Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

NCBI (National Center for Biotechnology Information)

General information

Description: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
Year founded: 1988
Last update: 2017-02-14
Version:
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: National Center for Biotechnology Information
Address: Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
City: Bethesda
Province/State: MD
Country/Region: United States
Contact name (PI/Team): Eric W. Sayers
Contact email (PI/Helpdesk): sayers@ncbi.nlm.nih.gov

Record metadata

Created on: 2016-01-12
Curated by:
Lina Ma [2019-04-21]
huma shireen [2018-08-30]
Lina Ma [2018-05-29]
Dong Zou [2018-02-08]
Dong Zou [2018-02-07]
zhang yang [2018-01-27]
Qi Wang [2018-01-27]
Qi Wang [2018-01-26]
Tongkun Guo [2018-01-26]
Shixiang Sun [2017-02-21]
Shixiang Sun [2017-01-10]
Lina Ma [2016-04-11]
Lin Liu [2016-03-27]
Zhang Zhang [2016-01-19]
Lina Ma [2016-01-18]
Lin Liu [2016-01-12]

Ranking

All databases:
30/4499 (99.355%)
Gene genome and annotation:
19/1199 (98.499%)
30
Total Rank
5,327
Citations
280.368
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Publications

27899561
Database Resources of the National Center for Biotechnology Information [PMID: 27899561]
NCBI Resource Coordinators

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include iCn3D, MutaBind, and the Antimicrobial Resistance Gene Reference Database; and resources that were updated in the past year include My Bibliography, SciENcv, the Pathogen Detection Project, Assembly, Genome, the Genome Data Viewer, BLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2017:45(D1) | 248 Citations (from Europe PMC, 2019-12-14)
28787666
ERas is constitutively expressed in full term placenta of pregnant cows. [PMID: 28787666]
Sante Roperto, Valeria Russo, Chiara Urraro, Brunella Restucci, Federica Corrado, Francesca De Falco, Franco Roperto,

ERas is a new gene recently found in mouse embryonic stem (ES) cells and localized on the X chromosome. It plays a role in mouse ES cell survival and is constitutively active without any mutations. It was also found to be responsible for the maintenance of quiescence of the hepatic stellate cells (HSCs), liver-resident mesenchymal stem cells, the activation of which results in liver fibrosis. This gene was not present in human ES cells. ERas was found to be activated in a significant population of human gastric cancer, where ERAS may play a crucial role in gastric cancer cell survival and metastases to liver via down-regulation of E-cadherin. ERas gene has been found to be expressed both in ES cells and adult tissues of cynomolgus monkey. Cynomolgus ERAS did not promote cell proliferation or induce tumor formation. ERAS was also detected in normal and neoplastic urothelium of the urinary bladder in cattle, where bovine ERAS formed a constitutive complex with platelet derived growth factor ? receptor (PDGF?R) resulting in the activation of AKT signaling. Here, molecular and morphological findings of ERAS in the full term placenta of pregnant cows have been investigated for the first time. ERAS was studied by reverse transcriptase PCR (RT-PCR). Alignment of the sequence detects a 100% identity with all transcript variant bovine ERas mRNAs, present in the GenBank database (http://www.ncbi.nlm.nih.gov). Furthermore, ERAS was detected by Western blot and investigated by real time PCR that revealed an amount of ERAS more than ERAS found in normal bovine urothelium but less than ERAS present in the liver. Immunohistochemical examination revealed the presence of ERAS protein both at the level of plasma membrane and in cytoplasm of epithelial cells lining caruncular crypts and in trophoblasts of villi. An evident ERAS immunoreactivity was also seen throughout the chorionic and uterine gland epithelium. Although this is not a functional study and further investigations will be warranted, it is conceivable that ERAS may have pleiotropic effects in the placenta, some of which, like normal urothelial cells, might lead to activation of AKT pathway. We speculate that ERAS may play a key role in cellular processes such as cell differentiation and movement. Accordingly, we believe it may be an important factor involved in trophoblast invasiveness via AKT signaling pathway. Therefore, ERas gene is a functional gene which contributes to homeostasis of bovine placenta.

Theriogenology. 2017:103() | 0 Citations (from Europe PMC, 2019-12-14)
26615191
Database resources of the National Center for Biotechnology Information. [PMID: 26615191]
NCBI Resource Coordinators.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Nucleic Acids Res. 2016:44(D1) | 306 Citations (from Europe PMC, 2019-12-14)
25398906
Database resources of the National Center for Biotechnology Information. [PMID: 25398906]
NCBI Resource Coordinators.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Nucleic Acids Res. 2015:43(Database issue) | 170 Citations (from Europe PMC, 2019-12-14)
26305468
A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis). [PMID: 26305468]
Lin He, Qing Li, Lihua Liu, Yuanli Wang, Jing Xie, Hongdan Yang, Qun Wang,

The accessory gland (AG) is an important component of the male reproductive system of arthropods, its secretions enhance fertility, some AG proteins bind to the spermatozoa and affect its function and properties. Here we report the first comprehensive catalog of the AG secreted fluid during the mature phase of the Chinese mitten crab (Eriocheir sinensis). AG proteins were separated by one-dimensional gel electrophoresis and analyzed by reverse phase high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). Altogether, the mass spectra of 1173 peptides were detected (1067 without decoy and contaminants) which allowed for the identification of 486 different proteins annotated upon the NCBI database (http://www.ncbi.nlm.nih.gov/) and our transcritptome dataset. The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700. An extensive description of the AG proteome will help provide the basis for a better understanding of a number of reproductive mechanisms, including potentially spermatophore breakdown, dynamic functional and morphological changes in sperm cells and sperm acrosin enzyme vitality. Thus, the comprehensive catalog of proteins presented here can serve as a valuable reference for future studies of sperm maturation and regulatory mechanisms involved in crustacean reproduction.

PLoS One. 2015:10(8) | 1 Citations (from Europe PMC, 2019-12-14)
24259429
Database resources of the National Center for Biotechnology Information. [PMID: 24259429]
NCBI Resource Coordinators.

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page.

Nucleic Acids Res. 2014:42(Database issue) | 193 Citations (from Europe PMC, 2019-12-14)
24319143
MMDB and VAST+: tracking structural similarities between macromolecular complexes. [PMID: 24319143]
Thomas Madej, Christopher J Lanczycki, Dachuan Zhang, Paul A Thiessen, Renata C Geer, Aron Marchler-Bauer, Stephen H Bryant

The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

Nucleic Acids Res. 2014:42(Database issue) | 59 Citations (from Europe PMC, 2019-12-14)
23193264
Database resources of the National Center for Biotechnology Information. [PMID: 23193264]
NCBI Resource Coordinators.

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page.

Nucleic Acids Res. 2013:41(Database issue) | 238 Citations (from Europe PMC, 2019-12-14)
22140104
Database resources of the National Center for Biotechnology Information. [PMID: 22140104]
Eric W Sayers, Tanya Barrett, Dennis A Benson, Evan Bolton, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael Dicuccio, Scott Federhen, Michael Feolo, Ian M Fingerman, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, Sergey Krasnov, David Landsman, David J Lipman, Zhiyong Lu, Thomas L Madden, Tom Madej, Donna R Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Anna Panchenko, Lon Phan, Kim D Pruitt, Gregory D Schuler, Edwin Sequeira, Stephen T Sherry, Martin Shumway, Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Yanli Wang, W John Wilbur, Eugene Yaschenko, Jian Ye

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2012:40(Database issue) | 320 Citations (from Europe PMC, 2019-12-14)
21097890
Database resources of the National Center for Biotechnology Information. [PMID: 21097890]
Eric W Sayers, Tanya Barrett, Dennis A Benson, Evan Bolton, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M Fingerman, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J Lipman, Zhiyong Lu, Thomas L Madden, Tom Madej, Donna R Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna Panchenko, Lon Phan, Kim D Pruitt, Gregory D Schuler, Edwin Sequeira, Stephen T Sherry, Martin Shumway, Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Yanli Wang, W John Wilbur, Eugene Yaschenko, Jian Ye

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2011:39(Database issue) | 336 Citations (from Europe PMC, 2019-12-14)
19910364
Database resources of the National Center for Biotechnology Information. [PMID: 19910364]
Eric W Sayers, Tanya Barrett, Dennis A Benson, Evan Bolton, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael Dicuccio, Scott Federhen, Michael Feolo, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J Lipman, Zhiyong Lu, Thomas L Madden, Tom Madej, Donna R Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna Panchenko, Kim D Pruitt, Gregory D Schuler, Edwin Sequeira, Stephen T Sherry, Martin Shumway, Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Yanli Wang, W John Wilbur, Eugene Yaschenko, Jian Ye

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2010:38(Database issue) | 251 Citations (from Europe PMC, 2019-12-14)
18940862
Database resources of the National Center for Biotechnology Information. [PMID: 18940862]
Eric W Sayers, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J Lipman, Thomas L Madden, Donna R Maglott, Vadim Miller, Ilene Mizrachi, James Ostell, Kim D Pruitt, Gregory D Schuler, Edwin Sequeira, Stephen T Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko, Jian Ye

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2009:37(Database issue) | 476 Citations (from Europe PMC, 2019-12-14)
18940865
The National Center for Biotechnology Information's Protein Clusters Database. [PMID: 18940865]
Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T.

Rapid increases in DNA sequencing capabilities have led to a vast increase in the data generated from prokaryotic genomic studies, which has been a boon to scientists studying micro-organism evolution and to those who wish to understand the biological underpinnings of microbial systems. The NCBI Protein Clusters Database (ProtClustDB) has been created to efficiently maintain and keep the deluge of data up to date. ProtClustDB contains both curated and uncurated clusters of proteins grouped by sequence similarity. The May 2008 release contains a total of 285 386 clusters derived from over 1.7 million proteins encoded by 3806 nt sequences from the RefSeq collection of complete chromosomes and plasmids from four major groups: prokaryotes, bacteriophages and the mitochondrial and chloroplast organelles. There are 7180 clusters containing 376 513 proteins with curated gene and protein functional annotation. PubMed identifiers and external cross references are collected for all clusters and provide additional information resources. A suite of web tools is available to explore more detailed information, such as multiple alignments, phylogenetic trees and genomic neighborhoods. ProtClustDB provides an efficient method to aggregate gene and protein annotation for researchers and is available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters.

Nucleic Acids Res. 2009:37(Database issue) | 166 Citations (from Europe PMC, 2019-12-14)
18045790
Database resources of the National Center for Biotechnology Information. [PMID: 18045790]
David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael Dicuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, Oleg Khovayko, David Landsman, David J Lipman, Thomas L Madden, Donna R Maglott, Vadim Miller, James Ostell, Kim D Pruitt, Gregory D Schuler, Martin Shumway, Edwin Sequeira, Steven T Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2008:36(Database issue) | 424 Citations (from Europe PMC, 2019-12-14)
17170002
Database resources of the National Center for Biotechnology Information. [PMID: 17170002]
David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y Geer, Yuri Kapustin, Oleg Khovayko, David Landsman, David J Lipman, Thomas L Madden, Donna R Maglott, James Ostell, Vadim Miller, Kim D Pruitt, Gregory D Schuler, Edwin Sequeira, Steven T Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2007:35(Database issue) | 442 Citations (from Europe PMC, 2019-12-14)
18287687
Using GenBank. [PMID: 18287687]
David Wheeler,

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

Methods Mol Biol. 2007:406() | 1 Citations (from Europe PMC, 2019-12-14)
16381840
Database resources of the National Center for Biotechnology Information. [PMID: 16381840]
David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, David L Kenton, Oleg Khovayko, David J Lipman, Thomas L Madden, Donna R Maglott, James Ostell, Kim D Pruitt, Gregory D Schuler, Lynn M Schriml, Edwin Sequeira, Stephen T Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tugba O Suzek, Roman Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2006:34(Database issue) | 262 Citations (from Europe PMC, 2019-12-14)
16963425
[The informatics of human genome and traditional Chinese medicine]. [PMID: 16963425]
Qiao Lin, Mi-Qu Wang, Bin Wu, Wei-Jun Ding, Wei-Hong Li, Tian-E Zhang,

Guided by the theory and methodology of yin-yang set derived from Changing Book and Medicine Canon, and using genetics as a bridge, we have tried to bring together the ancient functional systematology and modern structural one as well as Eastern and Western medicine, thereby promoting the modernization of traditional Chinese medicine (TCM) in theory and in clinical practice. Herein, we used virtual technology to transform the genetic information in OMIM of NCBI (National Center for Biotechnology Information of USA, http://www.ncbi.nlm.nih.gov ) into a secondary database in the form of webpages. There are sixteen kinds of the database named gene morbidity ones as followings as: the nature of gene, the profile of common phenotype, a interaction of endogenous, the disease of a organ or a viscera pathogenesis phenomenon, TCM, the sign of diagnosis of western medicine, the gene response to environment, syndrome, disease, nerve and -endocrine, tumor and cancer, psychology and behavior, morbidity, endo-factor of molecular information, expression, the interaction between endogenous and exogenous in which there is 4 711 words, files. The advantages of the database are its aptness for using human fuzzy intelligence to recognize things, suitability to uncovering the noumenon (yinyang) nature of an object and applicability to clinical use.

Yi Chuan. 2006:28(9) | 0 Citations (from Europe PMC, 2019-12-14)
16776646
Books for free? How can this be? - A PubMed resource you may be overlooking. [PMID: 16776646]
Ann K Corsi,

The NCBI (National Center for Biotechnology Information) at the National Institutes of Health collects a wide range of molecular biological data, and develops tools and databases to analyse and disseminate this information. Many life scientists are familiar with the website maintained by the NCBI (http://www.ncbi.nlm.nih.gov), because they use it to search GenBank for homologues of their genes of interest or to search the PubMed database for scientific literature of interest. There is also a database called the Bookshelf that includes searchable popular life science textbooks, medical and research reference books and NCBI reference materials. The Bookshelf can be useful for researchers and educators to find basic biological information. This article includes a representative list of the resources currently available on the Bookshelf, as well as instructions on how to access the information in these resources.

Biol Cell. 2006:98(7) | 2 Citations (from Europe PMC, 2019-12-14)
15608222
Database resources of the National Center for Biotechnology Information. [PMID: 15608222]
David L Wheeler, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L Kenton, Oleg Khovayko, David J Lipman, Thomas L Madden, Donna R Maglott, James Ostell, Joan U Pontius, Kim D Pruitt, Gregory D Schuler, Lynn M Schriml, Edwin Sequeira, Steven T Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O Suzek, Roman Tatusov, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2005:33(Database issue) | 267 Citations (from Europe PMC, 2019-12-14)
14681353
Database resources of the National Center for Biotechnology Information: update. [PMID: 14681353]
David L Wheeler, Deanna M Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L Madden, Joan U Pontius, Gregory D Schuler, Lynn M Schriml, Edwin Sequeira, Tugba O Suzek, Tatiana A Tatusova, Lukas Wagner

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, PubMed, PubMed Central, LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SARS Coronavirus Resource, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2004:32(Database issue) | 179 Citations (from Europe PMC, 2019-12-14)
12519941
Database resources of the National Center for Biotechnology. [PMID: 12519941]
David L Wheeler, Deanna M Church, Scott Federhen, Alex E Lash, Thomas L Madden, Joan U Pontius, Gregory D Schuler, Lynn M Schriml, Edwin Sequeira, Tatiana A Tatusova, Lukas Wagner

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2003:31(1) | 472 Citations (from Europe PMC, 2019-12-14)
11752242
Database resources of the National Center for Biotechnology Information: 2002 update. [PMID: 11752242]
David L Wheeler, Deanna M Church, Alex E Lash, Detlef D Leipe, Thomas L Madden, Joan U Pontius, Gregory D Schuler, Lynn M Schriml, Tatiana A Tatusova, Lukas Wagner, Barbara A Rapp

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human inverted exclamation markVMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2002:30(1) | 116 Citations (from Europe PMC, 2019-12-14)
11125038
Database resources of the National Center for Biotechnology Information. [PMID: 11125038]
D L Wheeler, D M Church, A E Lash, D D Leipe, T L Madden, J U Pontius, G D Schuler, L M Schriml, T A Tatusova, L Wagner, B A Rapp

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap'99, Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri-tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov.

Nucleic Acids Res. 2001:29(1) | 146 Citations (from Europe PMC, 2019-12-14)
10592169
Database resources of the National Center for Biotechnology Information. [PMID: 10592169]
D L Wheeler, C Chappey, A E Lash, D D Leipe, T L Madden, G D Schuler, T A Tatusova, B A Rapp

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov

Nucleic Acids Res. 2000:28(1) | 252 Citations (from Europe PMC, 2019-12-14)