Integrating data publishing with workflows

in biodiversity research

Lyubomir Penev, Teodor Georgiev, Pavel Stoev, Jordan Biserkov, Laurence Livermore,

Jeremy Miller, David Roberts, Vincent Smith, Daniel Mietchen

ViBRANT

43rd Annual Meeting of the Ecological Society of Germany, Austria and Switzerland, Potsdam, September 9-13, 2013

Think about a dataset...

...and how it came to be...

...what it means to you...

...what it could enable...

...who knows about it...

...how they got to know about it...

...who actually uses it...

...and how we can improve that...

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 of 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 the 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 does BDJ do 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

DwC terms visible in text

Compose plates

Pick up a reference

Cite a reference

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

PensoWri ngTool(PWT)

Collabora veonlinewri ng

Authors

PensoJournalSystem(PJS)

Editor

PublicCommunity

Closed

Review

requests

Peer-reviewop ons

All reviewsassembledintoasingleonlineversion

Review

Review

Review

Nominatedreviewers

Publicreviewers

Panel reviewers

Editorialdecision&feedback

Onlineedi ng

Author’srevisedmanuscript

Publica on&

dissemina onOnlineedi ng

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

Implementation in other domains welcome!

Now what about your dataset?

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!

LOW COST!

I Open Access!

and….

ViBRANT

PLAZI

Drawings: slavenapeneva.com

Classifications

Import co-author’s profile

Describe new taxon

Structure of the checklist filed

External links

External links

DwC Template

DwC Template

DwC Template

Key preview