Sherborn: Penev - ZooKeys: Streamlining the registration – to – publication pipeline
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Transcript of Sherborn: Penev - ZooKeys: Streamlining the registration – to – publication pipeline
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Streamlining the registration- to-
publication pipeline
Lyubomir Penev, Teodor Georgiev, Pavel Stoev
Sherborn Meeting, NHM London, 28 Oct 2011
ViBRANT
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The registration workflow for taxonomic names and acts
TAXONOMICPUBLICATION
AUTHOR PUBLISHER
PRE-PUBLICATION REGISTRATION
POST-PUBLICATION RECORDING
AUTHOR
XML MARK UP
Structured text (data!)
ARTICLESOccurr-
ence dataTaxon namesTaxon treatments
Plazi
BHL
Wiki COL
Biblio-graphies
Index AnimaliumZoological RecordIndex Kewensis, IPNIIndex Fungorum
ZooBank MycoBankIPNIIndex Fungorum
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bn
XML-based publication and dissemination workflow
Scratchpads- generated manuscripts
GBIF-generated manuscripts from
metadata descriptions
PENSOFT MARK UP TOOL(PMT)
Manuscripts writtenvia customized
online forms
Marked up final publicationin PDF, HTML and XML
formats
Manuscripts generated from
authors’ databases
Upfront pre-submission marked up manuscripts
Non-tagged manuscripts (MS Word, Open Office)
Peer-review, editorial and publication process
ARTICLES
Automated dissemination, archiving, indexing, harvesting
Occurrence data Taxon namesTaxon treatments
Plazi
BHL
Wiki COL
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But why doing all this ?
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Semantic enhancements to published texts
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The challenges of the registration process
Four different groups of players: data managers, registry editors, authors, publishers
Who will be “allowed” to register new data in electronic registries?
Who will control the quality of (validate) registered records?
Who will supply the record ID numbers to the publishers?
Who and when will add/correct the article metadata after publication?
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Automated workflow
MANUSCRIPT SUBMISSION
MANUSCRIPT ACCEPTED
XML Response
ARTICLEPUBLISHED
Taxon name available (effectively published)
XML article metadata
XML Query
Peer review
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The technical solution:
Pensoft Writing Tool (PWT)
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PWT combines: (1) writing of a taxonomic manuscript (2) upfront markup of the text (3) submission to an appropriate journal into one and the same process (tool)
PWT is a core module of the forthcoming Biodiversity Data Journal (BDJ)
Short taxonomic treatments or even single nomenclatural acts, single records, biological and ecological observations, local checklists, larger taxonomic revisions, etc.
Compliant to the two Biological Codes (bacteria still missing)
Can be used as educational environment for the future taxonomists
PWT – Main functionalities
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Acknowledments
ViBRANT
Plazi
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“ Semi-automatically generated semantic, enhanced e-publications are the only way to describe the missing 10 M species, and to deal with an increasing flood of data.”
Donat Agosti
All this is not easy, but......
... it is truly exciting
...but
... is possible only through Open Access!
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Thank you for your attention!
I Open Access!