Rutger Vos and Wayne Maddison University of British Columbia Nexml Rutger Vos and Wayne Maddison University of British Columbia

Introduction (1/5) The idea A file format like nexus, but: Fixes (some) problems with nexus Gives access to data at higher level Extensible Exposes data to xml goodies

Introduction (2/5) Nexus problems Hard/impossible to validate No explicit versions Nothing ever deprecated No public extensions Leads to hacks such as ‘mixed’ data, ‘hot comments’ Phylogenetics post-’80s in private blocks

Introduction (3/5) Higher level data access Processing nexus data involves lexing + parsing + processing XML allows choosing a parser library, data can be processed as a structure that hides tokenization issues

Introduction (4/5) Extensibility ‘Extensible’ file format should, more robustly than NEXUS, provide the ability to: define new data types that implement described ‘interfaces’ attach typed data structures to core types attach custom XML

Introduction (5/5) XML goodies Large stack of off-the-shelf tools: XML parser libraries Webservices Native XML databases Editors/IDEs Serialization tools

Design (1/4) Design principles Re-use of prior art Follow design patterns Referencing Verbose and compact representations

Design (2/4) Re-use of prior art Generic key/value attachments following apple’s plist semantics: <dict> <key>prior</key> <float>0.78</float> </dict> Trees and networks following graphml General file structure following nexus concepts, i.e. blocks that reference each other

Design (3/4) XML design patterns http://www.xmlpatterns.com “Declare before use” “Metadata first” “Venetian blinds” Abstract inheritance through extension, concrete inheritance through restriction

Design (4/4) Referencing Elements sometimes refer to other elements, much like in nexus In nexml, elements refer to the id of other elements by the name of the referenced element: <taxon id="t1"/> <!-- i.e. OTU, referenced later as: --> <node id="n1" taxon="t1"/>

Nexml (1/8) Approach Schema design Community feedback through wiki, email, telecon, meetings (evoinfo, ppod) etc. Processors (perl+mesquite+python) development in parallel Experiments with xml tools (ws, db, serialization)

Nexml (2/8) root element version="1.0" generator="mesquite" Versioned namespace: xmlns:nex="http://www.nexml.org/1.0"

Nexml (3/8) inheritance tree for elements “Base”, optional base/lang/href attributes extends “Annotated”, optional dict elements extends “Labelled”, optional label attribute extends “IDTagged”, required id attribute extends “AbstractElement”, in root schema restricts “ConcreteElement”, in instance document

Nexml (4/8) anatomy of a “block” Name (e.g. "characters"), id attribute, xsi:type concrete subclass attribute (e.g. "nex:DnaSeq"), possible reference to other element: <characters id="c1" xsi:type="nex:DnaSeqs" taxa="t1"> </characters> Metadata attachment: <dict><key>desc</key><string>description…</string></dict> Contents…

Nexml (5/10) Character Classes Granularity Sequence Cells DNA nex:DnaSeqs nex:DnaCells RNA nex:RnaSeqs nex:RnaCells Protein nex:ProteinSeqs nex:ProteinCells Standard nex:StandardSeqs nex:StandardCells Continuous nex:ContinuousSeqs nex:ContinuousCells Restriction nex:RestrictionSeqs nex:RestrictionCells Data type

Nexml (6/10) Tree Classes Float Int Network Tree Branch type nex:FloatNetwork nex:IntNetwork Tree nex:FloatTree nex:IntTree Topology

Nexml (7/10) blocks, current status Done: OTUs characters: dna, rna, nucleotide, protein, categorical, continuous, restriction (compact and verbose) trees: graphml trees and networks

Nexml (8/10) blocks, current status To do: sets (in progress, using class identifiers) substitution model descriptions (KS progress) more restricted vocabulary attachments (Darwin core) distances splits cross-reference with glossary, ontology follow up on earlier feedback (small fixes)

Nexml (9/10) Experiments XML parsers: expat, libxml2, jdom Processed schema using xmlbeans Included schema in soap wsdl Indexed files in dbxml Created large files from tolweb, rbcl XInclude with tinyseq xml REST service described using nexml

Nexml (10/10) Resources GSoC Base URL SVN Wiki SourceForge repository https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Phylogenetic_XML Base URL http://www.nexml.org SVN http://nexml07gsoc.googlecode.com/svn/trunk/ Wiki https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard SourceForge repository

Acknowledgements Contributions: Jason Caravas, Mark Holder, Peter Midford, Jeet Sukumaran Feedback: wg-evoinfo, pPOD Additional funding, support: NESCent, GSoC