Scratchpads introductory presentation 45mins
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Scratchpads are virtual research environments that allow taxonomic and biodiversity data to be collected, curated, analyzed, published, and shared in a digital, open, and linked manner. They provide a seamless workflow for data by hosting websites for communities to enter and structure data using standardized modules. This facilitates dissemination of research through open access publishing of datasets, descriptions, keys, and more without reformatting. Major projects like e-Monocot demonstrate Scratchpads' ability to aggregate data from various sources into an integrated portal.
![Character matrices – Key construction
Quantitative or qualitative characters
Auto generation of keys
Taxon based matrices
[Specimens based character matrices]
The main features](https://image.slidesharecdn.com/scratchpadsintroductorypresentation-45mins-130523073350-phpapp02/85/Scratchpads-introductory-presentation-45mins-33-320.jpg)
Scratchpads introductory presentation 45mins
- 1. Scratchpads Virtual Research Environments for taxonomic and biodiversity related data
- 2. Scratchpads introductory presentation. Dimitrios Koureas, Laurence Livermore. figshare. 2013. doi:10.6084/m9.figshare.640101 Where to find and how to cite this presentation
- 3. Publications based on countless specimens, images, maps, ke ys and datasets Current taxonomic data production Typically generated by small communities for “local” research projects Figure from Costello M.J et al, 2013. doi: 10.1126/science.1230318
- 4. On the other hand: 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
- 5. Expected volume of taxonomic and biodiversity data Need of extracting, aggregating and linking data on a global level
- 6. 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
- 7. Data curation Data analysis Data publishing The four nodes of data workflow Data collection & generation What are the bottlenecks in the workflow?
- 8. Data curation Data analysis Data publishing What we need is… Data collection & generation a seamless workflow
- 9. 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…
- 10. Scratchpads Virtual Research Environments Making taxonomy digital, open & linked
- 12. What are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible
- 13. 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
- 14. A Scratchpad is a website that holds data for you and your community The Scratchpads concept Your data External data & services
- 16. Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) ProjectsConservation Regions Societies Examples of use:
- 17. Red List conservation assessments Examples of use:
- 18. Examples of use: Bulbous monocot genera listed in CITES
- 19. Global Invasive Alien Species Information Partnership Examples of use:
- 20. Major integrated projects • Online resource for monocot plants • Collaboration between Kew, Oxford University and NHM • Data to be open and usable by other scientists
- 21. 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
- 22. 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/
- 23. 65,000 unique visitors/month Per month unique visitors to Scratchpads sites 580Scratchpads Communities by 8,185active registered users covering 155,607taxa in 653,274 pages. Are Scratchpads sustainable? In total more than 1,200,000 visitors
- 24. Are Scratchpads sustainable? 2007 2011 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline Proposals?
- 26. Classification term oriented system Biological classifications Non-biological classifications Taxonomies Hierarchical controlled vocabularies The main features
- 27. Dynamic Biological Classifications Manually entered or imported Auto generated The main features
- 28. Taxon pages Overview of data related to taxon Generated from tagged content The main features
- 29. Bibliography management Faceted browsing An inbuilt Bibliography manager Taxon tagging and free keywords Import from and export to all major formats The main features
- 30. Specimen/Observation data Linked to images and georeferenced Annotated full specimen/observation records The main features
- 31. Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data The main features
- 32. Example regional distribution The main features
- 33. Character matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices] The main features
- 34. Media handling Bulk upload Metadata (incl. EXIF) Media galleries The main features
- 35. Generation of custom pages Tagged or not External RSS Twitter feeds Media files The main features
- 36. Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments Enhanced communication tools The main features
- 37. analytical tools OBOE service i.a. Ecological informatics, Phylogenetics, Sequence alignment The main features
- 39. data mobilisation more on the way… External services Integration
- 45. Allow submission of datasets for publication without reformatting and restructuring Working in a single environment based on standardised XML schema
- 47. XML Figures and Tables References Manuscript text Submitting your data Author names and affiliations Taxon descriptions Specimen data
- 49. Submission & enhanced peer review • Manuscript data validation • One-click submission to BDJ • Traditional peer review and optional panel/public review
- 50. XML Figures and Tables Keys References Texts The publication module Author names and affiliations Taxon descriptions Specimen data
- 51. The data workflow MANUSCRIPT PUBLISHED (XML, PDF) PENSOFT JOURNAL SYSTEM (PJS 2.0) XML submission SCRATCHPADS Community Taxon namesOccurrence datadatasetsArchive Taxon treatments Plazi Wiki
- 52. 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
- 53. Scratchpads are an integrated system to Enter, Curate, Mark-up, Link and Publish data taxonomic workflow in a single virtual environment
- 54. 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 Pensoft team Our 8000 users Acknowledgements
- 55. Help & Support • In-site Support • Wiki • Training Courses (12 in 2012) • Ambassadors Programme • Embedded Issues Queue • Sandbox Site http://help.scratchpad.eu
- 58. Authors and Contributors Lead author Contributors (mentor, linguis c editor, copy editor, poten al reviewer, colleague/friend) Co-authors Invite Invite Template- based manuscript crea on Taxon treatment Interac ve key Checklist Data paper Authoring Authoring Contribu ng Manuscript ready to submit
- 59. • 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.
Editor's Notes
- #11: 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
- #22: 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.
- #23: 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.
- #29: 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.
- #50: 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.