National Center for Biotechnology Information

Last updated
National Center for
Biotechnology Information
AbbreviationNCBI
Founded1988;34 years ago (1988)
Headquarters Bethesda, Maryland
Location
Coordinates 38°59′45″N77°05′56″W / 38.9959°N 77.0989°W / 38.9959; -77.0989 Coordinates: 38°59′45″N77°05′56″W / 38.9959°N 77.0989°W / 38.9959; -77.0989
Official language
English
Director
Stephen Sherry
(since Sept 26, 2022)
Parent organization
United States National Library of Medicine
Affiliations National Institutes of Health
Website ncbi.nlm.nih.gov

The National Center for Biotechnology Information (NCBI) [1] [2] is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.

Contents

The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, [2] one of the original authors of the BLAST sequence alignment program [3] and a widely respected figure in bioinformatics.

GenBank

NCBI had responsibility for making available the GenBank DNA sequence database since 1992. [4] GenBank coordinates with individual laboratories and other sequence databases, such as those of the European Molecular Biology Laboratory (EMBL) and the DNA Data Bank of Japan (DDBJ). [4]

Since 1992, NCBI has grown to provide other databases in addition to GenBank. NCBI provides Gene, Online Mendelian Inheritance in Man, the Molecular Modeling Database (3D protein structures), dbSNP (a database of single-nucleotide polymorphisms), the Reference Sequence Collection, a map of the human genome, and a taxonomy browser, and coordinates with the National Cancer Institute to provide the Cancer Genome Anatomy Project. The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5]

The NCBI has software tools that are available through internet browsers or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.

NCBI Bookshelf

The NCBI Bookshelf [6] is a collection of freely accessible, downloadable, online versions of selected biomedical books. The Bookshelf covers a wide range of topics including molecular biology, biochemistry, cell biology, genetics, microbiology, disease states from a molecular and cellular point of view, research methods, and virology. Some of the books are online versions of previously published books, while others, such as Coffee Break , are written and edited by NCBI staff. The Bookshelf is a complement to the Entrez PubMed repository of peer-reviewed publication abstracts in that Bookshelf contents provide established perspectives on evolving areas of study and a context in which many disparate individual pieces of reported research can be organized.[ citation needed ]

Basic Local Alignment Search Tool (BLAST)

BLAST is an algorithm used for calculating sequence similarity between biological sequences, such as nucleotide sequences of DNA and amino acid sequences of proteins. [7] BLAST is a powerful tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and posts the results back to the person's browser in the chosen format. Input sequences to the BLAST are mostly in FASTA or GenBank format while output could be delivered in a variety of formats such as HTML, XML formatting, and plain text. HTML is the default output format for NCBI's web-page. Results for NCBI-BLAST are presented in graphical format with all the hits found, a table with sequence identifiers for the hits having scoring related data, along with the alignments for the sequence of interest and the hits received with analogous BLAST scores for these. [8]

Entrez

The Entrez Global Query Cross-Database Search System is used at NCBI for all the major databases such as Nucleotide and Protein Sequences, Protein Structures, PubMed, Taxonomy, Complete Genomes, OMIM, and several others. [9] Entrez is both an indexing and retrieval system having data from various sources for biomedical research. NCBI distributed the first version of Entrez in 1991, composed of nucleotide sequences from PDB and GenBank, protein sequences from SWISS-PROT, translated GenBank, PIR, PRF, PDB, and associated abstracts and citations from PubMed. Entrez is specially designed to integrate the data from several different sources, databases, and formats into a uniform information model and retrieval system which can efficiently retrieve that relevant references, sequences and structures. [10]

Gene

Gene has been implemented at NCBI to characterize and organize the information about genes. It serves as a major node in the nexus of the genomic map, expression, sequence, protein function, structure, and homology data. A unique GeneID is assigned to each gene record that can be followed through revision cycles. Gene records for known or predicted genes are established here and are demarcated by map positions or nucleotide sequences. Gene has several advantages over its predecessor, LocusLink, including, better integration with other databases in NCBI, broader taxonomic scope, and enhanced options for query and retrieval provided by the Entrez system. [11]

Protein

Protein database maintains the text record for individual protein sequences, derived from many different resources such as NCBI Reference Sequence (RefSeq) project, GenBank, PDB, and UniProtKB/SWISS-Prot. Protein records are present in different formats including FASTA and XML and are linked to other NCBI resources. Protein provides the relevant data to the users such as genes, DNA/RNA sequences, biological pathways, expression and variation data, and literature. It also provides the pre-determined sets of similar and identical proteins for each sequence as computed by the BLAST. The Structure database of NCBI contains 3D coordinate sets for experimentally-determined structures in PDB that are imported by NCBI. The Conserved Domain database (CDD) of protein contains sequence profiles that characterize highly conserved domains within protein sequences. It also has records from external resources like SMART and Pfam. There is another database of proteins known as Protein Clusters database, which contains sets of proteins sequences that are clustered according to the maximum alignments between the individual sequences as calculated by BLAST. [12]

Pubchem database

PubChem database of NCBI is a public resource for molecules and their activities against biological assays. PubChem is searchable and accessible by Entrez information retrieval system. [13]

See also

Related Research Articles

In bioinformatics, BLAST is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.

In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable.

<span class="mw-page-title-main">Entrez</span> Cross-database search engine for health sciences

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National Library of Medicine (NLM), which is itself a department of the National Institutes of Health (NIH), which in turn is a part of the United States Department of Health and Human Services. The name "Entrez" was chosen to reflect the spirit of welcoming the public to search the content available from the NLM.

A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and search one or more databases for information related to that sequence. Summaries and aggregate results are provided in standardized format describing the information that would otherwise have required visits to many smaller sites or direct literature searches to compile. Many sequence profiling tools are software portals or gateways that simplify the process of finding information about a query in the large and growing number of bioinformatics databases. The access to these kinds of tools is either web based or locally downloadable executables.

The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

HomoloGene, a tool of the United States National Center for Biotechnology Information (NCBI), is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

<span class="mw-page-title-main">David J. Lipman</span> American biologist

David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics. In 2017, he left NCBI and became Chief Science Officer at Impossible Foods.

The Biomolecular Object Network Databank is a bioinformatics databank containing information on small molecule structures and interactions. The databank integrates a number of existing databases to provide a comprehensive overview of the information currently available for a given molecule.

formatdb is a discontinued software tool that was used in molecular bioinformatics to format protein or nucleotide databases for BLAST. It has been replaced by makeblastdb and the NCBI "strongly encourage[s]" users to stop using formatdb.

UniGene was a NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that appear to stem from the same transcription locus. Information on protein similarities, gene expression, cDNA clones, and genomic location is included with each entry.

Warren Richard Gish is the owner of Advanced Biocomputing LLC. He joined Washington University in St. Louis as a junior faculty member in 1994, and was a Research Associate Professor of Genetics from 2002 to 2007.

<span class="mw-page-title-main">DGLUCY</span> Protein-coding gene in the species Homo sapiens

DGLUCY is a protein that in humans is encoded by the DGLUCY gene.

The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. RefSeq was first introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes.

<span class="mw-page-title-main">TSBP1</span> Protein-coding gene in the species Homo sapiens

TSBP1 is a protein that in humans is encoded by the TSBP1 gene. C6orf10 is an open reading frame on chromosome 6 containing a protein that is ubiquitously expressed at low levels in the adult genome and may play a role during fetal development. C6orf10 has been found to be linked to both neurodegenerative and autoimmune diseases in adults. Expression of this gene is highest in the testis but is also seen in other tissue types such as the brain, lens of the eye and the medulla. TSBP1 was previously known as C6orf10.

<span class="mw-page-title-main">UGENE</span>

UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.

<span class="mw-page-title-main">TSR3</span>

TSR3, or TSR3 Ribosome Maturation Factor, is a hypothetical human protein found on chromosome 16. Its protein is 312 amino acids long. and its cDNA has 1214 base pairs It was previously designated C16orf42.

<span class="mw-page-title-main">METTL26</span>

METTL26, previously designated C16orf13, is a protein-coding gene for Methyltransferase Like 26, also known as JFP2. Though the function of this gene is unknown, various data have revealed that it is expressed at high levels in various cancerous tissues. Underexpression of this gene has also been linked to disease consequences in humans.

<span class="mw-page-title-main">Transmembrane protein 44</span>

Transmembrane protein 44 is a protein that in humans is encoded by the TMEM44 gene.

<span class="mw-page-title-main">C19orf44</span> Mammalian protein found in Homo sapiens

Chromosome 19 open reading frame 44 is a protein that in humans is encoded by the C19orf44 gene. C19orf44 is an uncharacterized protein with an unknown function in humans. C19orf44 is non-limiting implying that the protein exists in other species besides human. The protein contains one domain of unknown function (DUF) that is highly conserved throughout its orthologs. This protein is most highly expressed in the testis and ovary, but also has significant expression in the thyroid and parathyroid. Other names for this protein include: LOC84167.

References

  1. "The Human Genome Project". The New York Times .
  2. 1 2 "Research Institute Posts Gene Data on Internet". The New York Times . June 26, 1997.
  3. "Sense from Sequences: Stephen F. Altschul on Bettering BLAST". 2000. Archived from the original on 2007-10-07.
  4. 1 2 Mizrachi, Ilene (22 August 2007). GenBank: The Nucleotide Sequence Database. National Center for Biotechnology Information (US) via www.ncbi.nlm.nih.gov.
  5. "Home - Taxonomy - NCBI". www.ncbi.nlm.nih.gov.
  6. USA (2019-05-06). "Home - Books - NCBI". Ncbi.nlm.nih.gov. Retrieved 2019-06-12.
  7. Altschul Stephen; Gish Warren; Miller Webb; Myers Eugene; Lipman David (1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/s0022-2836(05)80360-2. PMID   2231712.
  8. Madden T. (2002). The NCBI Handbook, 2nd edition, Chapter 16, The BLAST Sequence Analysis Tool
  9. NCBI Resource Coordinators (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20.
  10. Ostell J. (2002). The NCBI Handbook, 2nd edition, Chapter 15, The Entrez Search and Retrieval System
  11. Maglott D., Pruitt K. & Tatusova T. (2005). The NCBI Handbook, 2nd edition, Chapter 19, Gene: A Directory of Genes
  12. Sayers E. (2013). The NCBI Handbook, 2nd edition, NCBI Protein Resources
  13. Wang Y. & Bryant S H. (2014). The NCBI Handbook, 2nd edition, NCBI PubChem BioAssay Database