSRProj 数据库包含来自 380 多个资助来源的 36,000 个主动卫生服务研究项目）；找到 1800 个基本数据集、数据收集工具和相关文献（卫生服务研究资源数据库）；并查找当前新闻、报告和数据（PHPartners 和 HSR 信息中心门户）。