1. TaxPub: An Extension of JATS for Taxonomic Descriptions Terry Catapano 2010-11-02

2. Taxonomic Descriptions “Treatment” Discussion of the features/distribution of a related group of organisms, “taxon” Formal conventions ICZN, ICBN, etc... Frequently parts of publications Cited as discrete objects 200+ year history

3. Linnaeus, Systema Naturae, 10th Edition, 1767- 1770

4. Taekul, C., N. F. Johnson, L. Masner, A. Polaszek and Rajmohana K.. 2010. World species of the genus Platyscelio Kieffer (Hymenoptera, Platygastridae). ZooKeys 50: 97-126.

5. Treatment Components Nomenclature o Name o Authority o Status, etc… Description Materials Examined o Specimens  Collection  Deposit Diagnosis, Distribution, Etymology, Key, etc…

6. Background: TaxonX NSF/DFG Funded Project Extraction of species data from taxonomic literature of Ants TaxonX schema for markup of corpus c. 500 publications; c. 11,000 treatments Development continued by Plazi

7. Independent Not-for-Profit Association Based in Switzerland Members from varied domains Pro Bono Open Access to Scientific Literature o Legal  "...[T]axonomic treatments as well as the metadata of the publications – are in the public domain and can therefore be used for further scientific research without any restriction, whether or not contained in copyrighted publications."  Agosti D, Egloff W (2009). "Taxonomic information exchange and copyright: the Plazi approach". BMC Research Notes 2:53. doi:10.1186/1756-0500-2-53.

8. Open Data: Technical Activities o GoldenGate Markup Editor o Treatment Repository: Literature of Ants o Treatments provided to Encyclopedia of Life (EOL) o Collaborations and Participation: – Journals: ZooKeys, Zootaxa – "Fine-Grained Markup of Descriptive Data for Knowledge Applications in Biodiversity Domains", Hong Cui, U. of Arizona PI. (NSF) – “The Hymenoptera Ontology: Part of a Transformation in Systematics and Genome Sciences" Andrew Deans, N.C. State PI (NSF) – Global Biodiversity Information Facility (GBIF) o Implemented TAPIR o Implemented Species Profile Model (SPM) o Report on Knowledge Organization Systems – TaxonX & TaxPub

9. TaxPub

10. Legacy Literature: Challenges Text accuracy Formal/Editorial Variety Condensed Information Loose schema, higher costs of application

11. New Literature: Rationale Matt Yoder et al., Development of the Hymenoptera Anatomy Ontology: Implications for Systematics and Literature Mark-up

12. TaxPub Extension of Publishing (“Blue”) DTD Parsimony: largely rely on base DTD “tp:” namespace Available throughout o : scientific names o : morphology o : specimens; gene sequences Within o + subelements

13. "Common" TaxPub Elements

14. A further undescribed Nixonia species related to N. lamorali emerged from processing of samples collected in Kogelberg Biosphere Reserve (50km east of Cape Town). This species may usurp N. gigas...

15. , con't @reg: regularized form of name object-id: identifier(s) for name o semantics of xlink attrs? @*-part-type: semantics for name components o string o use URI's: here terms from Darwin Core vocabulary (http://rs.tdwg.org/dwc/terms/) N. lamorali

16. Relatively undeveloped Modeling of descriptions challenging o complex, if formal, natural language Segment text o Delineate components o Normalize/Annotate o

17. ... Length 7.0 mm ; completely black, tarsi lighter (figs. 2A, B); wings infuscate throughout, brownish...... tarsi lighter...

18. ... tarsi lighter...

19. : how, when collected o : where collected : current location

20. , con't 1 male, South Africa Western Cape" Langberg Farm, (3 km 270° W Langebaanweg) 32°58.461’S 18°07.344’E 12–19 Mar 2003, S. van Noort, Malaise trap, LW02-N2-M175, Sand Plain Fynbos, SAM-HYM-P030184, OSUC 256954 ), ( SAMC ) tp:location: o @location-type:  URI (Darwin Core)  string named-content: all other components

21. tp:treatment and Sub-Elements

22. o bibliographic metadata for treatments o standalone treatments : required o : required o other elements... o @sec-type

23. Nixonia masneri van Noort & Johnson sp. n. Figures 1A–F

24. Nixonia Masner, 1958, 101 Original description. Type: Nixonia pretiosa Masner, by monotypy and original designation. For subsequent taxonomic literature see Johnson (1992) or The Genera of Platygastroidea of the World ( http://purl.oclc.org/NET/ hymenoptera/platygastroidea ).

26. Type material Holotype... Diagnosis Most similar to... Etymology Named in honour of Lubomír Masner,... Distribution and habitat association Currently only known from two widely spaced localities.... Description..., con't

27. Keys Indentify subordinate taxa within higher taxon (e.g., species in genus) No model in TaxPub Use existing JATS table model Use or

28. Keys, con't Key to species of Nixonia Online interactive key...> 1 Third antennal segment shorter than, or subequal to, second antennal segment 2

29. Test Implementations “Data-driven” publication –OSU Virtual Systematics Lab –Database morphological data –Export taxon descriptions as TaxPub ZooKeys –ZooKeys 50 –Archived by PubMed Central

32. Status and Future SourceForge project –http://sourceforge.net/projects/taxpubhttp://sourceforge.net/projects/taxpub Subversion Updated Documentation, examples, tools (conversion and profiling) Next release December 2010 Call for comment December 2010 Version 1: March 2011 Expand Zoological focus Morphology markup Vocabularies for type attributes, etc... Continued modeling, maintenance infrastructure, hand off... Data-driven treatment publication

33. Reflections, Self-Criticisms, Doubts

34. Problems, Issues “Treatments” –Undefined –Conventional, but not Regular Zoological focus to date Prospective/Retrospective blurry Data/Publication –Scenarios? (XHTML + RDFa, ePub, extraction of data for analysis) –Inline vs. Linked –Metadata and Packaging Page breaks –Code requirements –Citation practices

35. DTD Perceived as “old-fashioned”, “superseded” Unfamiliar Complex Technical Limitations –Datatypes: (really an issue for taxonomic pubs?) –Namespaces: (e.g., Keys; existing schemas; embed?) –Tools, libraries: (processing preferences) Embedded XML documentation

36. Super Set Customization Necessary? “Structural” elements: – + @sec-type adequate? has own content model Restrictions to enable lower costs of creation/application ZooKeys: too restrictive (PCDATA), hard to model in generic JATS Otherwise semantic sugar adequate? TaxPub mostly isomorphic with Blue (e.g., ZooKeys > PMC) So...why? Schema Validation Applications (not yet) Convenience Social/Market value Reifies; focuses efforts

37. Profiling Customization is not just Extension files –Documention on use of Extension –Documention on use of Blue DTD –Samples –Tools Semantic and Structural Layers Use or develop vocabularies for type attributes –e.g., DarwinCore –Model and Publish own –Enumerate in DTD, Schematron Express usage rules –Subset –Schematron