"I love NeXML - phylogenetic data as xml"

2022-05-09 13:10:18

NeXML - phylogenetic data as xml Skip to: Site menu | Main content [NeXML] Rich phyloinformatic data The future data exchange standard is here! NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process. Overview The NEXUS flat file format is a commonly used syntax forphylogenetic data. Unfortunately, over time, non-compliant NEXUS implementationshave overloaded the standard - which has caused variousproblems. Meanwhile, mature technologies around theXML standard haveemerged. These technologies have the potential to greatlysimplify and improve robustness in the processing of rich phylogeneticdata. This website is the home for the community-driven NeXML project, whichseeks to leverage XML technologies in the development of a data standardthat translates NEXUS concepts into a syntax that is more easily validatedand processed. This approach promises several advantages:Syntax validation — some of the issues hamperinginteroperability are caused by the fact that no formalspecification exists for NEXUS and other flat files, and no unambiguous wayto validate them. Using XML Schema we have defined a versioned grammar against whichdata files can be validated syntactically. In addition, this website has a validationservice (the orange box in the center of every page) that also checks the semanticsof uploaded NeXML files beyond ways that can be expressed in XSD schema language.Semantic annotation — an issue in current fileformats is that their semantics are not well-defined. For example, what doesit mean to use an ambiguity code in a matrix? Is it uncertainty or polymorphism?With the wider EvoInfo working group we are developing an ontology on which we are mapping NeXML schema types so that the semanticsof data files become well-defined. In addition, NeXML has a facility forannotating fundamental phylogenetic data objects (such as trees, characterstate matrices and taxa) with ontology predicates and objects usingRDFa.Web services — a number of differenttechnologies (such as XML-RPC,RESTand SOAP) haveemerged allowing disparate, xml-based services to be glued togetherover the internet. For example, thePhyloWSinitiative seeks to develop conventions for RESTful phylogenetic webservices for which NeXML is one of the preferred response formats.Because of the advantages of NeXML over current standards, developers of phylogenetic software have come together as part of the NESCent working group for evolutionary informatics to develop thisnew data exchange standard based on XML technologies.We have recently published a description of NeXML in SystematicBiology. If you use NeXML in your research, please consider citingdoi:10.1093/sysbio/sys025 [ Back to top ]What are we doing about it?NeXML development is being undertaken along a number of tracks:In the first place, there's an XML schema. Thisschema (currently designated as namespace http://www.nexml.org/2009)is explained on ourwiki andformally documented; the latest version is available fromgit.Secondly, the community is implementing NeXML read and/or write abilities in anumber of software applications: Carl Boettiger and Scott Chamberlain have developed an excellent NeXML library for R for rOpenSci.TreeBASE supports serialization to NeXML.The Mesquite projectsupports readingand writing of NeXML. Wayne Maddison and Peter Midfordhelped start an implementation for this that is currently beingmaintained by Rutger Vos. Xuhua Xia's DAMBEversion 5.2.31 for Windows Vista/7 reads and writes NeXMLdata.The PhenoScape project uses NeXML to annotate complex morphological characterstates with ontology terms in itsPhenex editor.Jeet Sukumaran has implemented NeXML I/O for python in the DendroPy package.There are many DendroPycode samplesfor dealing with NeXML data in the wiki manual.Chase Miller has implementedBio::NexmlIO forBioPerl, which underthe hood reuse Rutger Vos'sBio::Phyloparser libraries.Anurag Priyam and Rutger Vos have developed a NeXML I/O pluginfor theBioRuby open source bioinformatics library for Ruby.Jaime Huerta-Cepas' team is working on NeXML I/O for theETE Python environment for tree exploration.Matt Yoder has implemented NeXML serialization for themx collaborative web-based content management system for evolutionary systematists.Andrew Hill has added NeXML support to PhyloBox.Sam Smits has made it so that the jsPhyloSVG tree visualization widget can now show NeXML trees.Mike Keesey has added NeXML support to Names On Nodes,a web application that automatically applies biological nomenclature to datasets.Daniel Huson's DendroScopedevelopment team has adopted NeXML as its primary file format for storing visualization (styling)metadata. However, at present, its implementation is not fullycompliant so should not be taken as a template to generate NeXML output.For the 2011 Google Summer of Code, Apurv Verma has addedNeXML reading capability tophyloGeoRef.Mark Jensen has implemented NeXML compatability for theHIVQuery webapplication.Third, we're crossreferencing the NeXML schema with theCharacter Data Analysis Ontologywhich is being developed by other members of the EvoInfo working group. [ Back to top ] Get involved! If you are interested in being involved in the NeXML project in any way, please do! Here are some ways to get involved:Get informed — information about the NeXMLproject is distributed over the manual(for an overview of vision, plans, implementation),documentation(for formal description of the schema) and themailing list(for immediate plans and discussion).Try it out — the download section of thewebsite has nightly builds of bindings for various languages.Take these for a spin!Contribute — if you are a programmer interestedin extending NeXML support, please contact us through the mailinglist to get commit support for the subversion repository. [ Back to top ]AcknowledgementsThe research leading to these results has received funding from the [EuropeanCommunity's] Seventh Framework Programme ([FP7/2007-2013] under grant agreementn° [237046]. [ Back to top ]Suggested citationRutger A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, P. E. Midford, A. Priyam, J. Sukumaran, X. Xia, and A. Stoltzfus. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61(4): 675-689 [doi:10.1093/sysbio/sys025] [ Back to top ] Quick links: Manual Schema documentation NeXML publication Example files Slide show Libraries: Java | Python | Perl | C++ | JavaScript | Ruby | Top of page External links nexml@github NeXML wiki CDAO PhyloWS Site implementation and technology: © Rutger Vos. Site design: © Andreas Viklund of Jokkmokk.