NeXML is an exchange standard for representing phyloinformatic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

1. Nexml A future data exchange standard for phylogenetics Rutger Vos

2. 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

3. 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

12. 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

15. 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

16. 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

17. Implementation (4/6) anatomy of a “block” <characters id=&quot;c1&quot; xsi:type=&quot;nex:DnaSeqs&quot; otus=&quot;t1&quot;> </characters> <meta id=&quot;m1&quot; datatype=&quot;xsd:string” xsi:type=&quot;nex:LiteralMeta” property=&quot;dwc:catalogNumber&quot; content=&quot;12345&quot;/> 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

18. 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

19. 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