2024: Domino Containers - The Next Step. News from the Domino Container commu...
NeXML
1. NeXML A future data exchange standard for phylogenetics Rutger Vos University of British Columbia
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 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
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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
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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="c1" xsi:type="nex:DnaSeqs" otus="t1"> </characters> <dict> <key>desc</key> <string>description … </string> </dict> 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
