Results [193]
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AccessGUDID AccessGUDID contains key device identification information submitted to the FDA about medical devices that have Unique Device Identifiers (UDI).
The API provides developers with RESTful API functions for retrieving AccessGUDID data.
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Alma Library Services Platform NLM uses for core library operations including acquisitions, cataloging, collection management, and circulation. Alma provides a Z39.50 protocol for fielded search and retrieval of MARC bibliographic records.
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ASN.1 Format Summary An International Standards Organization (ISO) data representation format used to achieve interoperability between platforms.
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Assembly Database A database provides information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.
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Batch Entrez Retrieve records from Entrez databases by uploading a file of GI or accession numbers from the Nucleotide or Protein databases, or a file of unique identifiers from other Entrez databases. Save results in various formats.
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BioProject A collection of genomics, functional genomics, and genetics studies and links to their resulting datasets. This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases.
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BioSample Database containing descriptions of biological source materials used in experimental assays.
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Biotechnology Information Molecular biology, computational biology and related software tools.
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BLAST (Basic Local Alignment Search Tool) Find regions of local similarity between sequences and compare nucleotide or protein sequences to sequence databases and calculate the statistical significance of matches.
BLAST Tutorials and Guides has links for a selection guide for BLAST algorithms, descriptions of BLAST output formats, explanations of parameters for stand-alone BLAST, directions for setting up stand-alone BLAST on local machines.
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BLAST (Stand-alone) Suite of BLAST tools that utilize the NCBI C++ Toolkit.
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BLAST - Global Align Find global similarity between two nucleotide or protein sequences.
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BLAST - Multiple Alignment (also called COBALT) A protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from a conserved domain database and sequence similarity, using RPS-BLAST and BLASTP.
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BLAST - VecScreen Finds segments of a nucleic acid sequence that may be of vector origin to help identify and remove any segments of vector origin before you analyze or submit sequences.
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BLAST API API for Basic Local Alignment Search Tool (BLAST) services which find regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
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BLAST Databases Sequence databases for use with the stand-alone BLAST programs. The files in this directory are pre-formatted databases that are ready to use with BLAST.
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BLAST+ (in a Docker Image) A version of regular BLAST+ using Docker image to run BLAST analysis on a cloud platform.
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Bookshelf A collection of online biomedical books whose full text can be searched through the Entrez system.
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CDTree A stand-alone application for classifying protein sequences and investigating their evolutionary relationships. CDTree can import, analyze and update existing Conserved Domain (CDD) records and hierarchies, and also allows users to create their own.
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Circulating Now Explore historical research, rare materials, and collections activities related to the History of Medicine.
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Citing Medicine Provides guidance for citing published and unpublished material, ranging from print books and journal articles to blogs, wikis and preprint materials.
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Clinical Table Search Service A web API service which software programs can use for querying clinical data tables, such as drug names, medical conditions, ICD-10-CM, NPI, and many others. The tables may also be accessed through FHIR APIs: https://clinicaltables.nlm.nih.gov/fhir.html
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ClinVar A resource under development to provide a public, tracked record of reported relationships among human variation and observed health status.
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Cn3D A stand-alone application for viewing 3-dimensional structures from NCBI Entrez retrieval service. Runs on Windows, Macintosh, and UNIX and can be configured to receive data from most popular Web browsers.
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COBALT COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.
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Coffee Break A collection of short stories and interactive tutorials about recent biomedical discoveries.
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Computational Resources from NCBI Structure Group A centralized resource covering databases and tools to help in the study of macromolecular structures, conserved domains and protein classification, small molecules and their biological activity, biological pathways, and systems.
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Consensus CDS (CCDS) A collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
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Conserved Domain Search Service (CD Search) Identifies the conserved domains present in a protein sequence. CD-Search uses RPS-BLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-specific score matrices that have been prepared from conserved domain alignments present in the Conserved Domain Database (CDD).
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Conserved Domains Database (CDD) Collection of sequence alignments and profiles representing protein domains conserved in molecular evolution.
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DailyMed DailyMed contains drug information in SPL (Structured Product Label) format for US marketed drugs.
The DailyMed RESTful API is a web service for accessing current SPL information.
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Data Discovery at NLM A platform to provide access to datasets from selected NLM resources. Users can explore, filter, visualize, and export data in a variety of formats, including Excel, JSON, XML, as well as access and build with these datasets via API.
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Database of Genomic Structural Variation (dbVar) The dbVar archives information associated with large scale genomic variation, including large insertions, deletions, translocations and inversions. dbVar also stores associations of defined variants with phenotype information.
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Database of Genotype and Phenotype (dbGaP) Data from genome wide association (GWA) studies, which aim to establish associations between genotype and phenotype information to elucidate the link between genes and disease.
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Database of Short Genetic Variations (dbSNP) A repository containing single nucleotide variations, microsatellites, and small-scale insertions and deletions. dbSNP contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral variations and clinical mutations.
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Digital Collections NLM's online repository of digitized and born digital resources including books, still images, videos, and maps.
The API provides access to metadata and full-text OCR of all resources in the Digital Collections repository in XML format. Developers can use the Web service to incorporate NLM historical monographs, films and other resources into their own applications.
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DOCLINE NLM’s automated interlibrary loan (ILL) request routing and referral system. The web-based system provides efficient resource sharing of biomedical literature via ILL among libraries in the
National Network of Libraries of Medicine (NNLM) and beyond.
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Download MEDLINE/PubMed Data NLM distributes MEDLINE/PubMed data in XML to individuals and organizations for use in accordance with NLM Terms and Conditions.
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ElasticBLAST A cloud-based tool to run BLAST searches for a large number of queries. See the
documentation .
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Entrez Search the biomedical databases of the Entrez Molecular Biology System.
Entrez Programming Utilities - tools that provide access to data within the NCBI Entrez system outside of the regular Web query interface. Entrez tasks are automated within applications and each specialized retrieval task can be used simply by writing a specially formatted URL.
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FDA Notices of Judgment Collection Archive of digitized court case summaries published between 1906-1965 for foods, drugs, cosmetics, and medical devices seized by the FDA under the 1906 Pure Food and Drug Act. Gateway to the 2,400+ box collection of prosecution’s evidence files. The Web Service API provides access to metadata and full-text OCR of all resources in the repository in XML format.
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Finding and Using Health Statistics This course describes different types of health statistics, how they are collected, and where they can be found. The data are collected by government, private, and non-profit agencies and organizations. The health statistics reported by these groups are integral to monitoring trends in the health status of populations, planning the allocation of health care resources, and evaluating the effectiveness of public health interventions.
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GenBank NIH Genetic sequence database, an annotated collection of all publicly available DNA sequences. For information on how to submit data to GenBank go to:
Submit Data
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GenBank: BankIt A Web-based sequence submission tool for one or a few submissions to the GenBank database, designed to make the submission process quick and easy.
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Gene Database of gene-specific information. Each record represents a single gene from a given organism and can include, as available, nomenclature, map, sequence, expression, structure, functional, and homology data.
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Gene Expression Omnibus (GEO) GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Submitted data is stored in two databases (GEO Profiles and GEO Datasets) with tools to help users query and download experiments and curated gene expression profiles.
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Gene Expression Omnibus (GEO) Data Submission Submit functional genomics study information and data, such as next-generation sequence, microarray or mass spectrometry datasets to NCBI GEO.
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Gene Expression Omnibus (GEO) Datasets A component of the Gene Expression Omnibus (GEO) repository that contains submitter-supplied records (known as "GEO Series"), which summarize individual experiments, plus GEO DataSets that are assembled by GEO staff.
For information about GEO DataSets, go to https://www.ncbi.nlm.nih.gov/geo/info/datasets.html
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Gene Expression Omnibus (GEO) Profiles This database stores individual gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository.
For detailed information about GEO Profiles, go to: https://www.ncbi.nlm.nih.gov/geo/info/profiles.html
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GeneRIF GeneRIF provides a simple mechanism to allow scientists to add to the functional annotation of genes in the Gene database.
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Genes and Disease Summary information for more than 80 genetic disorders with discussions of the underlying mutation(s) and clinical features, as well as links to related databases and organizations.
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Genetic Codes Displays the genetic codes for organisms in the Taxonomy database in tables and on a taxonomic tree.
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Genetic Relationship and Fingerprinting (GRAF) Genetic Relationship and Fingerprinting (GRAF) is a rapid statistical method to detect duplicates and closely related samples in large genomic datasets to be used as a quality assurance tool in dbGaP data processing. For more information, see this
abstract in PubMed .
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Genetic Testing Registry (GTR) [NOTE: replaces GeneTests] A free, centralized voluntary registry of comprehensive genetic test information covering clinical and research tests for Mendelian disorders and drug responses including multigenic, array-based, biochemical, cytogenetic, and molecular tests.
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Genome Sequence and map data from the whole genomes of organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress.
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Genome Data Viewer (GDV) GDV is a genome browser supporting the exploration and analysis of more than 500 eukaryotic RefSeq genome assemblies. GDV replaced the Map Viewer.
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Genome Reference Consortium (GRC) Maintains responsibility for the human and mouse reference genomes and works to correct misrepresented loci and to close remaining assembly gaps. Also seeks to provide alternate assemblies for complex or structurally variant genomic loci.
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Genomic Basic Local Alignment Search Tool (BLAST) Genome BLAST compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST) algorithm.
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GenPept The protein sequences corresponding to the translations of coding sequences (CDS) in GenBank are collected for each GenBank release. Please see the README file in the directory for more information.
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Health Information Technology and Health Data Standards at NLM NLM participation in activities relating to nationwide implementation of an interoperable health information technology infrastructure to improve the quality and efficiency of health care.
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Health Service Research (HSR) PubMed Queries Preformulated specialized PubMed searches on healthcare quality and costs, based on a search filter designed by Haynes RB.
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Health Services Research & Public Health Information Programs Provides access to the resources of the National Information Center on Health Services Research and Health Care Technology, including databases, web portals, webinars, preformulated PubMed searches, tutorials, and e-texts.
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Health Services Research Projects (HSRProj) This resource has been discontinued as of June 2021. See the archived HSRProj data about grants and contracts in health services research.
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History of Medicine Exhibitions, historical scholarship, and images in medicine.
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History of Medicine Finding Aids HMD Finding Aids is the central access point for electronic finding aids provided by the Archives and Modern Manuscripts and Prints and Photographs collections. It also includes historic audiovisual collections.
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HIV-1, Human Protein Interaction Database Information about known interactions of HIV-1 proteins with proteins from human hosts. It provides annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data.
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HomoloGene System for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
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I-MAGIC I-MAGIC is an interactive tool to demonstrate how the
SNOMED CT to ICD-10-CM map can be used to generate ICD-10-CM codes from clinical problems coded in SNOMED CT. It simulates a problem list entry interface in which the user searches for problem terms which are mapped to SNOMED CT codes in the back end. The SNOMED CT codes are then used to derive ICD-10-CM codes using the Map.
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IgBLAST A tool to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.
For more information, see
this abstract in PubMed, and the
documentation .
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Images from the History of Medicine Images from the History of Medicine (IHM) in NLM Digital Collections provides online access to images from the historical collections of the U.S. National Library of Medicine. IHM includes image files of a wide variety of visual media including fine art, photographs, engravings, and posters that illustrate the social and historical aspects of medicine dating from the 15th to 21st century.
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IndexCat User interface that provides access to the digitized version of the printed Index-Catalogue of the Library of the Surgeon General’s Office; eTK for medieval Latin texts; and eVK2 for medieval English texts. XML data are available for download.
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Influenza Virus Resource Provides researchers with a growing collection of virus sequences essential to the identification of the genetic determinants of influenza pathogenicity.
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Interlibrary Loan Interlibrary loan services are available only to libraries.
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Journal Article Tag Suite (JATS) Is an application of NISO Z39.96.2019, which defines a set of XML elements and attributes for describing the textual and graphical content of journal articles and describes three article models.
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Journals in NCBI Databases Look up journals cited in NCBI databases, including PubMed.
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LactMed (Drugs and Lactation Database) Find information about maternal and infant drug levels, possible effects on lactation and on breastfed infants, and alternative drugs to consider.
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Learning Resources Database The Learning Resources Database collects educational materials created by NLM. These materials include videos, tutorials, webinars, and other resources that provide user education on NLM products and services.
The REST API provides identifiers to allow the user to search by title, subject, and description. This returns the information in JSON allowing Web pages to parse and display the information for end users.
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Library LinkOut Third parties can link directly from PubMed and other Entrez database records to relevant Web-accessible resources beyond the Entrez system. Includes full-text publications, biological databases, consumer health information and research tools.
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LiverTox Provides up-to-date, accurate, and easily accessed information on the diagnosis, cause, frequency, patterns, and management of liver injury attributable to prescription and nonprescription medications, herbals and dietary supplements.
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LocatorPlus Catalog Provides public access to NLM bibliographic data for journals, books, audiovisuals, electronic resources and other materials. Integrated with NLM’s Alma system, enabling real-time display of holdings information.
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MAGPIE (Map Assisted Generation of Procedure and Intervention Encoding) [DEMO] MAGPIE is an interactive tool to help users (e.g., professional coders, researchers, clinicians) find SNOMED CT and ICD-10-PCS codes for medical procedures and interventions. MAGPIE is an NLM research tool (it has not been tested in a production environment), and is developed primarily for the 2018 version of ICD-10-PCS. MAGPIE combines lexical and map-assisted searching strategies to look for SNOMED CT, ICD-9-CM, and ICD-10-PCS codes sequentially.
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Martin Cummings and the NLM Citation to access speeches, articles, and Congressional Appropriations testimonies by former NLM director Martin M. Cummings, based on the collection of his papers in HMD’s Modern Manuscripts collection. Also, search the
NLM Digital Collection .
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MedGen A portal to information about medical genetics. MedGen includes term lists from multiple sources and organizes them into concept groupings and hierarchies.
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Medical Text Indexer (MTI) A system for producing indexing recommendations to assist in the indexing process at NLM. Currently provides indexing recommendations to more than 100 journals based on the NLM Medical Subject Headings (MeSH) vocabulary.
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MEDLINE/PubMed References including abstracts to articles in thousands of biomedical journals.
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MEDLINE/PubMed Baseline Repository (MBR) Resources related to the annual baseline files. Includes a query tool for Web-based searching for use by NLM registered MEDLINE/PubMed licensees.
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MedlinePlus Health information for patients, families and health care providers. Also in Spanish.
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MedlinePlus Connect A free service that allows electronic health record (EHR) systems to link to relevant and authoritative health information from MedlinePlus.
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MedlinePlus en Español Health information for patients, families and health care providers in Spanish.
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MedlinePlus: For Developers These services (Web Service, XML files, and applications) allow developers to build on and point to information from MedlinePlus. All are available at no cost and without requiring any registration or licensing
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MedPix MedPix is a database of patient cases integrating images and textual information. The content material is organized by disease location (organ system), pathology category, patient profiles, and by image classification and caption.
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MeSH Browser Medical Subject Heading search tool.
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MeSH Database NLM controlled vocabulary used for indexing articles for MEDLINE/PubMed. MeSH terminology provides a consistent way to retrieve information that may use different wording for the same concepts.
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MeSH on Demand MeSH on Demand identifies MeSH Terms in your text using the NLM Medical Text Indexer (MTI) program. After processing, MeSH on Demand returns a list of MeSH Terms relevant to your text as well as a list of related articles from PubMed.
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MeSH RDF Medical Subject Headings (MeSH) linked data. Includes a SPARQL endpoint, lookup service, RESTful interface and bulk download of MeSH RDF data.
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MetaMap Highly configurable program to map biomedical text to the UMLS Metathesaurus or, equivalently, to discover Metathesaurus concepts referred to in text. More information is available at this
site . Use MetaMap via a Web API. The MetaMap Java API and the MetaMap UIMA Annotator allow users to access MetaMap directly through their Java-based application(s).
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Multiple Sequence Alignment (MSA) Viewer An interactive Web application that enables users to visualize multiple alignments created by database search results or other software applications. The MSA Viewer allows users to upload an alignment and set a master sequence and to explore the data using features such as zooming and changing of coloration. It can be embedded in a wide variety of web pages and with a large number of options.
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Musings from the Mezzanine Innovations in health information from Dr. Patricia Flatley Brennan, NLM director.
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NCBI C++ Toolkit Manual A comprehensive manual on the NCBI C++ toolkit, including its design and development framework, a C++ library reference, software examples and demos, FAQs and release notes. It is searchable online and can be downloaded as a series of PDF documents.
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NCBI Data Specifications Specifications for NCBI data in ASN.1 or DTD format. The “NCBI_data_conversion.html” links to the conversion tool.
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NCBI Datasets-Beta NCBI Datasets is a resource that allows you to gather data from across the NCBI databases. A web interface enables users to find and download gene, transcript, protein and genome sequences, annotation and metadata. Special data packages for SARS-CoV-2 genomes are also available. For programmatic access, use the NCBI Datasets command line interface or API.
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NCBI Glossary Part of the NCBI Handbook, this glossary contains descriptions of NCBI tools and acronyms, bioinformatics terms and data representation formats.
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NCBI Handbook An extensive collection of articles about NCBI databases and software.
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NCBI Help Manual Accessed through the NCBI Bookshelf, the Help Manual contains documentation for many NCBI resources, including PubMed, PubMed Central, the Entrez system, Gene, SNP and LinkOut. All chapters can be downloaded in PDF format.
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NCBI Insights The Blog provides perspective on NCBI resources, introduces new resources, explains how to perform specific tasks, and explores current topics in science, and how to find relevant NCBI resources for further exploration.
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NCBI Learn Links to tutorials and training materials, including PowerPoint slides and print handouts.
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NCBI Pathogen Detection Project A project involving the collection and analysis of bacterial pathogen genomic sequences originating in food, environmental sources, and patients. It quickly clusters and identifies related sequences to uncover potential food contamination sources, helping public health scientists investigate foodborne disease outbreaks.
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NCBI Website Search A database of static NCBI Web pages, documentation, and online tools. Includes specialized online sequence analysis tools, back issues of newsletters, legacy resource description pages, sample code, and other miscellaneous resources.
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NIH Common Data Elements (CDE) Repository The NIH Common Data Elements (CDE) Repository has been designed to provide access to structured human and machine-readable definitions of data elements that have been recommended or required by NIH Institutes and Centers and other organizations for use in research and for other purposes.
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NIH Manuscript Submission System (NIHMS) The NIH Public Access Policy requests that researchers funded by NIH submit their final, peer-reviewed manuscripts, which have been accepted for publication, to PubMed Central.
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NIH Public Access The NIH Public Access Policy ensures that the public has access to the published results of NIH-funded research. The NIH Manuscript Submission System is a mechanism for authors to deposit their NIH-funded manuscripts.
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NLM Catalog Provides public access to NLM bibliographic data under NLM/NCBI Entrez platform. Links to NLM holdings information in LocatorPlus.
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NLM Classification A classification scheme for the arrangement of medical library collections.
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NLM Technical Bulletin Web-based newsletter for NLM online searchers.
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Nucleotide Contains nucleotide sequence data from organisms. Includes data from a number of sources databases such as GenBank, RefSeq, TPA, and PDB.
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Nursing Resources for Standards and Interoperability A nursing terminologies resource for systems development. Describes the role of SNOMED CT and Laboratory Observation Identifiers Names and Codes (LOINC) in implementing Meaningful Use in the U.S., specifically for the nursing and care domain.
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OLDMEDLINE Data The subset in PubMed® represents journal article citations from two print indexes: Cumulated Index Medicus (CIM) and the Current List of Medical Literature (CLML). Created by the National Library of Medicine® (NLM®), there are approximately 2,011,000 article citations from international biomedical journals that cover the fields of medicine, preclinical sciences and allied health sciences from 1946 through 1965.
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Online Exhibitions and Digital Projects Enhancing the public and scholarly awareness and appreciation of National Library of Medicine collections.
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Online Oral Histories History of Medicine Division's XML-encoded online oral histories provide access to a wealth of digitized transcripts, and audio when available.
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Open Reading Frame Finder (ORF Finder) A graphical analysis tool that finds all open reading frames in a user's sequence or in a sequence already in the database.
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Open-i Open-i service provides search and retrieval of abstracts and images (including charts, graphs, clinical images, etc.) from the open source literature, and biomedical image collections. Searching may be done by text queries as well as by query images.
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OSIRIS A public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols.
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Phenotype-Genotype Integrator (PheGenI) Supports finding human phenotype/genotype relationships with queries by phenotype, chromosome location, gene, and SNP identifiers. Currently includes information from dbGaP, the National Human Genome Research Institute (NHGRI) genome-wide association study (GWAS) Catalog, and Genotype - Tissue Expression (GTeX).
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Physician’s Lives in the Shenandoah Valley XML-encoded transcriptions and images of 828 handwritten letters (1786-1907) from the History of Medicine's Henkel Family correspondence collection; comprised largely of letters to and from Caspar C. Henkel (1835-1908).
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PMC Open Access Subset API Provides access to metadata of all items in the PMC archive, and the full text of a subset of these items. PMC-OAI is an implementation of the Open Archives Initiative Protocol for Metadata Harvesting.
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PMC Open Access Web Service The service allows users to discover downloadable resources from the PMC Open Access Subset by providing an API to allow discovery of resources related to articles.
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PopSet Sets of DNA sequences that have been collected to analyze the evolutionary relatedness of a population.
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Prescribable RxNorm API The Prescribable RxNorm API is a web service for accessing the current RxNorm current prescribable content.
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Primer-BLAST The Primer-BLAST tool uses Primer3 to design PCR primers to a sequence template. The potential products are then automatically analyzed with a BLAST search against user specified databases, to check the specificity to the target intended.
Documentation
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Profiles in Science Archival collections of leaders in biomedical research and public health.
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ProSplign A utility for computing alignment of proteins to genomic nucleotide sequence based on a variation of the Needleman Wunsch global alignment algorithm and specifically accounts for introns and splice signals.
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Protein Contains protein sequences from organisms. Includes data from a number of source databases such as GenPept (translations from annotated coding regions in GenBank), RefSeq, SwissProt, PIR, PRF, and PDB.
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Protein Clusters A collection of Reference Sequence (RefSeq) proteins, from the complete genomes of prokaryotes, plasmids, and organelles, that have been grouped and annotated based on sequence similarity and protein function.
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PubChem PubChem is organized as three linked databases (PubChem Substance, PubChem Compound, PubChem BioAssay) within the Entrez system. Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties. PubChem provides several ways for programmatic access to its data. Go to: https://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access.
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PubChem BioAssay Contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure.
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PubChem Compound Derived from PubChem Substance this NCBI database provides a non-redundant view of the chemically validated substances in PubChem Substance. There is one PubChem Compound record for each unique substance, and for each unique substance component.
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PubChem Power User Gateway (PUG) The PubChem Power User Gateway (PUG) provides access to PubChem services via a programmatic interface for retrieving information on the biological activities of small molecules. PUG provides access to these PubChem services: Data Download (substance and compound), Compound Structure Search, BioAssay Data Download and Structure Standardization.
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PubChem Standardization Service Standardization, in PubChem terminology, is the processing of chemical structures in the same way used to create PubChem Compound records from contributors' original structures. Users can see how PubChem handles structures they would like to submit.
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PubChem Substance Chemical substance information electronically submitted to PubChem by depositors. This includes any chemical structure information submitted, as well as chemical names, comments, and links to the depositor's Web site.
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PubChem Upload Use this site to contribute new data to PubChem and/or test data upload procedures. Create a test account to test the deposition procedures and to preview data records then move on to a deposition account to upload data to the public database.
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PubChem Web-based and Programmatic Download Services These services provide several ways for users to download a single record, record datasets or custom datafiles. Numerous download files are available including TXT, SDF, XML, CSV, and JSON.
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PubMed PubMed comprises more than 34 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher Web sites.
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PubMed Central (PMC) Free digital archive of full text biomedical and life sciences journal literature.
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PubMed Central Open-Access Subset This small subset of articles in PMC are made available under a Creative Commons or similar license that generally allows more liberal redistribution and reuse than a traditional copyright. Refer to the license statement in each article for details.
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PubMed Clinical Queries A specialized PubMed search form targeted to clinicians and health services researchers. The page simplifies searching by clinical study category, finding systematic reviews and searching the medical genetics literature.
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PubMed Special Queries Directory of topic-specific PubMed queries including AIDS, Bioethics, Cancer, Space Life Sciences as well as Clinical Queries along with many other search strategies.
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PubMed Tutorial The NLM comprehensive tutorial on PubMed scope, content and features, including an in-depth explanation of PubMed Automatic Term Mapping (ATM).
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Reference Sequence (RefSeq) A collection of curated, non-redundant genomic DNA, transcript (RNA), and protein sequences produced by NCBI. Provides a stable reference for genome annotation, gene identification and characterization, and comparative analysis.
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RefSeqGene RefSeqGene, a subset of NCBI's Reference Sequence (RefSeq) project, defines genomic sequences to be used as reference standards for well-characterized genes. These sequences, are labeled with the keyword RefSeqGene in NCBI's nucleotide database.
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Retrovirus Resources A collection of resources designed to support the research of retroviruses, including a genotyping tool, alignment tool for global alignment of multiple sequences, a HIV-1 automatic sequence annotation tool, and annotated maps of many retroviruses.
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RxClass An application for exploring drug classes and their RxNorm drug members. RxClass provides access to various drug classification systems, including ATC, NDF-RT, DailyMed and MeSH. The API provides developers with functions for linking RxNorm drugs to various drug classification systems. Typical use cases for the APIs include finding the class(es) for a given drug and finding all the drug members in a given class. The API RESTful is available for retrieving drug class information.
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RxMix An interface for building applications that allows users to combine functions of various NLM drug APIs, including the RxNorm, RxClass, RxTerms, and NDF-RT APIs. Sequences of functions can be executed interactively or in batch mode.
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RxNav An application for navigating RxNorm drugs. This applications displays relations among drug entities in RxNorm and provides additional information about RxNorm drugs, including drug classes, pill images and drug-drug interactions. RxNav is supported by several drug APIs.
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RxNav-in-a-Box RxNav-in-a-Box provides users with a locally-installable version of
RxNav and RESTful companion APIs, including RxNorm, RxTerms, RxClass, and drug-drug interactions.
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RxNorm A standardized nomenclature for clinical drugs. The RxNorm API provides developers with functions for retrieving RxNorm data from the most current RxNorm data set. Typical use cases include mapping drug codes to RxNorm and linking among drug entities in RxNorm (e.g., branded drug to ingredient).
RxTerms is a drug interface terminology derived from RxNorm for prescription writing or medication history recording. RxTerms URL: https://lhncbc.nlm.nih.gov/MOR/RxTerms/.
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RxTerms RxTerms is a drug interface terminology derived from RxNorm for prescription writing or medication history recording (e.g. in e-prescribing systems, PHRs).
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SARS-CoV-2 Resources at the NLM Access the following SARS-CoV-2 resources: SARS-CoV-2 sequences (RefSeq reference genome, GenBank nucleotide and GenPept protein sequences, and SRA nextgen reads), PubChem’s SARS-CoV-2-related chemical compounds, GEO expression studies, as well as PubMed, LitCovid, and ClinicalTrials.gov records. and more literature, clinical/genetic resources, and resources for accessing and analyzing SARS-CoV-2 Sequences and other molecular data.
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Semantic Knowledge Representation (SKR) API Indexing Initiative Web API provides access to the entire suite of Indexing Initiative and Semantic Knowledge Representation tools including MetaMap, Medical Text Indexer (MTI), and SemRep, and allows programmatic access to the Indexing Initiative Batch and Interactive facilities.
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Sequence Read Archive (SRA) The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System®, Helicos Biosciences Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.
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Sequence Read Archive (SRA) Download Facility This site contains next-generation sequencing data organized by the submitted sequencing project.
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SNOMED CT SNOMED CT is one of a suite of designated standards for use in U.S. Federal Government systems for the electronic exchange of clinical health information and is also a required standard in interoperability specifications of the U.S. Healthcare Information Technology Standards Panel.
The SNOMED CT Status API is a web service for accessing the current status of SNOMED CT concept.
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SPDI Variation Service This genetic variation services interconvert and transform short genetic variants between HGVS expressions, VCF format, and the new SPDI (Sequence Position Deletion Insertion) format, based on alignment datasets used by ClinVar and dbSNP.
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Splign Compute cDNA-to-Genomic sequence alignments.
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Structure (Molecular Modeling Database) General information about the National Center for Biotechnology Information (NCBI) Structure Group and its research projects, as well as access to the Molecular Modeling Database (MMDB) and related tools.
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Structured Abstracts Information about abstracts with distinct, labeled sections (e.g., Introduction, Methods, Results, discussion) that appear in MEDLINE.
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Submission Portal A unified system for multiple submission types. Currently only ribosomal RNA (rRNA), rRNA-ITS, metazoan mitochondrial COX1, Influenza, Norovirus, Dengue or SARS-CoV-2 sequences can be submitted with the GenBank component of this tool. Genome and Transcriptome Assemblies can be submitted through the Genomes and TSA portals, respectively. This will be expanded in the future to include other types of GenBank submissions.
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Taxonomy Contains the names and lineages of organisms, both living and extinct, that are represented in the genetic databases with at least one nucleotide or protein sequence. New organisms are added to the database as sequence data are deposited for them.
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Taxonomy Browser Search the taxonomy tree using partial taxonomic names, common names, wild cards and phonetically similar names.
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Taxonomy Common Tree Generates a taxonomic tree for a selected group of organisms. Users can upload a file of taxonomy IDs or names, or they can enter names or IDs directly.
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Taxonomy Statistics Displays the number of taxonomic nodes in the database for a given rank and date of inclusion.
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Taxonomy Status Reports Displays the current status of a set of taxonomic nodes or IDs.
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Third Party Annotation (TPA) Database A database that contains sequences built from the existing primary sequence data in GenBank. The sequences and corresponding annotations are experimentally supported and have been published in a peer-reviewed scientific journal.
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UCUM Web API Service A web API service for validating and converting unit expressions from the Unified Code for Units of Measure (UCUM).
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UCUM-LHC A JavaScript package that can be included in webpages or programs and used for validating and converting unit expressions from the Unified Code for Units of Measure (UCUM).
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Unified Medical Language System (UMLS) Database of biomedical vocabularies (including SNOMED CT), and related semantic and lexical resources for system developers. Unified Medical Language System (UMLS) Terminology Services API is Intended for application developers to perform Web service calls and retrieve UMLS data within their own applications. Documentation provides a suite of Web Services Description Language (WSDL) files, API installation instructions, and sample code.
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UniGene (Archived Data) An automated analytical system for producing organized views of the transcriptome from a growing number of organisms. UniGene was retired in July 2019; however, you will continue to be able to access archived data.
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UniVec UniVec and UniVec_Core databases in FASTA format.
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Value Set Authority Center (VSAC) The VSAC is a repository and authoring tool for public value sets created by external programs such as Centers for Medicare & Medicaid Services (CMS) electronic Clinical Quality Measures (eCQMs), HL7 Consolidated Clinical Document Architecture (C-CDA), and the CMS Core Clinical Data Elements & Hybrid Measures. Retrieve value set expansions via the VSAC SVS API or the FHIR Terminology Service.
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VecScreen Quickly identifying segments of a nucleic acid sequence that may be of vector origin.
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Vector Alignment Search Tool (VAST) A computer algorithm that identifies similar protein 3-dimensional structures. Structure neighbors for every structure in MMDB are pre-computed and accessible via links on the MMDB Structure Summary pages.
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Viral Genomes Curated sequence data and related information for the community.
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Viral Genotyping Tool This tool helps identify the genotype of a viral sequence.
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Virus Variation Extension of the Influenza Virus Resource to other organisms, providing an interface to download sequence sets of selected viruses; analysis tools, including virus-specific BLAST pages; and genome annotation pipelines (in progress).
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Visible Human Project Three-dimensional representations of the human male and female bodies.
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Water Emergency Response for Libraries Steps on what you should do after a water emergency in your library or cultural heritage institution.
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Whole Genome Shotgun Sequences Whole genome shotgun sequence data organized by the 4-digit project code. Data include GenBank and GenPept flat files, quality scores and summary statistics.
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