National Biomedical Information Services

National Library Of Medicine

Investigators

Linked publications & trials

Abstract

In FY2021, NLM National Biomedical Information Services continued to grow and enhance access to data, information, and tools to accelerate biomedical research and public health. In addition, NLM supported the response to the COVID-19 pandemic by making new data and information related to COVID-19 readily available to scientists, clinicians, public health officials, and the public. In FY2021, NLM: Added 1.5 million citations to PubMed, now with 33+ million citations to biomedical journal articles. Expanded the LitCOVID curated literature hub of information on 160,000+ SARS-CoV-2 articles in PubMed. Indexed 1.1+ million MEDLINE citations with Medical Subject Headings (MeSH), providing data access points using advanced natural language processing mappings to PubMed citations. Added 900,000 articles to PubMed Central, which provides free public access to 7.1 million full text journal articles, 4 million+ of which are downloadable via cloud providers in machine-readable forms supporting automated analysis. Expanded the NIH Preprint Pilot, now with 2,600+ preprints from NIH-funded COVID-19 research. Provided nearly 200,000 coronavirus articles via PMC Public Health Emergency COVID-19 Collection of freely available articles in machine readable formats, accessed 200 million times. Added 39,000 new clinical research studies and 6,000+ new results summaries to ClinicalTrials.gov, now with a total of 395,000 studies and 51,000 results summaries, including 7,000 COVID-19 related clinical studies, with another 5,000 displayed that are accessible from the WHO database. Continued ClinicalTrials.gov modernization by enhancing technical infrastructure and stakeholder engagement. Added 292 million genetic sequences and 697,000 complete SARS-CoV-2 genome records to GenBank (database of all publicly available DNA sequences). Added 39.4 million records to RefSeq, a database of reference sequences including genomic, transcript, and protein data that also generates comprehensive human genome annotation results. Added 200,000+ human genome sequence variants to ClinVar, which reports on relationships among human genome variations and human phenotypes. Human conditions described in submissions are mapped to reference sequences and reported according to the Human Genome Variation Society (HGVS) standard. Provided 16 million SRA data records in two formats (50 petabytes of genetic sequence data) on 2 cloud providers, including a post-processed version available through the AWS Open Data Program, which provides free data download for all users. Continued the COVID-19 Genome Sequence Dataset, providing free cloud-based access to SARS-CoV-2 SRA data. Supported the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance consortium, coordinating U.S. efforts to provide publicly accessible SARS-CoV-2 sequence data in GenBank and SRA. Developed SARS-CoV-2 metadata packages and improved SARS-CoV-2 data submissions and data validation processes to SARS-CoV-2 virus resource; added graphic interfaces and supported viral lineage data retrieval. Participated in FNIH ACTIV TRACE project to develop processes and infrastructure to monitor and evaluate emerging SARS-CoV-2 variants and to standardize, gather, and share variant sequencing data. Developed data processing and analysis methods to support tracking frequency of SARS-CoV-2 sequence variants and predict their impact on vaccine and biologic interventions. Provided test information for 70+ COVID-19 tests in Genetic Testing Registry. Processed genome sequence data for 250,000 samples via the Pathogen Detection pipeline to identify sources of human illnesses such as Salmonella, E. coli, and Listeria. Provided real-time U.S. foodborne pathogen surveillance used by FDA to support 700+ actions, thus reducing consumer risk of foodborne illness. Provided access to antimicrobial resistance information for 900,000+ pathogens via AMRFinderPlus. Coordinated clinical data standards for HHS and provided resources for facilitating interoperability of clinical health data and support certified electronic health record interoperability requirements. Updated terminology resources by expanding the SNOMED International edition with 3,500 new concepts, 12 relating to COVID-19, and the U.S. Extension, with 570 new concepts, 4 relating to COVID-19, including concepts to capture COVID-19 test data requested by CDC; adding 1,300 new lab test and observation codes to LOINC, including 120 COVID-19-related; expanding the RxNorm drug terminology resource to include investigational COVID-19 related drugs; and adding 40+ new Supplementary Concept Records for SARS-CoV-2 and COVID-19 detection and treatment to MeSH. Enhanced the Common Data Element (CDE) Repository to improve user experience and facilitate COVID-19 data services; added 230+ CDEs from the Rapid Acceleration of Diagnostics program; and added 245,000 devices to AccessGUDID. Processed 20+ COVID-19 related provisional files, for inclusion in the Value Set Authority Center (VSAC).Updated FHIR Terminology Service for VSAC Resources documentation page with use cases for all FHIR API calls into VSAC database and ability of VSAC FHIR API to retrieve value set expansions for logically-defined value sets. Expanded drug information available in the Drug Information Portal; DailyMed (drug labeling information from package inserts for 139,000+ drugs); and LactMed (effects of 1,600 drugs, dietary supplements, and diagnostic agents on breastfeeding mothers and their nursing infants); Added 1,200 chemical items to ChemIDplus, including 220+ drugs related to COVID-19. Integrated health services research products and services to PubMed, ClinicalTrials.gov, NLM Bookshelf, and digitized Health Policy and Services Research Collection to better serve users. Developed Bookshelf collection of 60 COVID-19 guidelines and reviews. Provided trusted consumer information on health conditions, medical tests, drugs, and supplements via MedlinePlus. Merged Genetics Home Reference into MedlinePlus and added content on effects of genetic variation on human health. Responded to 150+ million electronic requests from health IT systems via MedlinePlus Connect. Restructured NIH MedlinePlus Magazine, an important part of NIH's outreach and engagement. Reconfigured (and renamed) the Network of the National Library of Medicine (8,800+ libraries, information centers, and other organizations) through the award of five-year cooperative agreements to seven Regional Medical Libraries and four centers of excellence. Increased innovative virtual engagement nationwide to promote diversity, equity, and inclusion, e.g., educating communities underrepresented in biomedical research about digital literacy, the NIH All of Us Research Program, and COVID vaccines and clinical trials through partnership with NIH Community Engagement Alliance. Trained public library staff to use high-quality health information; trained health sciences librarians in research data management and data science; and encouraged citizen science. Conducted 1,700+ virtual activities reaching 89,000+ participants (220 organizations led projects). Reached over 1000 NLM staff through DataScienceNLM, including 26 NLM staff in Data Science Fundamentals mentoring program - a model for federal data science workforce development. Expanded public outreach via: 30+ online exhibitions (600,000 visitors), including 4 new exhibitions, linking to 1400+ pages of digitized collection materials and a virtual lecture on race and African American health; selecting 3 Michael E. DeBakey Fellows in the History of Medicine to conduct research using NLM historical collections. Hosted two Ada Lovelace Computational Health talks featuring contributions of computational innovation to biomedical research and health.