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Nexml A future data exchange standard for phylogenetics
Rutger Vos University of British Columbia
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Introduction (1/7) The problem
EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (1/7) The problem Increased automation in evolutionary informatics is hampered by poorly defined “standards”
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Introduction (2/7) EvoInfo interests
The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (2/7) EvoInfo interests Semantics: CDAO Syntax: Nexml Transport: PhyloWS Addressing interoperability problems by coding our way out of it
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Introduction (3/7) This subproject’s mission
The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (3/7) This subproject’s mission To create a file format like nexus*, but: Fix (some) problems with nexus Give access to data at higher level Be extensible Expose data to xml goodies *Maddison, Swofford and Maddison, NEXUS: An Extensible File Format for Systematic Information. Syst. Biol. 46(4):
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Introduction (4/7) Nexus problems
The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (4/7) 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
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Introduction (5/7) Parsing plain text versus parsing XML
The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (5/7) Parsing plain text versus parsing XML Processing nexus data involves lexing + parsing + processing XML allows choosing a parser library, data can be processed as a structure that hides tokenization issues
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Introduction (6/7) Extensibility
The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (6/7) Extensibility ‘Extensible’ file format should provide the ability to: define new data types that implement described ‘interfaces’ attach typed data structures to core types attach custom XML
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Introduction (7/7) XML goodies
The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Introduction (7/7) XML goodies Large stack of off-the-shelf tools: XML parser libraries Web service toolkits Native XML databases Editors / IDEs Serialization / data binding tools
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Design (1/5) Design principles
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Design (1/5) Design principles Re-use of prior art Follow design patterns Referencing Verbose and compact representations
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Design (2/5) Re-use of prior art
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Design (2/5) 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
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Design (3/5) XML design patterns
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Design (3/5) XML design patterns “Declare before use” “Metadata first” “Venetian blinds” Abstract inheritance through extension, concrete inheritance through restriction
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Design (4/5) Inheritance
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Design (4/5) Inheritance “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
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Design (5/5) Referencing
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Design (5/5) 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: <otu id="t1"/> <!-- i.e. OTU, referenced later as: --> <node id="n1" otu="t1"/>
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Implementation (1/6) Approach
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Implementation (1/6) Approach Schema design Community feedback through wiki, , telecon, projects (evoinfo, ppod, MIAPA) etc. Processors (perl, java, python, c++, VB) development in parallel Experiments with xml tools (ws, db, data binding tools)
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Implementation (2/6) root element
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Implementation (2/6) root element version="1.0" generator="mesquite" Versioned namespace: xmlns:nex="
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Implementation (3/6) inheritance tree for elements
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Implementation (3/6) inheritance tree for elements
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Implementation (4/6) anatomy of a “block”
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Implementation (4/6) anatomy of a “block” <characters id="c1" xsi:type="nex:DnaSeqs" otus="t1"> </characters> <dict> <key>desc</key> <string>description…</string> </dict> Contents…
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Implementation (5/6) Character Classes
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Implementation (5/6) Character Classes Granularity Sequence Cells DNA DnaSeqs DnaCells RNA RnaSeqs RnaCells Protein ProteinSeqs ProteinCells Standard StandardSeqs StandardCells Continuous ContinuousSeqs ContinuousCells Restriction RestrictionSeqs RestrictionCells Data type
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Implementation (6/6) Tree Classes
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Implementation (6/6) Tree Classes Branch type Float Int Network FloatNetwork IntNetwork Tree FloatTree IntTree Topology
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Current status (1/4) Schema blocks
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Current status (1/4) Schema blocks Done: OTUs characters: dna, rna, nucleotide, protein, categorical, continuous, restriction (compact and verbose) trees: graphml trees and networks, various edge formats and rootings
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Current status (2/4) Parsers and writers
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Current status (2/4) Parsers and writers Nexml parsers and writers: mesquite, java, using xmlbeans Bio::Phylo, perl pyNexml, python DAMBE, Visual Basic stubs for c++ xmlbeans plans for ruby?
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Current status (3/4) Experiments
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Current status (3/4) Experiments Included schema in soap wsdl Indexed files in dbxml Created large files from tolweb, rbcl XInclude with tinyseq xml REST service described using nexml
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Current status (4/4) To do
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Current status (4/4) To do Cross-reference with glossary, ontology Substitution model descriptions Publish standard Follow up on earlier feedback (small fixes) Sets (in progress, using class identifiers) more restricted vocabulary attachments (Darwin core) Distances Splits
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Resources Base URL Wiki SourceForge project
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach Example Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources Resources Base URL Wiki SourceForge project
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Acknowledgements Contributions: Jason Caravas, Mark Holder, Peter Midford, Jeet Sukumaran, Xuhua Xia Feedback: wg-evoinfo, pPOD, Wayne Maddison, David Maddison Additional funding, support: NESCent, GSoC
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