publishing biodiversity: the interplay between scratchpads and the new biodiversity data journal

Publishing Biodiversity:The interplay between Scratchpads and

the new Biodiversity Data Journal

Koureas D.N.1, Rycroft S. 1, Baker E. 1, Livermore L. 1, Scott B. 1, Heaton A.1, Bouton K.1, Penev L.2, Roberts D.1 and Smith V.S.1

1 The Natural History Museum London2 Pensoft Publishers

• 15-20k new spp. described annually (2M total)1

• 30k nomenclatural acts (12M total) 1

• 20k phylogenies (750k total)2

• 31k taxa sequenced (360k taxa total)3

• 800k BioMed papers (40M total pp. of taxonomy) 4

• Countless specimens, images, maps, keys and datasets

Our current taxonomic data production

Typically generated by small communities for “local” research projects

Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

The four nodes of data workflow

1. We collect and generate data

2. We curate, link and structure data

3. We analyse data

4. We publish data

Data curation

Data curation

Data analysis

Data analysis

Data publishing

Data publishing

The four nodes of data workflow

Data collection &generation

Data collection &generation

What are the

bottlenecks

in the workflow?

bottleneck

bottleneck

Data curation

Data curation

Data analysis

Data analysis

Data publishing

Data publishing

What we need is…

Data collection &generation

Data collection &generation

aseamless

workflow

Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001

This requires data, information & knowledge to be…

•Digital Not printed paper

•Openly accessible Not behind barriers (e.g. paywalls)

•Linked-up Not in silos

“Link together evolutionary data… by developing

analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses”

To achieve this…

Global Systematics

ScratchpadsVirtual Research Environments

Making taxonomy digital, open & linked

so…

what are

the

Scratchpads?

What are Scratchpads?

• Hosted websites for biodiversity data

• Virtual research & publication platform

• Completely open access & open source

• Modular & flexible

What are Scratchpads?

development of online research communities

facilitate

standardized environment of entering and curating data

through

sharing and interlinking

that allow

dissemination of research products

and

A Scratchpad is a website that holds data for you and your community

The Scratchpads concept

Your data External data & services

Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic

& morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies

Examples of use:

65000 unique visitors/month

Per month unique visitors to Scratchpads sites

464 Scratchpads Communities

by 6,407 active registered users

covering 52,661 taxa

in 559,488 pages.

Are Scratchpads sustainable?

In total more than

1,200,000 visitors

Are Scratchpads sustainable?

2007 2011 2014

ViBRANTVirtual Biodiversity Research

& &

Other grants in the pipelineProposals?

the main

features

Dynamic Biological Classifications

Manually entered or imported

Auto generated

The main features

Taxon pages

Overview of data related to taxon

Generated from tagged content

The main features

Bibliography management

Faceted browsing

An inbuilt Bibliography manager

Taxon tagging and free keywords

Import from and export to all major formats

The main features

Specimen/Observation data

Linked to images and georeferenced

Annotated full specimen/observation records

The main features

Distribution maps

Google maps based

Data layers

Occurrence data

Distribution dataTDWG regions

GBIF data

The main features

Character matrices – Key construction

Quantitative or qualitative characters

Auto generation of keys

Taxon based matrices [Specimens based character matrices]

The main features

Media handling

Bulk upload

Metadata (incl. EXIF)

Media galleries

The main features

Generation of custom pages

Tagged or not

External RSS

Twitter feeds

Media files

The main features

Working groups

Forums

Blog entries

Webforms

Newsletters

RSS syndication

Inbuilt comments

Enhanced communication tools

The main features

analytical tools

OBOE service

i.a.

Ecological informatics,

Phylogenetics,

Sequence alignment

The main features

data

mobilisation

more on the way…

The main features

The

Publication module

Open-accessjournal

The main features

What will BDJ publish?

• Single taxon treatments and nomenclatural acts

• Local or regional checklists• Sampling reports and occasional

inventories• Habitat-based checklists and inventories• Ecological and biological observations of

species and communities?• Single identification keys • biodiversity-related databases, including

genomic, ecological and environmental data (data papers)

• Biodiversity-related software tools

How do

Scratchpads and

BDJ interact?

Allow submission of

datasets for publication

without reformatting and restructuring

Working in a single environment

based on standardised XML schema

Author names and affiliations

Data included in manuscript in a structured annotated format

The publication module

Taxon descriptions

The publication module

Specimen data

The publication module

XMLXMLFigures and Tables

Keys

References

Texts

The publication module

Author names and affiliations

Taxon descriptions

Specimen data

The data workflow

MANUSCRIPT PUBLISHED(XML, PDF)

MANUSCRIPT PUBLISHED(XML, PDF)

PENSOFT JOURNAL SYSTEM (PJS 2.0)

XML submission

SCRATCHPADS

Com

mun

ity

Taxon namesOccurrence datadatasetsArchive Taxon treatments

PlaziPlazi Wiki

veng

Collaboraonline wri

Authors

Scratchpads

The editorial workflow

Example papers via Scratchpads…Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: 79–90.

doi: 10.3897/zookeys.50.506Faulwetter S, Chatzigeorgiou G, Galil BS, Nicolaidou A,

Arvanitidis C (2011. ZooKeys 150: 327–345. doi: 10.3897/zookeys.150.1877

Brake I, von Tschirnhaus M (2010). ZooKeys 50: 91–96. doi: 10.3897/zookeys.50.505

http://milichiidae.info/node/14995http://polychaetes.marbigen.org/node/35http://sciaroidea.info/node/44428

Live (updated) versions of these papers

Scratchpads technical development- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Bouton

Scratchpads outreach- Laurence Livermore, Isa van deVelde & Dimitris Koureas

e-Monocot- Paul Wilkin & the Kew team, Charles Godfray & the Oxford team

ViBRANT- Vince Smith, Dave Roberts & Lucy Reeve

Pensoft- Lyobomir Penev and the team

Our 7000 users

Acknowledgements

Thank you Data

curation

Data curation

Data analysis

Data analysis

Data publishing

Data publishing

Data collection &generation

Data collection &generation

Authors and Contributors

Manuscript ready to submit