National Biomedical Information Services

国家生物医学信息服务

• 批准号: 10927115
• 负责人: Michael Huerta
• 金额: $ 35884.77万
• 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/10927115
• 关键词: 2019-nCoV; Acceleration; Adoption; African American; Alaska Native; American Indians; Antimicrobial Resistance; Artificial Intelligence; Asian Americans; Authorization documentation; Automated Indexing; Awareness; Bioinformatics; Biological; Biomedical Engineering; Biomedical Research; Biotechnology; Black American; Books; COVID-19; COVID-19 pandemic; Chemicals; ClinVar; Clinical; Clinical Data; Clinical Research; Clinical Trials; Code; Collaborations; Collection; Common Data Element; Communities; Comparative Genomic Analysis; Computational Science; Coronavirus; DNA Sequence; Data; Data Analyses; Data Science; Data Set; Data Storage and Retrieval; Databases; Development; Discipline; Diverse Workforce; Drug Labeling; Early Intervention; Ecosystem; Electronic Health Record; Emergency response; Ensure; Epidemiology; Escherichia coli; Ethnic Origin; Family; Federal Government; Feedback; Frequencies; Funding; Genbank; Genetic; Genome; Genomics; Goals; Health; Health Professional; Health Services; Health Services Research; Health Technology; Healthcare; Hispanic; History of Medicine; Human; Human Genetics; Human Genome; Individual; Information Dissemination; Information Services; Information Systems; Infrastructure; Interlibrary Loans; International; Intramural Research Program; Journals; Knowledge; Latino; Leadership; Libraries; Linguistics; Listeria; Literature; Local Government; Logical Observation Identifiers Names and Codes; MEDLINE; Machine Learning; Maintenance; Manuscripts; MeSH Thesaurus; Medical Device; Medical Informatics; Medical Libraries; MedlinePlus; Methods; Minority; Minority-Serving Institution; Modernization; Molecular Biology; Monitor; Mutation; Names; National Heart, Lung, and Blood Institute; Native-Born; Operations Research; Organism; Pacific Islander; Pathogen detection; Patients; Persons; Pharmaceutical Preparations; Phenotype; Play; Policies; Population; Population Group; Positioning Attribute; Preparation; Prevention Measures; Printing; Process; Proteins; Provider; PubMed; Public Health; Readability; Recording of previous events; Records; Reduce health disparities; Reporting; Research; Research Personnel; Research Support; Resources; Role; Route; SARS-CoV-2 genome; SARS-CoV-2 variant; Salmonella; Sampling; Science; Sequence Read Archive; Services; Source; Standardization; State Government; Strategic Planning; System; Systematized Nomenclature of Medicine; Techniques; Technology; Terminology; Text; Therapeutic; Time; Training; Transcript; Translating; Tribes; Trust; Underrepresented Populations; United States National Institutes of Health; United States National Library of Medicine; Update; Vaccines; Validation; Variant; Viral; Visualization; analytical tool; archive data; authority; automated analysis; biomedical informatics; biomedical information system; cloud based; cloud platform; community engagement; comparative; comparative genomics; computerized data processing; coronavirus disease; data reduction; data standards; data submission; digital; digital medicine; electronic health record system; exhibitions; experience; foodborne illness; foodborne pathogen; genome annotation; genome resource; genome sequencing; genomic data; graphical user interface; health data; health disparity; health management; improved; indexing; innovation; interoperability; journal article; knowledgebase; lectures; online resource; open data; outreach; pathogen; petabyte; preservation; programs; public health emergency; repository; research and development; research study; scientific computing; statistics; tool; virus resource; web site

In FY 2023, NLM's national biomedical information services expanded and enhanced access to data and information to accelerate biomedical research and public health. Provided access to biomedical literature Indexed 1+ million MEDLINE citations with medical subject headings (MeSH). Added 1.6 million citations to PubMed, growing it to 36+ million citations to biomedical literature. Expanded LitCovid to provide enhanced access to 360,000+ SARS-CoV-2 article citations in PubMed. Added nearly 1 million articles to PubMed Central (PMC) to provide free public access to 9+ million full-text journal articles, 5+ million of which are downloadable in machine-readable forms to support automated analysis through bulk download or at scale in the cloud using machine learning and artificial intelligence. Provided immediate access to 350,000+ coronavirus articles in machine-readable formats through the PMC Public Health Emergency COVID-19 Collection. Expanded the NIH Preprint Pilot to provide access to 10,000+ preprints reporting on NIH-funded research. Digitized 372,000 pages from print books and journals, making them accessible worldwide through NLMs Digital Collections and PMC. Expanded and maintained other digital collections by adding 5,100+ web resources to a collection that now provides access to 20,000+ resources documenting the COVID-19 pandemic, including content from federal, state, and local governments, aid organizations, and NGOs websites on topics ranging from prevention measures and vaccines. Filled 56,000 interlibrary loan (ILL) requests. Enabled ILL activities between approximately 1,780 medical libraries to fulfill an estimated 545,000 requests through the NLM DOCLINE ILL request and routing system. Provided trusted information for biomedical research, public health, and health care management Registered 37,000 new clinical research studies and added 4,000+ new results summaries to ClinicalTrials.gov, which provides access to 466,000+ studies and 60,000+ results summaries, including 9,000+ COVID-19-related studies. Launched a modernized ClinicalTrials.gov website after a multiyear effort to improve the user experience. Added 968 million genetic sequences, including 1.5 million SARS-CoV-2 genome sequence records, to the GenBank database of all publicly available DNA sequences. Added 41.7 million records to RefSeq, a database of reference sequences including genomic, transcript, and protein data, which generates comprehensive human genome annotation results. Added 720,000+ annotated human genetic sequence variants to ClinVar, which reports on relationships among human genome variations and human phenotypes. Provided 25+ million SRA data records (87 petabytes of genetic sequence data) on two commercial cloud providers in three formats, including a post-processed version available through the AWS Open Data Program and a second post-processed version with a greatly reduced data storage footprint, available from commercial AWS and Google cloud platforms to enable the use of machine learning and artificial intelligence. These data included the COVID-19 Genome Sequence Dataset, providing free cloud-based access to SARS-CoV-2 SRA data and controlled access to human genome sequence data derived from research studies. Supported the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance consortium to provide publicly accessible SARS-CoV-2 sequence data in GenBank and SRA. Improved SARS-CoV-2 data submission and validation processes to SARS-CoV-2 virus resources and updated graphic interfaces for viral lineage data retrieval. Supported processes and infrastructure to monitor and evaluate emerging SARS-CoV-2 variants as part of NIH ACTIV TRACE, and standardized, gathered, and shared variant sequencing data. Supported data processing and analysis methods to track the frequency of SARS-CoV-2 sequence mutations and variants using different genome sequencing technologies and predict their impact on vaccine and biologic early interventions. Provided results of this standardized analysis to support the findability of individual samples and large-scale analysis across the entire dataset. Continued to develop the NIH Comparative Genomics Resource to facilitate comparative genomics analyses for eukaryotic organisms through an ecosystem of NLM repositories and community-created knowledgebases offering integrated cloud-ready data, tools, and interfaces compatible with community-provided organism resources. Conducted outreach to support a strategy of stakeholder feedback and community engagement. Submitted manuscripts and released tools to improve the quality of genomic data submitted to GenBank for comparative analyses, to assist users to find and download genomic data, and to visualize and identify sequences. Processed genome sequence data for 416,000+ samples via the Pathogen Detection Pipeline to identify sources of human illnesses such as Salmonella, E. coli, and Listeria. Provided real-time foodborne pathogen surveillance used by the U.S. FDA, resulting in 1,000+ actions to protect consumers from foodborne illness. Provided access to antimicrobial resistance information for nearly 1.2 million pathogens via AMRFinderPlus. Expanded DailyMed drug labeling information for 145,000+ drugs and added information for 460,000+ medical devices in the AccessGUDID database of more than 4 million medical devices. Provided trusted health information to an estimated 500 million visitors through MedlinePlus and nearly 200 million patients via electronic health record (EHR) systems via MedlinePlus Connect. Transitioned MedlinePlus Connect to the cloud for faster, more reliable access to critical health information. Provided information to evaluate online health information. Supported the development and use of health data standards Coordinated clinical data standards for HHS and provided resources to facilitate interoperability of clinical health data and confirmation of federal EHR interoperability requirements. Updated health data standards resources by expanding the SNOMED International Edition and the U.S. Extension with more than 7,000 and 300 concepts respectively. Added 600+ codes to LOINC and expanded the RxNorm drug terminology by 200+ concepts. Added 1,700+ federally recognized American Indian and Alaskan Native tribal names and ethnic and ethnolinguistic minority terms designated as "Population Groups" to MeSH. Enhanced the Value Set Authority Center with new features to support maintenance, comparison, tracking of changes, and usage statistics of value sets. Enhanced the NIH Common Data Element (CDE) Repository to encourage adoption of CDEs in NIH-funded biomedical research. Added 12 CDEs from the NHLBI Collaborating Network of Networks for Evaluating COVID-19 and Therapeutic Strategies program to the NIH-Endorsed CDEs and curated 4 COVID and 5 non-COVID-related CDE submissions in preparation for NIH endorsement, including submission of 30 CDEs from the NIH Science collaborative for Health disparities and Artificial intelligence bias Reduction. Enhanced public engagement and creation of a diverse workforce Supported minority-serving institution libraries knowledge and use of the All of Us Researcher Workbench. Provided training on user conduct and access to All of Us data and data engagement techniques via the All of Us data training and engagement for academic libraries program. Improved public awareness of NLM resources by hosting 7 Michael E. DeBakey Fellows in the History of Medicine to support research using NLM historical collections, an Ada Lovelace Computational Health Lecture highlighting computational innovation efforts to biomedical research, 9 History Talks promoting awareness and use of NLMs historical collections for research, and 38 online exhibitions.

在2023财年，NLM的国家生物医学信息服务扩大并增强了对数据和信息的访问，以加速生物医学研究和公共卫生。 提供了对生物医学文学的访问 用医学主题标题（网格）索引1百万个Medline引用。在PubMed中增加了160万次引用，将其增加到36多个引用生物医学文献。扩大的litcovid可以增强对PubMed中360,000多个SARS-COV-2文章引用的访问。 向PubMed Central（PMC）添加了近100万篇文章，以免费提供9多个全文期刊文章的公共访问权限，其中500万篇文章可在机器可读表单中下载，以通过使用机器学习和人工智能在云中大规模下载或大规模支持自动分析。通过PMC公共卫生紧急COVID-19 Collection提供了以机器可读格式的350,000多个冠状病毒文章的立即访问。扩展了NIH预印试验，以提供有关NIH资助研究的10,000多个预印本报告的访问。 从印刷书籍和期刊中数字化了372,000页，使其通过NLMS数字收藏和PMC在全球范围内访问。通过向目前提供5,100多个Web资源添加5,100多个Web资源的收藏，该集合现在可以访问20,000多个资源，这些资源可访问20,000多个资源，记录了COVID-19的大流行，包括来自联邦，州和地方政府，援助组织和非政府组织网站的内容，涉及预防措施和疫苗的主题。 填写了56,000张间贷款（ILL）请求。启用了大约1,780个医疗库之间的不良活动，以通过NLM Dicline Ill请求和路由系统满足545,000个请求。 为生物医学研究，公共卫生和医疗保健管理提供了可信赖的信息 注册了37,000个新的临床研究，并将4,000多个新的结果摘要添加到临床中，该研究可访问466,000多种研究和60,000多个结果摘要，包括9,000多个与COVID-19与COVID相关的研究。经过多年的努力来改善用户体验，启动了现代化的临床。 在所有公开可用的DNA序列的GenBank数据库中增加了9.68亿个遗传序列，包括150万SARS-COV-2基因组序列记录。 RefSeq添加了4,170万个记录，RefSeq是一个参考序列的数据库，包括基因组，转录本和蛋白质数据，该数据产生了全面的人类基因组注释结果。在Clinvar中增加了720,000多个注释的人类遗传序列变异，该变异报告了人类基因组变异和人类表型之间的关系。 在两个商业云提供商方面提供了25多种SRA数据记录（87位遗传序列数据）的三种格式，包括可通过AWS Open Data Program获得的后加工版本和第二个后处理版本，并具有大大减少的数据存储足迹，可从商业AWS和Google Cloud Platpters获得，可启用机器学习和人造智能的使用。这些数据包括COVID-19基因组序列数据集，提供对SARS-COV-2 SRA数据数据的免费访问以及对从研究研究得出的人类基因组序列数据的控制访问。 支持SARS-COV-2测序，用于公共卫生应急响应，流行病学和监视财团，以在GenBank和SRA中提供公开访问的SARS-COV-2序列数据。改进了SARS-COV-2数据提交和验证过程，以提供SARS-COV-2病毒资源，并更新了病毒谱系数据检索的图形接口。 支持的过程和基础架构，以监视和评估新兴的SARS-COV-2变体作为NIH Activ Trace的一部分，并标准化，收集和共享的变体测序数据。支持数据处理和分析方法，以使用不同的基因组测序技术跟踪SARS-COV-2序列突变和变体的频率，并预测其对疫苗和生物早期干预措施的影响。提供了此标准化分析的结果，以支持整个数据集中各个样本的可发现性和大规模分析。 继续开发NIH比较基因组学资源，以通过NLM存储库的生态系统和社区创建的知识库来促进真核生物的比较基因组学分析，从而提供与社区预测的生物资源相吻合的集成云就已经准备就绪的数据，工具和互动。进行了宣传，以支持利益相关者反馈和社区参与的战略。提交的手稿和已发布的工具，以提高提交给GenBank的基因组数据的质量进行比较分析，以帮助用户查找和下载基因组数据，并可视化和识别序列。 通过病原体检测管道为416,000多种样品进行了处理的基因组序列数据，以鉴定人类疾病的来源，例如沙门氏菌，大肠杆菌和李斯特菌。提供了美国FDA使用的实时食源性病原体监测，导致1,000多种保护消费者免受食源性疾病的行动。通过AMRFINDERPLUS提供了近120万病原体的抗菌抗性信息。 扩展了Dailymed药物标记信息，可用于145,000多种药物，并在超过400万台医疗设备的AccessGudID数据库中添加了460,000多种医疗设备的信息。 通过MedlinePlus通过MedlinePlus Connect通过MedlinePlus（EHR）系统提供了可信赖的健康信息，估计通过MedlinePlus和近2亿名患者提供了可信赖的健康信息。过渡后的Medlineplus连接到云，以更快，更可靠地访问关键健康信息。提供的信息以评估在线健康信息。 支持健康数据标准的发展和使用 HHS协调的临床数据标准，并提供了资源以促进临床健康数据的互操作性并确认联邦EHR EHR互操作性要求。通过扩展Snomed International Edition和美国扩展，分别具有7,000多个概念，更新了健康数据标准资源。添加了600多个代码，以通过200多个概念扩展了RXNorm药物术语。 增加了1,700多种联邦认可的美洲印第安人和阿拉斯加土著部落名称，以及指定为“人口群体”的种族和民族语言少数族裔。通过新功能增强了价值设置的权限中心，以支持维护，比较，更改跟踪以及价值集的使用统计信息。 增强了NIH公共数据元素（CDE）存储库，以鼓励在NIH资助的生物医学研究中采用CD。在NHLBI合作网络网络中添加了12个CDE，用于评估NIH备受尊敬的CDE的COVID-19和治疗策略计划，并策划了4个COVID和5个与NIH Science Socorial Disebarity Diseparority Drestortan Parias和人为的CDE的NIH认可的无关CDE提交，以准备NIH Science Science CDES，包括30个CDES的认可。 增强了公众参与和创造多样化的劳动力 支持少数派服务机构图书馆的知识和使用我们所有人的研究人员工作台。提供了有关用户行为的培训，并通过我们所有的数据培训和学术图书馆计划访问我们所有数据和数据参与技术。 通过接待7个Michael E. Debakey Fellows，在医学史上提高了公众对NLM资源的认识，以支持NLM历史收藏的研究，ADA Lovelace计算健康演讲强调了生物医学研究的计算创新工作，9历史，促进了NLMS历史集合的认识和使用研究，以及38个在线展览。

项目成果

RefSeq curation and annotation of antizyme and antizyme inhibitor genes in vertebrates.

• DOI: 10.1093/nar/gkv713
• 发表时间: 2015-09-03
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Rajput B;Murphy TD;Pruitt KD
• 通讯作者: Pruitt KD

How to publish a new fungal species, or name, version 3.0.

• DOI: 10.1186/s43008-021-00063-1
• 发表时间: 2021-05-03
• 期刊: IMA fungus
• 影响因子: 5.4
• 作者: Aime MC;Miller AN;Aoki T;Bensch K;Cai L;Crous PW;Hawksworth DL;Hyde KD;Kirk PM;Lücking R;May TW;Malosso E;Redhead SA;Rossman AY;Stadler M;Thines M;Yurkov AM;Zhang N;Schoch CL
• 通讯作者: Schoch CL

RefSeq microbial genomes database: new representation and annotation strategy.

• DOI: 10.1093/nar/gkt1274
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Tatusova T;Ciufo S;Fedorov B;O'Neill K;Tolstoy I
• 通讯作者: Tolstoy I

The NCBI Taxonomy database.

• DOI: 10.1093/nar/gkr1178
• 发表时间: 2012-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Federhen S

RefSeq: an update on prokaryotic genome annotation and curation.

• DOI: 10.1093/nar/gkx1068
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Haft DH;DiCuccio M;Badretdin A;Brover V;Chetvernin V;O'Neill K;Li W;Chitsaz F;Derbyshire MK;Gonzales NR;Gwadz M;Lu F;Marchler GH;Song JS;Thanki N;Yamashita RA;Zheng C;Thibaud-Nissen F;Geer LY;Marchler-Bauer A;Pruitt KD
• 通讯作者: Pruitt KD