ArticleSystematic biology2012
NeXML: rich, extensible, and verifiable representation of comparative data and metadata.
Article in Systematic biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.Systematic biology · 2024Article
- Simple prerequisite of presequence for mitochondrial protein import in the unicellular red alga Cyanidioschyzon merolae.Journal of cell science · 2024Article
- The Tree Reconstruction Game: Phylogenetic Reconstruction Using Reinforcement Learning.Molecular biology and evolution · 2024Article
- Reorganization of the ancestral sex-determining regions during the evolution of trioecy in Pleodorina starrii.Communications biology · 2023Article
- Fidelity of hyperbolic space for Bayesian phylogenetic inference.PLoS computational biology · 2023Article
- Measuring Phylogenetic Information of Incomplete Sequence Data.Systematic biology · 2022Article
- A vectorial tree distance measure.Scientific reports · 2022Article
- Morphology, mating system and taxonomy of Volvox africanus (Volvocaceae, Chlorophyceae) from Thailand.Botanical studies · 2022Article
- FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example.Journal of biomedical semantics · 2021Article
- Revisiting Shao and Sokal'sJournal of mathematical biology · 2021Article
- Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.BMC bioinformatics · 2021Article
- Root Digger: a root placement program for phylogenetic trees.BMC bioinformatics · 2021Article
- Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees.Systematic biology · 2020Article
- Article
- On the minimum value of the Colless index and the bifurcating trees that achieve it.Journal of mathematical biology · 2020Article
- Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data.Molecular biology and evolution · 2020Article
- When mycologists describe new species, not all relevant information is provided (clearly enough).MycoKeys · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. 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. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input-output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.