NeXML - phylogenetic data as XML

Nexml A future data exchange standard for phylogenetics Rutger Vos

Increased automation in evolutionary informatics is hampered by poorly defined “standards” Introduction (1/7) The problem Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Addressing interoperability problems by coding our way out of it Introduction (2/7) EvoInfo.nescent.org interests Syntax: Nexml Semantics: CDAO Transport: PhyloWS Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance 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 , 1997. NEXUS: An Extensible File Format for Systematic Information. Syst. Biol. 46 (4):590-621
Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Introduction (4/7) Nexus issues
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 The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources https://www.nescent.org/wg_evoinfo/NEXUS_Problems

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

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

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

Design (1/5) Design principles
Re-use of prior art
Follow design patterns
Referencing
Verbose and compact representations

Design (2/5) Re-use of prior art
Generic key/value attachments using RDFa
Trees and networks following graphml
General file structure following nexus concepts, i.e. blocks that reference each other

Design (3/5) XML design patterns
http://www.xmlpatterns.com
“ Declare before use”
“ Metadata first”
“ Venetian blinds”
Abstract inheritance through extension, concrete inheritance through restriction

Design (4/5) Inheritance IDTagged (required id attribute) Labelled (optional label attribute) Annotated (optional dict elements) Base (optional base/lang/href attributes) AbstractElement (in root schema) ConcreteElement (in instance document) extends extends extends extends restricts Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance 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"/>

<node id="n1" otu="t1"/>

Implementation (1/6) Approach
Schema design
Community feedback through wiki, email, telecon, projects (evoinfo, ppod, MIAPA) etc.
Processors (perl, java, python, c++, javascript, VB) development in parallel
Experiments with xml tools (ws, db, data binding tools)

Implementation (2/6) Entity relationships Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

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 ERD Inheritance 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> <meta id="m1" datatype="xsd:string” xsi:type="nex:LiteralMeta” property="dwc:catalogNumber" content="12345"/> Contents… Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Implementation (5/6) Character Classes RestrictionCells RestrictionSeqs Restriction ContinuousCells ContinuousSeqs Continuous StandardCells StandardSeqs Standard ProteinCells ProteinSeqs Protein RnaCells RnaSeqs RNA DnaCells DnaSeqs DNA Cells Sequence Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Implementation (6/6) Tree Classes IntTree FloatTree Tree IntNetwork FloatNetwork Network Int Float Introduction The problem EvoInfo interests This subproject Nexus issues Parsing Extensibility XML goodies Design Principles Re-use Patterns Inheritance References Implementation Approach ERD Inheritance 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

Nexml parsers and writers:
Phenex
TreeBASE
Mesquite
Bio::Phylo
DendroPy
DAMBE
Etc.
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 ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Included schema in soap wsdl
Indexed files in dbxml
Created large files from tolweb, rbcl
XInclude with tinyseq xml
REST service described using nexml
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 ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Cross-reference with glossary, ontology
Substitution model descriptions
Publish standard
Compact trees
Distances
Splits
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 ERD Inheritance Anatomy Characters Trees Current status Schema blocks Parsers & writers Experiments To do Resources

Resources
NeXML Base URL: http://nexml.org
Wiki: /wiki
Mailing list: /mail
Issue tracker: /tracker
SVN repository: /code
EvoInfo: http://evoinfo.nescent.org

CDAO: http://www.evolutionaryontology.org

Acknowledgements
Contributions: Jason Caravas, Mark Holder, Peter Midford, Jeet Sukumaran, Xuhua Xia, Chase Miller, Anurag Priyam, Jaime Huerta-Cepas, Matt Yoder, Andrew Hill, Sam Smits, Mike Keesey, Apurv Verma, Mark Jensen
Feedback: wg-evoinfo, pPOD, Wayne Maddison, David Maddison
Additional funding, support: NESCent, GSoC

NeXML - phylogenetic data as XML

by Rutger Vos on Jan 19, 2012

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