Xenopus laevis and tropicalis biology and genomics resource

Abbreviation:Xenbase

Recommended

General Information

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the literature, large scale screens and community submissions.

Homepage http://www.xenbase.org

Countries that developed this resource Canada , United States

Created in 2007

Taxonomic range

Xenopus

Xenopus laevis

Xenopus tropicalis

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: Xenbase; Xenopus laevis and tropicalis biology and genomics resource; DOI: https://doi.org/10.25504/FAIRsharing.jrv6wj; Last edited: April 17, 2019, 8:15 p.m.; Last accessed: Jan 18 2021 11:15 p.m.

This record is maintained by xenbase

Record updated: April 17, 2019, 7:45 p.m. by xenbase.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.jrv6wj' by 'xenbase' at 19:45, 17 Apr 2019 (approved):

	'contactORCID' has been modified:
		Before: 
		After: https://orcid.org/0000-0003-3217-3590

	'countries' has been modified:
		Before:
			Canada
			France
			Japan
			United Kingdom
			United States
		After:
			Canada
			United States
		Added:
		Removed:
			France
			Japan
			United Kingdom

	'yearOfCreation' has been modified:
		Before: None
		After: 2007

	'onto_disciplines' has been modified:
		Before:
			Anatomy
			Developmental Biology
			Life Sciences
		After:
			Anatomy
			Developmental Biology
			Life Sciences
			Ontology and Terminology
			Proteomics
		Added:
			Ontology and Terminology
			Proteomics
		Removed:

	'onto_domains' has been modified:
		Before:
			Bibliography
			ChIP-seq assay
			Gene expression data
			RNA-seq assay
			genome
			immunoglobulin complex, circulating
			miRNA
			reagent
		After:
			Bibliography
			ChIP-seq assay
			Differential gene expression analysis
			Differential protein expression analysis
			GO-term enrichment report
			Gene expression data
			RNA-seq assay
			disease process modeling objective
			genome
			immunoglobulin complex, circulating
			miRNA
			phenotype
			reagent
			strain
		Added:
			Differential gene expression analysis
			Differential protein expression analysis
			GO-term enrichment report
			disease process modeling objective
			phenotype
			strain
		Removed:

	'publications' has been modified:
		Before:
			Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes|JB Karpinka, JD Fortriede, KA Burns, C James-Zorn; VG Ponferrada; J Lee; K Karimi; AM Zorn; PD Vize |Nucleic Acids Res.|2014
			The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud|K Karimi and PD Vize |Database|2014
			Xenbase: gene expression and improved integration.|Bowes JB,Snyder KA,Segerdell E,Jarabek CJ,Azam K,Zorn AM,Vize PD|Nucleic Acids Res|2009
			Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.|Segerdell E,Ponferrada VG,James-Zorn C,Burns KA,Fortriede JD,Dahdul WM,Vize PD,Zorn AM|J Biomed Semantics|2013
			Xenopus genomic data and browser resources.|Vize PD,Zorn AM|Dev Biol|2016
		After:
			Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes|JB Karpinka, JD Fortriede, KA Burns, C James-Zorn; VG Ponferrada; J Lee; K Karimi; AM Zorn; PD Vize |Nucleic Acids Res.|2014
			The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud|K Karimi and PD Vize |Database|2014
			Xenbase: gene expression and improved integration.|Bowes JB,Snyder KA,Segerdell E,Jarabek CJ,Azam K,Zorn AM,Vize PD|Nucleic Acids Res|2009
			Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.|Segerdell E,Ponferrada VG,James-Zorn C,Burns KA,Fortriede JD,Dahdul WM,Vize PD,Zorn AM|J Biomed Semantics|2013
			Xenopus genomic data and browser resources.|Vize PD,Zorn AM|Dev Biol|2016
			Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.|James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, Pells T, Wang Y, Vize PD, Zorn A.|Methods Mol Biol. 2018;1757:251-305.|2018
			Xenbase: Facilitating the Use of Xenopus to Model Human Disease.|Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM.|Front Physiol. 2019 Feb 26;10:154|2019
			Xenopus genomic data and browser resources.|Vize PD, Zorn AM.|Dev Biol. 2017 Jun 15;426(2):194-199. |2017
		Added:
			Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.|James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, Pells T, Wang Y, Vize PD, Zorn A.|Methods Mol Biol. 2018;1757:251-305.|2018
			Xenbase: Facilitating the Use of Xenopus to Model Human Disease.|Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM.|Front Physiol. 2019 Feb 26;10:154|2019
			Xenopus genomic data and browser resources.|Vize PD, Zorn AM.|Dev Biol. 2017 Jun 15;426(2):194-199. |2017
		Removed:

In Collections

NIH-supported data repositories

Data Citation Implementation

Open Science Prize

Support

General

forum	http://forums.xenbase.org
online documentation	http://wiki.xenbase.org/xenwiki
twitter	@Xenbase

Additional Information

Contact

Aaron Zorn ORCID

Tools

BLAST	http://www.xenbase.org/genomes/blast.do
TextPresso	http://www.xenbase.org/cgi-bin/textpresso/xenopus/home
GBrowse	http://gbrowse.xenbase.org/fgb2/gbrowse/

Access / Retrieve Data

Conditions of Use

Applies to: General

No reuse without permision

Data Access

Download

ftp://ftp.xenbase.org/pub

Publications

Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes

•JB Karpinka, JD Fortriede, KA Burns, C James-Zorn; VG Ponferrada; J Lee; K Karimi; AM Zorn; PD Vize
Nucleic Acids Res. 2014