Scratchpads 2.0: a Virtual Research Environment supporting ...
Publishing biodiversity: The interplay between Scratchpads and the new Biodiversity Data Journal
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Transcript of 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