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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/scratchpad-2014-introduction-140224111002-phpapp01/85/Scratchpad-2014-introduction-37-320.jpg)
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Scratchpad 2014-introduction
This document discusses Scratchpads, which are hosted websites that facilitate the digital curation and publication of taxonomic and biodiversity data. Scratchpads allow researchers to enter, link, and publish their data in a seamless, open access workflow. They support digital classifications, specimen records, bibliographies, distribution maps, and analytical tools. Major projects like e-Monocot use Scratchpads to aggregate data from over 45 researchers. Scratchpads currently involve over 7,000 users curating over 162,000 taxa. They integrate with services like GBIF, IUCN, and Plazi and allow publication in the open access Biodiversity Data Journal.
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Scratchpad 2014-introduction
- 1. Scratchpads Virtual Research Environments fortaxonomic and biodiversity related data Dr. Vince Smith Informatics Research Leader The Natural History Museum London
- 2. Where to findand how to cite this presentation: Smith, V.S., Koureas, D, & Livermore, L. 2014. Scratchpads introductory presentation. Slideshare. http://www.slideshare.net/vsmithuk/Scratchpad-2014-Introduction
- 3. Current taxonomic dataproduction Typically generated by small communities for “local” research projects Figure from Costello M.J et al, 2013. doi: 10.1126/science.1230318 Publications based on countless specimens, images, maps, ke ys and datasets
- 4. However… not publicly accessible lacksufficient contextual metadata published in formats that require time-consuming manual extraction difficulty in publishing valuable datasets (i.a. local or regional Floras, Faunas) Published knowledge cannot easily be mobilised Vast amounts of unpublished taxonomic “knowledge”
- 5. On the otherhand: Estimates of 7.5 million species still undescribed1 1How Many Species Are There on Earth and in the Ocean? Mora C et al. doi:10.1371/journal.pbio.1001127
- 6. Expected volume Need ofextracting, of taxonomic and aggregating and linking biodiversity data data on a global level
- 7. The four nodesof data cycle 1. We collect and generate data 2. We curate, link and structure data 3. We analyse data 4. We publish data
- 8. The four nodesof data cycle What are the bottlenecks Data in the workflow? collection & generation Data Data publishing curation Data analysis
- 9. What we needis… a seamless workflow Data collection & generation Data Data publishing curation Data analysis
- 10. To achieve this… Linktogether evolutionary data… by developing “ analytical tools and proper documentation and This requires data, information & knowledge to be… • Digital Not printed paper • Openly accessible Not behind barriers (e.g. paywalls) • Linked-up Not in silos then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
- 11. Scratchpads Virtual Research Environments Makingtaxonomy digital, open & linked
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- 13. What are Scratchpads? •Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible
- 14. What are Scratchpads? facilitate developmentof online research communities through standardized environment of entering and curating data that allow sharing and interlinking and dissemination of research products
- 15. The Scratchpads concept AScratchpad is a website that holds data for you and your community Your data External data & services
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- 17. Examples of use: Taxa (Classifications,taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
- 18. Examples of use: RedList conservation assessments
- 19. Examples of use: Bulbousmonocot genera listed in CITES
- 20. Examples of use: GlobalInvasive Alien Species Information Partnership
- 21. Examples of use: BelgianNetwork for DNA Barcoding
- 22. Major integrated projects •Online resource for monocot plants • Collaboration between Kew, Oxford University and NHM • Data to be open and usable by other scientists
- 23. Major integrated projects •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
- 24. Major integrated projects •Retrieve information on any Monocot plant • Rich downloadable data • Identification keys • Model example of linked attributed data eMonocot Portal: http://e-monocot.org/
- 25. Are Scratchpads sustainable? 665Scratchpads Communities by 7,334 active registered users covering 162,432 taxa in 735,660 pages. In total more than 1,300,000 visitors 81 paper citations in 2012 Per month unique visitors to Scratchpads sites 65,000 unique visitors/month
- 26. Are Scratchpads sustainable? 2007 2011 2014 ViBRANT VirtualBiodiversity Research & & Other grants in the pipeline New Proposals
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- 28. The main features Classificationterm oriented system Biological classifications Taxonomies Non-biological classifications Hierarchical controlled vocabularies
- 29. The main features DynamicBiological Classifications Manually entered or imported Auto generated
- 30. The main features Taxonpages Overview of data related to taxon Generated from tagged content
- 31. The main features Bibliographymanagement An inbuilt Bibliography manager Faceted browsing Taxon tagging and free keywords Import from and export to all major formats
- 32. The main features Specimen/Observationdata Annotated full specimen/observation records Linked to images and georeferenced Linked to GenBank accession numbers
- 34. The main features Distributionmaps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data
- 35. The main features Exampleregional distribution
- 36. Create phylogenetic trees Basedon Newick/NeXML Different views
- 37. The main features Charactermatrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices]
- 38. The main features Mediahandling Bulk upload Metadata (EXIF & Aubudon core) Media galleries
- 39. The main features Generationof custom pages Tagged or not External RSS Twitter feeds Media files
- 40. The main features Enhancedcommunication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments
- 41. The main features analytical tools OBOEservice i.a. Ecological informatics, Phylogenetics, Sequence alignment
- 42. Phylogenies MCMC methods toestimate the posterior distribution of model parameters Sequence alignment Multiple sequence alignment Microsatellite repeats finder
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- 47. Help & Support •In-site Support • Wiki • Training Courses (12 in 2012) • Ambassadors Programme • Embedded Issues Queue • Sandbox Site http://help.scratchpads.eu
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- 49. The vision Helping researcherstake credit for all research products
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- 52. What does theBDJ 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
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- 54. Working in asingle environment Allow submission of datasets for publication without reformatting and restructuring based on standardised XML schema
- 55. Assembling a manuscript •Work on multiple manuscripts • Allocate different people to different manuscripts • Handle permissions
- 56. Assembling a manuscript Dataincluded in manuscript in a structured annotated format Author names and affiliations
- 57. Assembling a manuscript Taxondescriptions
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- 60. Supplementary files Select fromexisting or upload new
- 61. Assembling a manuscript References Easilycite bibliography Auto compile list of references
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- 63. The publication module Authornames and affiliations Taxon descriptions Specimen data Figures and Tables XML Keys References Supplementary files Texts
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- 65. Submission & enhancedpeer review • Manuscript data validation • One-click submission to BDJ • Traditional peer review and optional panel/public review
- 66. Community T h ewo r k f lo w XML submission SCRATCHPADS PENSOFT JOURNAL SYSTEM (PJS 2.0) MANUSCRIPT PUBLISHED (XML, PDF) Archive datasets Occurrence data Taxon treatments Plazi Taxon names Wiki
- 67. Scratchpads are anintegrated system to Enter, Curate, Mark-up, Link and Publish data workflow in a single virtual environment taxonomic
- 68. Acknowledgements Scratchpads technical development -Vince Smith, Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton, Katherine Boutton 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 - Lyubomir Penev and the Pensoft team Our 7000+ users
- 69.
Editor's Notes
- #6 With almost 8 million species still to be described,
- #12 The Scratchpads platform is being developed for the last 5 years under this framework. To provide researchers with the necessary tools to make taxonomy digital, open and linked!To facilitate the development of virtual research environments
- #24 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.
- #25 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.
- #31 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.
- #57 No need to restructure, correctly format or gather additional data. Once entered in Scratchpad they can automatically be added to the publication.
- #66 Prior to submission all data are validated to ensure there are no important missing fields.Once you have finished your manuscript there is a simple one-click submission process where all your specified authors and contributors are given access to the article in the Pensoft Journal System and will be updated on the review process.