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![The main features
Character matrices – Key construction
Quantitative or qualitative characters
Auto generation of keys
Taxon based matrices
[Specimens based character matrices]](https://image.slidesharecdn.com/rycroftscratchpads-131209095939-phpapp01/85/Scratchpads-the-Virtual-Research-Environment-for-biodiversity-data-15-320.jpg)
Uploaded byVince Smith
Scratchpads: the Virtual Research Environment for biodiversity data
Scratchpads are open access, modular websites for biodiversity data that serve as virtual research and publication platforms. They support a wide range of data management features, including taxonomic classification, specimen records, and distribution mapping, facilitating collaboration among a growing community of scientists. The project has achieved significant user engagement with over 1.5 million unique monthly visitors and aims to integrate various data sources while providing tools for publication and communication.
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Scratchpads: the Virtual Research Environment for biodiversity data
- 1. Scratchpads The virtual researchenvironment for biodiversity data Simon Rycroft, Dave Roberts, Vince Smith, Alice Heaton, Katherine Bouton, Laurence Livermore, Dimitris Koureas, Ed Baker Natural History Museum, London
- 2. What are Scratchpads? •Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible
- 3. The Scratchpads concept AScratchpad is a website that holds data for you and your community Your data External data & services
- 4. Examples of use: Taxa (Classifications,taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
- 5. Major integrated project •21+ open community sites and growing • Over 45 internationally collaborating scientists • Site data feeds into a “Portal” Site List: http://about.e-monocot.org/list-emonocot-scratchpads
- 6. Major integrated project •Retrieve information on any Monocot plant • Rich downloadable data • Identification keys • Model example of linked attributed data eMonocot Portal: http://e-monocot.org/
- 7. The main features DynamicBiological Classifications Manually entered or imported Auto generated
- 8. The main features Taxonpages Overview of data related to taxon Generated from tagged content
- 9. The main features Bibliographymanagement An inbuilt Bibliography manager Faceted browsing Taxon tagging and free keywords Import from and export to all major formats
- 10. The main features Specimen/Observationdata Annotated full specimen/observation records Linked to images and georeferenced Linked to GenBank accession numbers
- 12. The main features Distributionmaps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data
- 13. The main features Exampleregional distribution
- 14. Create phylogenetic trees Basedon Newick/NeXML Different views
- 15. The main features Charactermatrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]
- 16. The main features Mediahandling Bulk upload Metadata (EXIF & Audubon core) Media galleries
- 17. The main features Generationof custom pages Tagged or not External RSS Twitter feeds Media files
- 18. The main features Enhancedcommunication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments
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- 21. GBIF distribution dataintegration
- 23. Structured data Select, describe & annotatedata Publication module Publish, cite, disseminate & archive data Major repositories
- 24. Scratchpads Publication Module Scratchpadstemplates for publishing... • Taxon treatments • Nomenclatural acts • Checklists / inventories • Identification keys and trees • Metadata descriptions of databases • Descriptions of software tools Easy & intuitive • Draws on data from your site • Pre-submission validation • Submitted as structured XML • No reformatting
- 25. Are Scratchpads sustainable? 590Scratchpads Communities by 6,800 active registered users covering 91,631 taxa in 570,000 pages. In total more than 1,500,000 unique visitors Per month unique visitors to Scratchpads sites 65,000 visitors/month
- 26. Are Scratchpads sustainable? 2007 2011 2014 ViBRANT VirtualBiodiversity Research & & Other grants in the pipeline Horizon 2020
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Editor's Notes
- #6 In the project there are more than 21 eMonocot Scratchpads which have over 45 international collaborating scientists.The eMonocot Scratchpads cover over 15 families with more planned with additional workshops which will take place this year at Monocots V in New York.The Scratchpad to eMonocot Portal link is now active and available for the public to browse all the Scratchpad data combined with other external monocot resources.
- #7 All of the information is brought together in the eMonocot portal. The information presented here will be especially useful for anyone studying the ecology or evolution of the monocot plants, or who wants to understand monocot biodiversity and conservation.The portal provides taxon descriptions, distribution maps, taxonomies and keys, all of which are downloadable and attributed to the author and contributing site.
- #9 Intuitive professional looking layout.Easy to compile taxon pages without any knowledge of web design.Taxonomy provides the crucial backbone, linking content together and is easily updateable.On this page you can see the classification browser in the side bar, detailed nomenclatural information, images and a diagnostic summary.
- #24 The Scratchpad Publication Module fixes that by allowing you to select your structured data, describe it an annotate in an easy-to-use manuscript template and submit this to Pensoft Publishers for formal publication online as a peer-reviewed article.Your paper is then citable, widely disseminated to major services and data aggregators and all the data archived.
- #25 The Scratchpads Publication Module