Nexus XML
Names
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Nexus XML
metasource: Fairsharing.org
version: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
NeXML
metasource: Fairsharing.org
version: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
Nexus XML
metasource: Fairsharing.orgversion: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
NeXML
metasource: Fairsharing.orgversion: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
Nexus XML
metasource: Fairsharing.orgversion: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
NeXML
metasource: Fairsharing.orgversion: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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
Description
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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
metasource: Fairsharing.orgversion: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://www.nexml.orgWebpage
More detailed information about this field from each metasource.
http://www.nexml.org
metasource: Fairsharing.orgversion: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
NeXML: rich, extensible, and verifiable representation of comparative data and metadata
PMID: 22357728
metasource: Fairsharing.org
version: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
NeXML: rich, extensible, and verifiable representation of comparative data and metadata
PMID: 22357728
metasource: Fairsharing.org
version: FAIRsharing.org: NeXML; Nexus XML; DOI: https://doi.org/10.25504/FAIRsharing.knrb06; Last edited: Jan. 8, 2019, 1:30 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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NeXML: rich, extensible, and verifiable representation of comparative data and metadata
PubMed citations: 42.
42 articles citing: NeXML: rich, extensible, and verifiable representation of comparative data and metadata
A vectorial tree distance measure. PMID:35347186
Morphology, mating system and taxonomy of Volvox africanus (Volvocaceae, Chlorophyceae) from Thailand. PMID:35061120
Understanding the Nature of Metadata: Systematic Review. PMID:35014967
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. PMID:34823588
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. PMID:34187366
Root Digger: a root placement program for phylogenetic trees. PMID:33932975
When mycologists describe new species, not all relevant information is provided (clearly enough). PMID:32982558
Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen Phytophthora infestans. PMID:32576669
Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees. PMID:31769837
Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data. PMID:31633786
Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases. PMID:31428595
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. PMID:31331268
Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update. PMID:31076745
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. PMID:30576485
phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. PMID:30045713
The Biological Object Notation (BON): a structured file format for biological data. PMID:29941895
Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes. PMID:29325126
IcyTree: rapid browser-based visualization for phylogenetic trees and networks. PMID:28407035
Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building. PMID:27855645
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes. PMID:27145223
Two Influential Primate Classifications Logically Aligned. PMID:27009895
WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States. PMID:26949580
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens. PMID:26424081
Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PMID:26385966
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. PMID:26018570
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. PMID:25972520
Phylesystem: a git-based data store for community-curated phylogenetic estimates. PMID:25940563
MatrixConverter: Facilitating construction of phenomic character matrices. PMID:25699217
A synthetic phylogeny of freshwater crayfish: insights for conservation. PMID:25561670
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. PMID:25411634
Enriched biodiversity data as a resource and service. PMID:25057255
Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. PMID:24990571
Best practices for data sharing in phylogenetic research. PMID:24987572
The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction. PMID:24891820
Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach. PMID:24565381
The importance and application of the ancestral recombination graph. PMID:24133504
GraphML specializations to codify ancestral recombinant graphs. PMID:23967010
DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. PMID:23564938
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. PMID:23327936
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. PMID:23088596
Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. PMID:22909249
TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. PMID:22724002
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