Date post: | 10-May-2015 |
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Revolution in publication:
Data and text publishing integrated
in theBiodiversity Data JournalLyubomir Penev, Teodor Georgiev, Pavel Stoev,
Jordan Biserkov, Laurence Livermore, Jeremy Miller, David Roberts, Vincent Smith
ViBRANT
Biodiversity Informatics Horizons 2020 September 3-6, 2013, Rome
Revolution?Again??
…but if there is a bottleneck, then expect a revolution!
The “Publishing Bottleneck in Biodiversity”?
What is that?
Massive sampling/data gathering
‘Dark Taxa’ increase dramatically!
Rod Page, iPhylo blogspot, 12 April 2011
The paper/PDF impediment
… the burden or OCR, double-keying and markup of paper/PDF literature
Low uptake of open data publishing/sharing
The “impact factor” pressure
The “peer review” pressure
The solution?
Launch date
http://biodiversitydatajournal.com
Novel conceptsAuthoring, reviewing and publishing in one place, for first time!Upfront markup!“Small” data imported in and downloadable from text Large datasets published as data papers Text stored and treated as dataCommunity peer-reviewed and community owned interoperable data Text and data integrated publishing!
How BDJ does that?
COMMUNITY PEER-REVIEW (OPTIONS FOR PUBLIC AND
OPEN REVIEW)ALL ONLINE!
COLLABORATIVE ARTICLE AUTHORING (PENSOFT WRITING
TOOL)
MANUSCRIPT PUBLISHEDXML TEXT + DATA
Authors, Reviewers, Editors, Mentors, Copyeditors
Automatedsubmission
Revisions online
ARTICLESOccurr-
ence dataTaxon namesTaxon treatments
Plazi Wiki COL
Biblio-graphies
Novel work flows
AuthoringPeer-reviewPublishing and dissemination
Article templates
Classifications
Import co-author’s profile
Describe new taxon
Structure of the checklist filed
External links
External links
DwC Template
DwC Template
DwC Template
DwC terms visible in text
Compose plates
Pick up a reference
Cite a reference
Construction of keys
Key preview
No author guidelines! The tool will guide
you!
Authors do not need to markup or
hyperlink anything!It is done by the tool!
No layout stage!
Novel work flows
AuthoringPeer-reviewPublishing and dissemination
Community and public peer-review
Now imagine…
Consolidated Reviewers’ Version
Novel work flow
AuthoringPeer-reviewPublishing and dissemination
Article metadata
Download data
Map localities
Taxa and their usages
Taxon profile
Taxon profile
Tables and Figures
References
Possible solution for “dark” taxa
PWT – COLLABORATIVE ARTICLE AUTHORING TOOLDark taxon sequenced
BDJ – PEER-REVIEW
Automated submission to Pensoft Writing Tool
MANUSCRIPT PUBLISHED
BOLD Metadata: voucher specimen,
images, locality, etc.
MANUSCRIPT FINALIZATION & SUBMISSION
Automated update of bibliographic metadata, taxon names, Zoobank records, etc.
Automated pre-publication registration of new taxon names
MANUSCRIPT SUBMISSION
MANUSCRIPT ACCEPTED
XML Response
ARTICLEPUBLISHED
Taxon name available/valid (effectively published)
XML article metadata
XML Query
Peer review
Unified marked up final outputTaxon treatments, keys, images, localities, references
PROSPECTIVE PUBLISHING | HISTORICAL LITERATURE
Re-publishing of legacy literature
Content management systems &repositories (SCRATCHPADS, CDM, etc.)
PENSOFT WRITING TOOL
2nd DIGITAL EDITION semantically enhanced
HTML and XML
archivingSpecies-ID, Wikispecies
Wikipedia
Indexing (IPNI, ZooBank, Myco-
Bank, GNA)
Aggregators(EOL, GBIF)
Electronic archives; Data
Centers
END USERS
OCR, re-typing, markup, extracting images , tables
XML IMPORT
What will BDJ publish?
Single taxon treatments and acts Local/regional and habitat checklists, sampling reports, N2K inventoriesEcological and biological observations on species and communitiesIdentification keys Data papers describing dataDescriptions of software tools and work flows
Recruiting editors!
Editor Application Form http://pensoft.net/journals/bdj/editor_form.html
Why publish in BDJ?
Not just a journalEven not just a data journal!
A work flow and infrastructure to mobilize, review, publish, store, disseminate, make
interoperable, collate and re-use data through the act of publishing!
Implementation in other domains welcome!
LOW COST!
I Open Access!
and….
ViBRANT
PLAZI
Drawings: slavenapeneva.com