standards > model/format > DOI:10.25504/FAIRsharing.knrb06


ready Nexus XML

Abbreviation: NeXML


General Information
To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats

Homepage http://www.nexml.org

Countries that developed this resource Canada , India , Netherlands , United States

Created in 2011

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How to cite this record FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Apr 11 2021 10:27 p.m.


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Record updated: March 15, 2018, 10:16 a.m. by The FAIRsharing Team.

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NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A.
Systematic Biology 2012

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Related Databases (2)
TreeBase
TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa.

MorphoBank
MorphoBank provides a digital archive of biodiversity and evolutionary research data, specifically systematics (the science of determining the evolutionary relationships among species). MorphoBank aids development of the Tree of Life - the genealogy of all living and extinct species. Heritable features - both genotypes (e.g., DNA sequences) and phenotypes (e.g., anatomy, behavior, physiology) are stored as part of the Tree of Life project. While the genomic part of this work is archived at the National Center for Biotechnology Information (NCBI), MorphoBank is part of the infrastructure for storing and sharing phenotype data, including information on anatomy, physiology, behavior and other features of species. One can think of MorphoBank as two databases in one: one that permits researchers to upload images and affiliate data with those images (labels, species names, etc.) and a second database that allows researchers to upload morphological data and affiliate it with phylogenetic matrices. In both cases, MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived. The phylogenetic matrix aspect of MorphoBank is designed to aid systematists working alone or in teams to build large phylogenetic trees using morphology (anatomy, histology, neurology, or any aspect of phenotypes) or a combination of morphology and molecular data.

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  • 237046 (European Commission FP7)