Scratchpads The virtual research environment for biodiversity data Simon Rycroft, Dave Roberts, Vince Smith, Alice Heaton, Katherine Bouton, Laurence Livermore,

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Presentation transcript:

Scratchpads The virtual research environment for biodiversity data Simon Rycroft, Dave Roberts, Vince Smith, Alice Heaton, Katherine Bouton, Laurence Livermore, Dimitris Koureas, Ed Baker Natural History Museum, London

What are Scratchpads? Hosted websites for biodiversity data Virtual research & publication platform Completely open access & open source Modular & flexible

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) Projects Conservation RegionsSocieties Examples of use:

Major integrated project 21+ open community sites and growing Over 45 internationally collaborating scientists Site data feeds into a “Portal” Site List:

Major integrated project Retrieve information on any Monocot plant Rich downloadable data Identification keys Model example of linked attributed data eMonocot Portal:

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 Linked to GenBank accession numbers

Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data The main features

Example regional distribution The main features

Create phylogenetic trees Based on Newick/NeXML Different views

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 (EXIF & Audubon core) 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

data mobilisation more on the way… External services Integration

IUCN data integration

GBIF distribution data integration

Structured data Publish, cite, disseminate & archive data Select, describe & annotate data Publication module Major repositories

Scratchpads Publication Module Easy & intuitive Draws on data from your site Pre-submission validation Submitted as structured XML No reformatting Scratchpads templates for publishing... Taxon treatments Nomenclatural acts Checklists / inventories Identification keys and trees Metadata descriptions of databases Descriptions of software tools

65,000 visitors/month Per month unique visitors to Scratchpads sites 590 Scratchpads Communities by 6,800 active registered users covering 91,631 taxa in 570,000 pages. Are Scratchpads sustainable? In total more than 1,500,000 unique visitors

Are Scratchpads sustainable? ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Horizon 2020

About scratchpads.eu Code git.scratchpads.eu Try sandbox.scratchpads.eu