Scratchpad V irtual Research Environments: making your data work for you - PowerPoint PPT Presentation

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Scratchpad V irtual Research Environments: making your data work for you

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  1. Scratchpad VirtualResearch Environments:making your data work for you ICE 2012, Daegu, Korea, 20 August 2012 Vince Smith Natural History Museum, London vince@vsmith.info

  2. Our informatics grand challenge… “Link together evolutionary data across the great Tree of Life by developing analytical tools and proper documentation and 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

  3. Our informatics grand challenge… • This requires data, information & knowledge to be… • Digital • Not printed paper • Openly accessible • Not behind barriers • Linked-up • Not in silos “Link together evolutionary data across the great Tree of Life by developing analytical tools and proper documentation and 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

  4. The taxonomic data deluge? The Economist, 27th Feb. 2010

  5. Or taxonomic data drought? • 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… Mostly not digital, open or linked, generated by small communities Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

  6. ScratchpadVirtual Research Environments Making taxonomy digital, open & linked

  7. 2 Uploaded & tagged 3 1 “Published” & reviewed on your site Your data What is a Scratchpad? A website for you & your community Fast Intuitive Fit for use

  8. Scratchpads • EDIT (07-11), ViBRANT / eMonocot (11-13) • Hosted websites for taxonomists • Taxonomic, regional or societal • Research & publication platform • Supports the taxonomic workflow • Modular (Drupal) & flexible • Two full time developers • Ecosystem of communities (~450) http://scratchpads.eu

  9. Categories of Scratchpads Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies

  10. Scratchpad v.1 usage (2007- Mar. 2012) Nodes, 430, 948 Sites 326 Users 6809 Active Users 5733 (273 w / 759 m) Users Range: 1-1049 Mean: 15 Mode: 1 Sites • Prof. scientists • Amateur naturalists • Citizen scientists SP 2 ViBRANT

  11. Scratchpad 2 – the new version of Scratchpads • Launched March 2012 • 120 sites to date • EOL Fellows • SP1 migration ongoing • More professional • Easier to… • configure (workflows) • navigate (facets) • & populate (MS Excel templates) • Greater standardisation • Still highly flexible • Project profiles (eMonocot) • Framework for integration e.g. http://ihs.myspecies.info/

  12. What can Scratchpads do? +Specimens -Creating a record -Importing from a spreadsheet -Linking specimen & location records -Linking specimen & pub. records +Tasks -Creating a tasklist +Taxonomy -Importing from a spreadsheet -Importing from ClassificationBank -Starting from scratch -Taxonomy manager -Displaying a classification -Adding names -Deleting names -Taxonomy & panels +Users -Your settings -Adding a new user -User roles and permissions -Adding and editing user profile fields -Logging in +Webform -Creating and using webforms +Administration -Change your site information -Change you front page -Change your logo -Activity and access logs +Backup -Backing up your data -Restoring your data +Bibliography -Creating a record -Importing from a ref. manager -Exporting to a reference manager +Blog -Creating and adding a blog +Custom Content -Defining a CCK -Importing from a spreadsheet -Creating a custom view +Fileshare -Creating and using a fileshare +Forum -Altering the forum settings -Creating a container for a forum -Creating a new forum -Creating a new topic inside a forum +Groups -Creating a group -Subscribing to a group +Image -Uploading & basic annotation -Linking image & location records -Linking image & specimen records -Linking image & publication records -Overlay annotations on images +Layout -Change your theme -Menus -Blocks and sidebars +Locations -Creating a record -Importing from a spreadsheet +Pages -Creating, editing, cloning & deleting -Configuring the panels template +Panels -Adding & configuring content -Creating a new panel -Citing a Panels page +Phylogeny -Adding a phylogenetic tree

  13. Summary of what Scratchpads can do • Taxon pages, generated from tagged content (plant/animal) • Bibliography management • Character matrixes • Specimen records • Distribution maps (from specimens and regional) • Images, video and sound • Excel spreadsheet import (dynamically generated) • Darwin Core Archive export • Tabular data editing • Custom content • User management • Custom webforms • EOL data import (taxonomy, species information) • GBIF Map integration

  14. Sustainable training, support & development • Wiki • Training manuals, videos & glossary • In-site Support • One click help within your site • Training Courses (12 in 2012) • UK (6), Sweden, (2) Greece (1), Bulgaria (1), South Africa (1), Brazil (1) • Ambassadors Programme • Enthusiastic experienced users • Local support • Embedded Issues Queue • Bug reports • Feature requests • Sandbox Site • http://sandbox.scratchpad.eu • Open Source Development • http://scratchpad.eu/develop http://scratchpad.eu/help

  15. Online community revision • Taxonomy is in perpetual beta • Constantly evolving • Changing contributors • Small granular contributions • Sustainability • A permanent space to work • Guaranteed access (2015) • Easy ways to get the data out • Open science • Beyond Open Access • New ways of working • Data management plans • Need incentives to use • More efficient (functions & reuse) • Attribution & provenance • Credit via citation • New forms of publication Freeloader flies http://milichiidae.info

  16. Next generation article publishing XML HTML PDF http://scratchpads.eu > http://pensoft.net Paper assembled from Scratchpad database XML submission, peer review & marked-up publication by Pensoft doi:10.3897/zookeys.50.539 5-step workflow for selecting data, adding metadata & previewing Published in Zookeys & Phytokeys (worldwide coverage)

  17. Publishing observations & taxon data http://scratchpads.eu > http://gbif.org & http://eol.org Pushed to GBIF & EOL (requires site registration with GBIF & EOL) Specimen records & species pageson Scratchpads Darwin Core Archive (DwCA) >19K specimen records > 122k species pages >377M specimen records GBIF > 1 M species pages in EOL

  18. Biodiversity Data Journal