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

2. 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

3. 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

4. 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

5. 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

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

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

8. 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

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

10. 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"/>

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

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

13. 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

14. 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…

15. 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

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

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

18. 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)

19. 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

20. Nexml (10/10) Resources GSoC Base URL SVN Wiki SourceForge repository
Base URL
SVN
Wiki
SourceForge repository

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