ZHANG Zhi-Qiang 张 智 强

TDWG 2012 Conference Beijing, China 23 Oct 2012 Taxonomist & curator (mites) New Zealand Arthropod Collection, Landcare Research, Auckland

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Describer of biodiversity; user of biodiversity databases Commissioner International Commission on Zoological Nomenclature Chief editor & Founder, Zootaxa

Data of Zhang (2011)

“Without question, one indisputable publishing success in the field of zoological nomenclature is the taxonomic mega-journal Zootaxa ….. this publishing sensation has come from nowhere in 2001 to dominate the taxonomic publishing landscape as the world’s largest taxonomic journal .” “Zootaxa has helped defragment the publishing landscape for zoological taxonomy , making taxonomy findable , and enabling the disciple to benefit from the network effects of increased collaboration .” ---Vince Smith (2010) Systematic Biology 59(6): 759
“Zootaxa … is taxonomic publishing on a grand scale.” --- Rod Page (2010) http:// iphylo.blogspot.com/2010/08 / Chief editor & Founder, Zootaxa

196 links embedded to ZooBank using LSIDs and GUIDs for names, literature, CBOL, imagery and videos, and XML marked-up using standards in TaxonX .... Chief editor & Founder, Zootaxa

Journal data ------> biodiversity databases (retrospective)
Zootaxa fish and ant papers (2001-07) marked up using Golden Gate by Plazi
XML uploaded to Plazi
Distribution data to GBIF
Names data to ZooBank
Species accounts to EoL TaxPub : An Extension of the NLM DTD for Taxonomic Descriptions Describing and databasing biodiversity in e-publication era Reality
25 generations since Linnaeus have described only 1.5-2.0 million species on Earth, with 50-90% to be discovered and named (esp. invertebrates, Fungi, Protista, Bacteria & Archaea)
Only 20,000 new species are described each year at the present
Catalogue of described life is still a dream, let alone an EoL
Biodiversity crisis: we are at the present time living in an age of mass extinction

“Our generation is the first one and the last one to have the opportunity to discover and document all species on Earth before most of them are gone forever” (Quentin Wheeler)

The message
E-publication has a role to play via code-required journal-database interface How is e-publication allowed in amendments to the botanical & zoological codes? 2012 : taxonomy into e-publication era

Amendments to Amendments to botanical code (ICN) zoological code (ICZN) Starting date 1 Jan. 2012 4 Sept. 2012 ISSN/ISBN Required Required

Immutable fixed Required Required content/layout pdf Required explicitly pdf/A recommended

Registration of work Not required Required

Registration of names Not required, but for fungi, Not required from 2013 Archiving Not required Required

Latin diagnosis No longer required N/A (not required even before amendment) Consequences of allowing e-pub

• More and more print-only journals will become e-only • More and more print+online journals will become e-only • Journals from museums, small societies and others • Cost-saving by not printing • Possible investment in facilitating data distribution and archiving Consequences of allowing e-pub • More and more new e-only journals will be established • Reduced start-up costs • Reduced competitive edge of large commercial publishers as shown by new successful journals PLOS ONE (E-only) Zootaxa Phytotaxa Zookeys 2001 20 2002 107 2003 268 2004 396 2005 581 2006 137 1031 2007 1230 1128 2008 2717 1224 32 2009 4404 1506 18 156 2010 5934 1545 72 179 2011 ( impact factor ) 13785 ( 4.092 ) 1682 ( 0.927 ) 108 ( 1.797 ) 465 ( 0.879 ) Journal-database interface in e-pub era Catalogue of Life can be prospective
Coupling of e-pub with registration is a significant step but still incomplete
Code-required registration of fungus names in MycoBank (from 2013), unfortunately not for algae and plants
ICZN requires only registration of works so far; improved ZooBank to allow registration of all nomenclatural acts to couple with the development of the next edition of ICZN to require registration of all new names and nomenclatural acts

Bacteria has an Approved Lists with a starting point of 1980
International Committee on Taxonomy of Viruses (ICTV) has an authoritative database (ICTVdB) as of 2005 Increased e-publications need an aggregated journal portal for taxonomy

An international collaboration of museums, institutions, societies and other publishers for a shared integrated/aggregated journal web portal/publishing system where
taxonomic journals (large or small) by members will be hosted and
their back issues deposited/archived for perennial access (one of the conditions in the amendment of International Code of Zoological Nomenclature to allow e-only publication)
Members retain the identity of their journals and control; they themselves decide whether their journal(s) will be open access or subscription-based
A member-supported non-profit project/service
Self-sustaining
A permanent facility A non-profit permanent facility for defragmentation & partnership • This integrated/aggregated system
avoids duplicated efforts
enables other taxonomic publications to go online more easily
reduces cost for all participating journals
uses open sources software
Zootaxa/Phytotaxa will join this consortium from the start
upgrading the scale of the system (reducing cost via scale of economy)
Increased the visibility, access and impact of other smaller journals in the system
Better opportunities for using new technology • embedded hyperlinks to extended information • standardized semantic tags for better automatic extractions of data
Currently about a dozen committed journals (accounting for ca. 25% of all taxonomic papers) SYMPOSIUM: Biodiversity database and journal interface in e-publication era
Biodiversity database and journal interface in e- publication era: Zhi-Qiang Zhang
Making small data big: The Biodiversity Data Journal: Lyubomir Penev et al.
Semantic Annotation, Ontology Building, and Interactive Key Generation from Morphological Descriptions: Hong Cui et al.
Towards a Universal Bibliography – The RefBank approach: Guido Sautter et al.
From Taxonomic Literature to Cybertaxonomic Content: Jeremy Miller et al.
Highlighting fitness-for-use of published biodiversity data: Javier Otegui & Arturo H. Ariño