Format
Sort by
Items per page

Send to

Choose Destination

Selected items

Items: 9

1.
Nucleic Acids Res. 2011 Jan;39(Database issue):D1-6. doi: 10.1093/nar/gkq1243.

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. galperin@ncbi.nlm.nih.gov

Abstract

The current 18th Database Issue of Nucleic Acids Research features descriptions of 96 new and 83 updated online databases covering various areas of molecular biology. It includes two editorials, one that discusses COMBREX, a new exciting project aimed at figuring out the functions of the 'conserved hypothetical' proteins, and one concerning BioDBcore, a proposed description of the 'minimal information about a biological database'. Papers from the members of the International Nucleotide Sequence Database collaboration (INSDC) describe each of the participating databases, DDBJ, ENA and GenBank, principles of data exchange within the collaboration, and the recently established Sequence Read Archive. A testament to the longevity of databases, this issue includes updates on the RNA modification database, Definition of Secondary Structure of Proteins (DSSP) and Homology-derived Secondary Structure of Proteins (HSSP) databases, which have not been featured here in >12 years. There is also a block of papers describing recent progress in protein structure databases, such as Protein DataBank (PDB), PDB in Europe (PDBe), CATH, SUPERFAMILY and others, as well as databases on protein structure modeling, protein-protein interactions and the organization of inter-protein contact sites. Other highlights include updates of the popular gene expression databases, GEO and ArrayExpress, several cancer gene databases and a detailed description of the UK PubMed Central project. The Nucleic Acids Research online Database Collection, available at: http://www.oxfordjournals.org/nar/database/a/, now lists 1330 carefully selected molecular biology databases. The full content of the Database Issue is freely available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

PMID:
21177655
PMCID:
PMC3013748
DOI:
10.1093/nar/gkq1243
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
2.
Nucleic Acids Res. 2011 Jan;39(Database issue):D52-7. doi: 10.1093/nar/gkq1237. Epub 2010 Nov 28.

Entrez Gene: gene-centered information at NCBI.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20852, USA. maglott@ncbi.nlm.nih.gov

Abstract

Entrez Gene (http://www.ncbi.nlm.nih.gov/gene) is National Center for Biotechnology Information (NCBI)'s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis. The content represents the integration of curation and automated processing from NCBI's Reference Sequence project (RefSeq), collaborating model organism databases, consortia such as Gene Ontology and other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, genomic location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities) and for bulk transfer by FTP.

PMID:
21115458
PMCID:
PMC3013746
DOI:
10.1093/nar/gkq1237
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
3.
Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9. doi: 10.1093/nar/gkq1189. Epub 2010 Nov 24.

CDD: a Conserved Domain Database for the functional annotation of proteins.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. bauer@ncbi.nlm.nih.gov

Abstract

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership. Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

PMID:
21109532
PMCID:
PMC3013737
DOI:
10.1093/nar/gkq1189
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
4.
Nucleic Acids Res. 2011 Jan;39(Database issue):D15-8. doi: 10.1093/nar/gkq1150. Epub 2010 Nov 23.

The International Nucleotide Sequence Database Collaboration.

Author information

1
EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. cochrane@ebi.ac.uk

Abstract

Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

PMID:
21106499
PMCID:
PMC3013722
DOI:
10.1093/nar/gkq1150
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
5.
Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10. doi: 10.1093/nar/gkq1184. Epub 2010 Nov 21.

NCBI GEO: archive for functional genomics data sets--10 years on.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA. barrett@ncbi.nlm.nih.gov

Abstract

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

PMID:
21097893
PMCID:
PMC3013736
DOI:
10.1093/nar/gkq1184
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
6.
Nucleic Acids Res. 2011 Jan;39(Database issue):D38-51. doi: 10.1093/nar/gkq1172. Epub 2010 Nov 21.

Database resources of the National Center for Biotechnology Information.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA. sayers@ncbi.nlm.nih.gov

Abstract

In addition to maintaining the GenBankĀ® 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.

PMID:
21097890
PMCID:
PMC3013733
DOI:
10.1093/nar/gkq1172
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
7.
Nucleic Acids Res. 2011 Jan;39(Database issue):D908-12. doi: 10.1093/nar/gkq1146. Epub 2010 Nov 12.

NCBI Epigenomics: a new public resource for exploring epigenomic data sets.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA.

Abstract

The Epigenomics database at the National Center for Biotechnology Information (NCBI) is a new resource that has been created to serve as a comprehensive public resource for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). Epigenetics is the study of stable and heritable changes in gene expression that occur independently of the primary DNA sequence. Epigenetic mechanisms include post-translational modifications of histones, DNA methylation, chromatin conformation and non-coding RNAs. It has been observed that misregulation of epigenetic processes has been associated with human disease. We have constructed the new resource by selecting the subset of epigenetics-specific data from general-purpose archives, such as the Gene Expression Omnibus, and Sequence Read Archives, and then subjecting them to further review, annotation and reorganization. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes. Currently, there are 69 studies, 337 samples and over 1100 data tracks from five well-studied species that are viewable and downloadable in Epigenomics.

PMID:
21075792
PMCID:
PMC3013719
DOI:
10.1093/nar/gkq1146
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
8.
Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7. doi: 10.1093/nar/gkq1079. Epub 2010 Nov 10.

GenBank.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Abstract

GenBankĀ® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

PMID:
21071399
PMCID:
PMC3013681
DOI:
10.1093/nar/gkq1079
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central
9.
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21. doi: 10.1093/nar/gkq1019. Epub 2010 Nov 9.

The sequence read archive.

Author information

1
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. rasko@ebi.ac.uk

Abstract

The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequence data are deposited into the SRA. The SRA was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA, detail our support for sequencing platforms and provide recommended data submission levels and formats. We also briefly outline our response to the challenge of data growth.

PMID:
21062823
PMCID:
PMC3013647
DOI:
10.1093/nar/gkq1019
[Indexed for MEDLINE]
Free PMC Article
Icon for Silverchair Information Systems Icon for PubMed Central

Supplemental Content

Support Center