Database Commons

a catalog of biological databases

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

Database Profile

General information

URL: http://www.ncbi.nlm.nih.gov/
Full name: National Center for Biotechnology 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:
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Accessible
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Country/Region: United States
Data type:
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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

Publications

31602479
Database resources of the National Center for Biotechnology Information. [PMID: 31602479]
Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K, Ketter A, Kim S, Kimchi A, Kitts PA, Kuznetsov A, Lathrop S, Lu Z, McGarvey K, Madden TL, Murphy TD, O'Leary N, Phan L, Schneider VA, Thibaud-Nissen F, Trawick BW, Pruitt KD, Ostell J.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBankĀ® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Nucleic Acids Res. 2020:48(D1) | 23 Citations (from Europe PMC, 2020-11-21)
28787666
ERas is constitutively expressed in full term placenta of pregnant cows. [PMID: 28787666]
Roperto S, Russo V, Urraro C, Restucci B, Corrado F, De Falco F, Roperto F.

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() | 1 Citations (from Europe PMC, 2020-11-28)
26305468
A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis). [PMID: 26305468]
He L, Li Q, Liu L, Wang Y, Xie J, Yang H, Wang Q.

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, 2020-11-28)
24319143
MMDB and VAST+: tracking structural similarities between macromolecular complexes. [PMID: 24319143]
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.

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) | 81 Citations (from Europe PMC, 2020-11-21)
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) | 169 Citations (from Europe PMC, 2020-11-21)
18287687
Using GenBank. [PMID: 18287687]
Wheeler D.

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, 2020-11-28)
16963425
[The informatics of human genome and traditional Chinese medicine]. [PMID: 16963425]
Lin Q, Wang MQ, Wu B, Ding WJ, Li WH, Zhang TE.

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, 2020-11-28)
16776646
Books for free? How can this be? - A PubMed resource you may be overlooking. [PMID: 16776646]
Corsi AK.

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, 2020-11-28)

Ranking

All databases:
35/4722 (99.28%)
Gene genome and annotation:
20/1269 (98.503%)
35
Total Rank
5,676
Citations
283.8
z-index

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Record metadata

Created on: 2016-01-12
Curated by:
Lina Ma [2020-01-28]
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]