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Resource:Xenbase

Name: Resource:Xenbase
Description: Model organism database for Xenopus laevis and X. (Silurana) tropicalis serving as the principal centralized resource of genomic, development data and community information for Xenopus research. Xenbase gathers information for frog researchers, including both data about frogs as well as a frog stock center, a list of suppliers, meetings, and people working in the field. Xenbase welcomes data submissions from the Xenopus community. They are able to incorporate sequence data, expression data and images obtained using in situ hybridization or immunohistochemistry, protocols, and development movies. However, if you have other data that you feel would be valuable to the community, they will try to determine, how best to integrate your data.

Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis.

Gene pages are automatically assembled from data piped from the Entrez Gene, Gurdon Institute, JGI, Metazome, MGI, OMIM, PubMed, Unigene, Zfin, commercial suppliers and others. These data are then supplemented with in-house annotation.

Xenbase has implemented the Gbrowse genome browser and also provides a BLAST service that allows users to specifically search either laevis or tropicalis DNA or protein targets. A table of Xenopus gene synonyms has been implemented and allows the genome, genes, publications and high-throughput gene expression data to be seamlessly integrated with other Xenopus data and to external database resources, making the wealth of developmental and functional data from the frog available to the broader research community.

Through the Xenbase interface you may:

  • Blast Xenopus ESTs, unigene sets or the tropicalis sequence;
  • Search for Xenopus genes;
  • Browse the genome using the Xenbase or JGI genome browsers;
  • View development stages and cell fate maps;
  • Search publications about Xenopus;
  • Search for people, labs and organizations in the Xenopus Community. View job postings and events in the Xenopus community; and
  • Learn about research methods and protocols (e.g. antisense and morpholinos) and obtain materials.
Xenbase's core feature is the Gene Page, which presents genomic and functional information, sequence links, orthology, and publications, and will soon incorporate expression data.[1]
Other Name(s): Xenbase: Xenopus laevis and tropicalis biology and genomics resource
Abbreviation: Xenbase
Parent Organization: University of Calgary; Alberta; Canada
Supporting Agency: NICHD, NSF, Alberta Network for Proteomics Innovation
Grant: R01 HD045776, P41 HD064556, 9630621, 9983061
Resource Type(s): Database, Atlas, Data repository, Image repository
Resource: Resource
URL: http://www.xenbase.org/
*Id: nif-0000-01286
PMID: PMID 23125366, 19884130
Related application: Research
Related to: Resource:One Mind Biospecimen Bank Listing, North American Biobank, Resource:Monarch Initiative, Resource:OMICtools
Availability: No materials may be reproduced without permission, Acknowledgement requested, The community can contribute to this resource
Address: Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
Keywords: molecular neuroanatomy resource, DNA target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, BLAST, Development stage, publication, in situ hybridization, immunohistochemistry, Video resource, Organism-related portal, Experimental protocol, Organism supplier, Data analysis service, Gold standard or authority, developmental stage
Organism: Xenopus laevis, Xenopus tropicalis
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:Xenbase

Resource:Bgee: a dataBase for Gene Expression Evolution

Parts of Resource:Xenbase

Curation status: Uncurated

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References

  1. James-Zorn C et al. (2013) Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 41: D865-70 PubMed

Notes

This page uses this default form:Resource

Xref: OMICS_01665

News

| Twitter Handle: @Xenbase

Contributors

Aarnaud, Ccdbuser, Yazin, Zaidaziz



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:XenbaseRDF feed
AbbrevXenbase  +
AddressDepartment of Biological Sciences  +, University of Calgary  +, 2500 University Drive NW  +, Calgary  +, Alberta  +, and Canada  +
AvailabilityNo materials may be reproduced without permission  +, Acknowledgement requested  +, and The community can contribute to this resource  +
CurationStatuscurated  +
DefiningCitationhttp://www.xenbase.org/  +
DefinitionModel organism database for Xenopus laevis Model organism database for Xenopus laevis and X. (Silurana) tropicalis serving as the principal centralized resource of genomic, development data and community information for Xenopus research. Xenbase gathers information for frog researchers, including both data about frogs as well as a frog stock center, a list of suppliers, meetings, and people working in the field. Xenbase welcomes data submissions from the Xenopus community. They are able to incorporate sequence data, expression data and images obtained using in situ hybridization or immunohistochemistry, protocols, and development movies. However, if you have other data that you feel would be valuable to the community, they will try to determine, how best to integrate your data.

Data is collected from other databases, high-throughput screens and the scientific literature and integrated into a number of database modules covering subjects such as community, literature, gene and genomic analysis.

Gene pages are automatically assembled from data piped from the Entrez Gene, Gurdon Institute, JGI, Metazome, MGI, OMIM, PubMed, Unigene, Zfin, commercial suppliers and others. These data are then supplemented with in-house annotation.

Xenbase has implemented the Gbrowse genome browser and also provides a BLAST service that allows users to specifically search either laevis or tropicalis DNA or protein targets. A table of Xenopus gene synonyms has been implemented and allows the genome, genes, publications and high-throughput gene expression data to be seamlessly integrated with other Xenopus data and to external database resources, making the wealth of developmental and functional data from the frog available to the broader research community.

Through the Xenbase interface you may:

  • Blast Xenopus ESTs, unigene sets or the tropicalis sequence;
  • Search for Xenopus genes;
  • Browse the genome using the Xenbase or JGI genome browsers;
  • View development stages and cell fate maps;
  • Search publications about Xenopus;
  • Search for people, labs and organizations in the Xenopus Community. View job postings and events in the Xenopus community; and
  • Learn about research methods and protocols (e.g. antisense and morpholinos) and obtain materials.
Xenbase's core feature is the Gene Page, which presents genomic and functional information, sequence links, orthology, and publications, and will soon incorporate expression data.
and will soon incorporate expression data.
ExampleImageXenbase.PNG  +
GrantCategory:R01 HD045776   +, Category:P41 HD064556   +, Category:9630621   +, and Category:9983061   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, Atlas  +, Data repository  +, and Image repository  +
Idnif-0000-01286  +
Is part ofUniversity of Calgary; Alberta; Canada  +
KeywordsMolecular neuroanatomy resource  +, DNA target  +, Protein target  +, Gene  +, Genome  +, Function  +, Sequence  +, Orthology  +, Publication  +, Gene expression  +, Model organism  +, Genomics  +, Development  +, Annotation  +, BLAST  +, Development stage  +, In situ hybridization  +, Immunohistochemistry  +, Video resource  +, Organism-related portal  +, Experimental protocol  +, Organism supplier  +, Data analysis service  +, Gold standard or authority  +, and Developmental stage  +
LabelResource:Xenbase  +
ModifiedDate14 January 2014  +
PMID23125366, 19884130  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:One Mind Biospecimen Bank Listing  +, North American Biobank  +, Resource:Monarch Initiative  +, and Resource:OMICtools  +
Related applicationResearch  +
SpeciesXenopus laevis  +, and Xenopus tropicalis  +
SuperCategoryResource  +
Supporting AgencyNICHD  +, NSF  +, and Alberta Network for Proteomics Innovation  +
SynonymXenbase: Xenopus laevis and tropicalis biology and genomics resource  +
TwitterXenbase  +