standards > model/format > DOI:10.25504/FAIRsharing.665mts


ready Big Browser Extensible Data Format

Abbreviation: BigBed


General Information
The bigBed format stores annotation items that can either be simple, or a linked collection of exons, much as BED files do. BigBed files are created initially from BED type files, using the program bedToBigBed. The resulting bigBed files are in an indexed binary format. The main advantage of the bigBed files is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets bigBed is considerably faster than regular BED files.

Homepage http://genome.ucsc.edu/goldenPath/help/bigBed.html

Developed in United States

Created in 2009

Taxonomic range




How to cite this record FAIRsharing.org: BigBed; Big Browser Extensible Data Format; DOI: https://doi.org/10.25504/FAIRsharing.665mts; Last edited: Jan. 8, 2019, 1:28 p.m.; Last accessed: Mar 25 2019 3:59 a.m.


This record is maintained by BrianLee  ORCID

Record updated: Nov. 4, 2016, 12:09 p.m. by The FAIRsharing Team.

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Support

General

contact form http://genome.ucsc.edu/cgi-bin/hgUserSug ...
support email genome@soe.ucsc.edu

Additional Information

Contact Donna Karolchik

Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use





Publications

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Raney BJ,Dreszer TR,Barber GP,Clawson H,Fujita PA,Wang T,Nguyen N,Paten B,Zweig AS,Karolchik D,Kent WJ
Bioinformatics 2013

View Paper (PubMed) View Publication

BigWig and BigBed: enabling browsing of large distributed datasets.

Kent WJ,Zweig AS,Barber G,Hinrichs AS,Karolchik D
Bioinformatics 2010

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Implementing Databases (5)
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.
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.
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.
UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").
ENCODE Project
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build 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. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.

Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

Funds

Maintains

Grant Number(s)

  • 5P41HG002371-09 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)

  • 5U41HG004568-02 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)

  • P41HG002371 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)

  • R01HG007354 (U.S. National Library of Medicine)

  • U01ES017154 (U.S. National Library of Medicine)

  • U41HG004568 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)