Plazi: Prospects for Markup of Legacy and New Taxonomic Literature Terry Catapano TDWG Fremantle, WA October 21, 2008

NSF/DFG Grant (AMNH/University of Karlsruhe)‏ XML Markup of taxonomic publications for extraction of: Treatments Scientific Names Morphological Characters Distribution Data Collection locales/events For: Open Access Submission to db's Retrieval Ontology development

Markup Languages Provides grammar to define document types Delineate & identify document elements (atoms) in text Syntax: Structural relationships between elements (parent/child, cardinality, ordinality, id/idref, key/keyref)‏ Beyond the PDF‏

TaxonX schema Golden Gate Editor 250 Docs/7500 Treatments DSpace-based Digital Object Repository (handles)‏ SRS TAPIR (specimen data)‏ Species Profile Model/RDF (descriptive data)‏

Wildly heterogeneous Requires lax structuring of documents Need for regularization Requires editorial policy (reproduction: text of work or text of document) Defers much work of interoperability Benefits Treatments +names, subsections, localities, bibliographic references Extraction & representation in other services Costs GoldenGate configured for testbed: 3 minutes per page $5 page(?)‏

New Literature Different markup activity Different markup activity Prospective not Retrospective More optimal cost/benefit ratio? Strict modeling for consistent documents/data Increased regularization Increased sharing, re-use Decreased costs (potentially)‏: Application QC Adoption

TDWG Vocabularies supply many concepts NLM Journal Archiving and Interchange Tag Suite DTD's for markup of journal articles Archiving, Publishing, Authoring, other modules possible Wide adoption by publishers and aggregators; LOC Actively maintained Module for taxonomic treatments in Publishing

Inherit generic features from existing Tag Set Bibliographic references Tables Linking supporting material/data (xlink)‏ Linking to graphic and media objects (xlink)‏ Treatments Treatment sections Scientific names, Geographic names, Characters/States Specimens and other materials citations

Plazi: NLM conversion of Zootaxa and PLOS One articles Apply markup at earliest stage possible Develop tools to assist (probably easier than for “pure” legacy literature)‏ Extend codes and structures to handle electronic publication Shifts “illustrated narrative” complex digital objects METS, OAI-ORE, MPEG-21/DIDL

Text Materials Description Treatment Image Data Nomenclature

Linked Data Machines > Documents > Data Open documents, free data Reduced costs of use/re-use (e.g., SPM for EOL)‏ Broaden scope of application Accelerate velocity of information exchange