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Xenbase Data Downloads

Xenbase data downloads provide access to genomes, database content, and more. Most files are in a tab delimited format. Click the "readme" link to view information on the files, including the header row for these files. To download a file, click on the corresponding link on the far right side. More files are available on our data download site. If you have any questions about the content of the files, or would like a custom Data Report generated, please contact us. To submit your data to Xenbase, please contact us

Genomics

Genomes


Sequences

BLAST databases


Data Reports

Xenbase data reports are updated weekly.


Ontologies

Xenopus Anatomy Ontology (XAO)

The Xenopus Anatomy Ontology describes Xenopus anatomy and embryological development using a 'controlled vocabulary' of anatomy terms that are organized in an hierarchy with a graphical structure. Xenbase curators use XAO terms to describe gene expression, and the XAO is constantly being updated in response to the latest published Xenopus research.

XAO 10.0 [readme] Download as: obo owl

Xenopus Phenotype Ontology (XPO)

The Xenopus Phenotype Ontology (XPO) is a structured controlled vocabulary for the curation of abnormal phenotypes in Xenopus species. The XPO covers anatomical, behavioral, molecular function and biological process phenotypes. The XPO has been developed using design patterns adhering to templates provided by uPheno (https://github.com/obophenotype/upheno). The XPO is built from logical axioms connecting terms from other ontologies and incorporates elements of the XAO, GO, NBO and PATO ontologies.

XPO 2.0 [readme] Download as: obo owl json

Xenopus Small Molecules Ontology (XSMO)

The Xenopus small molecule ontology (XSMO) is a controlled vocabulary of chemical entities, The XSMO is used in Xenbase curation of experimental details for phenotypes and metadata curation for GEO processing. Chemical entities in the XSMO have synonyms and cross references to PubChem IDs where available.

XSMO 1.1 [readme] Download as: obo

Xenbase Experimental Data Ontology (XBED)

The Xenbase Experimental Data Ontology (XBED) is a structured controlled vocabulary covering many aspects of Xenbase curation. The XBED covers different classifications of article content, article copyright statuses, assay methods, experimental manipulation types and other factors required for curation.

XBED 1.2 [readme] Download as: obo