Scratchpads Publishing biodiversity: The interplay between Scratchpads and the Biodiversity Data Journal Dr Dimitrios Koureas Biodiversity Informatics.

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Presentation transcript:

Scratchpads Publishing biodiversity: The interplay between Scratchpads and the Biodiversity Data Journal Dr Dimitrios Koureas Biodiversity Informatics Group The Natural History Museum London

Data curation Data curation Data publishing Data publishing Data collection & generation Data collection & generation a seamless workflow Data analysis Data analysis The four nodes of data cycle

Incentivise researchers Enable data mobilisation Facilitate data flow We have to:

Helping researchers take credit for all research products The vision

Publication module The vision

The Publication module Open-access journal 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 the BDJ interact?

Allow submission of datasets for publication without reformatting and restructuring Working in a single environment based on standardised XML schema

Work on multiple manuscripts Allocate different people to different manuscripts Handle permissions Assembling a manuscript

Author names and affiliations Data included in manuscript in a structured annotated format Assembling a manuscript

Taxon descriptions Assembling a manuscript

Specimen data Assembling a manuscript

Figures and Tables

Supplementary files Select from existing or upload new

References Assembling a manuscript Easily cite bibliography Auto compile list of references

Assembling a manuscript Texts

XML Figures and Tables Keys References Texts The publication module Author names and affiliations Taxon descriptions Specimen data Supplementary files

Previewing your manuscript

Submission & enhanced peer review Manuscript data validation One-click submission to BDJ Traditional peer review and optional panel/public review

The workflow MANUSCRIPT PUBLISHED (XML, PDF) MANUSCRIPT PUBLISHED (XML, PDF) PENSOFT JOURNAL SYSTEM (PJS 2.0) XML submission SCRATCHPADS Community Taxon namesOccurrence datadatasets Archive Taxon treatments Plazi Wiki

Thank you Data curation Data curation Data analysis Data analysis Data publishing Data publishing Data collection & generation Data collection & generation

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 Our current taxonomic data production Figures from 1) Zhang, Zootaxa , 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.