- Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. [PMID: 25313157]
J Brad Karpinka, Joshua D Fortriede, Kevin A Burns, Christina James-Zorn, Virgilio G Ponferrada, Jacqueline Lee, Kamran Karimi, Aaron M Zorn, Peter D Vize
Nucleic acids research 2015:43(Database issue)
Citation (to be updated)
Abstract: Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and gene targeting. The two species are extremely similar and protocols, reagents and results from each species are often interchangeable. Xenbase imports, indexes, curates and manages data from both species; all of which are mapped via unique IDs and can be queried in either a species-specific or species agnostic manner. All our services have now migrated to a private cloud to achieve better performance and reliability. We have added new content, including providing full support for morpholino reagents, used to inhibit mRNA translation or splicing and binding to regulatory microRNAs. New genomes assembled by the JGI for both species and are displayed in Gbrowse and are also available for searches using BLAST. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- The Xenbase literature curation process. [PMID: 23303299]
Jeff B Bowes, Kevin A Snyder, Christina James-Zorn, Virgilio G Ponferrada, Chris J Jarabek, Kevin A Burns, Bishnu Bhattacharyya, Aaron M Zorn, Peter D Vize
Database : the journal of biological databases and curation 2013:2013
3 Citations (Google Scholar as of 2016-02-28)
Abstract: Xenbase (www.xenbase.org) is the model organism database for Xenopus tropicalis and Xenopus laevis, two frog species used as model systems for developmental and cell biology. Xenbase curation processes centre on associating papers with genes and extracting gene expression patterns. Papers from PubMed with the keyword 'Xenopus' are imported into Xenbase and split into two curation tracks. In the first track, papers are automatically associated with genes and anatomy terms, images and captions are semi-automatically imported and gene expression patterns found in those images are manually annotated using controlled vocabularies. In the second track, full text of the same papers are downloaded and indexed by a number of controlled vocabularies and made available to users via the Textpresso search engine and text mining tool.
- Xenbase: expansion and updates of the Xenopus model organism database. [PMID: 23125366]
Christina James-Zorn, Virgilio G Ponferrada, Chris J Jarabek, Kevin A Burns, Erik J Segerdell, Jacqueline Lee, Kevin Snyder, Bishnu Bhattacharyya, J Brad Karpinka, Joshua Fortriede, Jeff B Bowes, Aaron M Zorn, Peter D Vize
Nucleic acids research 2013:41(Database issue)
43 Citations (Google Scholar as of 2016-02-28)
Abstract: Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus and Xenopus data to workers using other model organisms. As an amphibian Xenopus serves as a useful evolutionary bridge between invertebrates and more complex vertebrates such as birds and mammals. Xenbase content is collated from a variety of external sources using automated and semi-automated pipelines then processed via a combination of automated and manual annotation. A link-matching system allows for the wide variety of synonyms used to describe biological data on unique features, such as a gene or an anatomical entity, to be used by the database in an equivalent manner. Recent updates to the database include the Xenopus laevis genome, a new Xenopus tropicalis genome build, epigenomic data, collections of RNA and protein sequences associated with genes, more powerful gene expression searches, a community and curated wiki, an extensive set of manually annotated gene expression patterns and a new database module that contains data on over 700 antibodies that are useful for exploring Xenopus cell and developmental biology.
- Xenbase: gene expression and improved integration. [PMID: 19884130]
Jeff B Bowes, Kevin A Snyder, Erik Segerdell, Chris J Jarabek, Kenan Azam, Aaron M Zorn, Peter D Vize
Nucleic acids research 2010:38(Database issue)
69 Citations (Google Scholar as of 2016-02-28)
Abstract: Xenbase (www.xenbase.org), the model organism database for Xenopus laevis and X. (Silurana) tropicalis, is the principal centralized resource of genomic, development data and community information for Xenopus research. Recent improvements include the addition of the literature and interaction tabs to gene catalog pages. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. Gene expression data are integrated into the gene catalog via an expression tab and is also searchable by multiple criteria using an expression search interface. The gene catalog has grown to contain over 15,000 genes. Collaboration with the European Xenopus Research Center (EXRC) has resulted in a stock center section with data on frog lines supplied by the EXRC. Numerous improvements have also been made to search and navigation. Xenbase is also the source of the Xenopus Anatomical Ontology and the clearinghouse for Xenopus gene nomenclature.
- Xenbase: a Xenopus biology and genomics resource. [PMID: 17984085]
Jeff B Bowes, Kevin A Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, Peter D Vize
Nucleic acids research 2008:36(Database issue)
99 Citations (Google Scholar as of 2016-02-28)
Abstract: Xenbase (www.xenbase.org) is a model organism database integrating a diverse array of biological and genomic data on the frogs, Xenopus laevis and Xenopus (Silurana) tropicalis. 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.