Standards > model/format > DOI:10.25504/FAIRsharing.mwmbpq


ready Browser Extensible Data Format

Abbreviation:BED


General Information
BED (Browser Extensible Data) format provides a flexible way to define the data lines that are displayed in an genome annotation track. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used.



How to cite this record FAIRsharing.org: BED; Browser Extensible Data Format; DOI: 10.25504/FAIRsharing.mwmbpq; Last edited: Feb. 22, 2018, 2:03 p.m.; Last accessed: Jul 16 2018 3:36 p.m.


Record updated: July 12, 2017, 10:54 a.m. by The FAIRsharing Team.




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Implementing Databases (12)
Encyclopedia of DNA Elements at UCSC
Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database.

HaploReg
HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

MAPPER-2
This resource provides information primarily on the upstream non-coding sequence data of genes in 3 genomes which gives insight into the transcription factors binding sites (TFBSs). For each transcript, the region scanned extends from 10,000bp upstream of the transcript start to 50bp downstream of the coding sequence start. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs.

modMine
modMine is an integrated web resource of data & tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

The Human OligoGenome Resource: A Database for Customized Targeted Resequencing Covering the Human Genome
Oligonucleotides for targeted resequencing of the human genome

UCSC Genome Browser database
Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

Human disease methylation database
The human disease methylation database, DiseaseMeth is a web based resource focused on the aberrant methylomes of human diseases. Until recently, bulks of large-scale data are avaible and are increasingly grown, from which more information can be mined to gain further information towards human diseases. Our mission is to provide a curated set of methylation information datasets and tools in the human genome, to support and promote research in this area. Especially, we provide a genome-scale landscape to show human methylaton information in a scalable and flexible manner.

GWASdb
GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications

Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis

The UCSC Archaeal Genome Browser
The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.

The MGA Data Repository
The Mass Genome Annotation (MGA) Data Repository stores published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) that, in conjunction with the ChIP-Seq and SSA servers, can be accessed and studied by scientists. The main characteristic of the MGA database is to store mapped data (in the form of genomic coordinates of mapped reads) and not sequence files. In this way, each sample present in the database has been pre-processed (for example sequence reads has been mapped to a genome) and presented in a standardized text format

MirGeneDB.org
MirGeneDB is a database of microRNA genes that have been validated and annotated. The initial version contained 1,434 microRNA genes for human, mouse, chicken and zebrafish. Version 2.0 contains more than 7,500 genes from 33 organisms representing nearly every major metazoan group, and these microRNAs can be browsed, searched and downloaded.

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