Presentation on theme: "TaxPub: An Extension of JATS for Taxonomic Descriptions Terry Catapano, Plazi Leiden, Netherlands 2013-02-14."— Presentation transcript:
TaxPub: An Extension of JATS for Taxonomic Descriptions Terry Catapano, Plazi Leiden, Netherlands 2013-02-14
JATS Journal Article Tag Suite Formerly NLM/NCBI Journal Archiving and Publishing Tag Suite Version 1, 2002 PubMed Central Widely adopted by STM publishers Now NISO JATS ANSI/NISO Z39.96-2012
JATS DTD Spectrum Legacy/Loose Prospective/Strict Archiving (Green) DTD Publishing (Blue) DTD Now also Authoring and Book DTDs Offers extensibility features
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
Linnaeus, Systema Naturae, 10th Edition, 1767- 1770
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.
Treatment Components Nomenclature o Name o Authority o Status, etc… Description Materials Examined o Specimens Collection Deposit Diagnosis, Distribution, Etymology, Key, etc…
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
Legacy Literature: Challenges Text accuracy Formal/Editorial Variety Condensed Information Loose schema, higher costs of application
New Literature: Rationale Matt Yoder et al., Development of the Hymenoptera Anatomy Ontology: Implications for Systematics and Literature Mark-up
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
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...
, 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
Relatively undeveloped Modeling of descriptions challenging o complex, if formal, natural language Segment text o Delineate components o Normalize/Annotate o
... Length 7.0 mm ; completely black, tarsi lighter (figs. 2A, B); wings infuscate throughout, brownish...... tarsi lighter...
Spreading shrub; stems erect, greenish http://ontology.org/plant/stem-colorhttp://ontology.org/plant/greenish. Leaves deciduous early in summer (particularly when infected with Diseasomyces), oblong, apex obtuse, glabrous or weakly hirsute; stipules sharply pointed, 3,2mm wide, http://ontology.org/plant/stipule-color black or darkish brown, extremely rarely yellow, often shallowly joined around the node; spines stout.
: how, when collected o : where collected : current location
, 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
o bibliographic metadata for treatments o standalone treatments : required o : required o other elements... o @sec-type
Nixonia masneri van Noort & Johnson sp. n. Figures 1A–F
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 ).
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
Keys Indentify subordinate taxa within higher taxon (e.g., species in genus) No model in TaxPub Use existing JATS table model Use or
Keys, con't Key to species of Nixonia Online interactive key...> 1 Third antennal segment shorter than, or subequal to, second antennal segment 2
Future Work Extension to “Green”/Archiving DTD o For legacy literature Descriptive data (i.e., keys, characters, states, etc...) Tools XSLT stylesheets for rendition/proofing XSLT stylesheets for conversion to external formats Development of supporting vocabularies Schematron for profiling Stand-alone validator Implementations EJT Smithsonian Zootaxa