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Scratchpads Virtual Research Environments for taxonomic and biodiversity related data Dr. Vince Smith Informatics Research Leader The Natural History Museum London
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Smith, V.S., Koureas, D, & Livermore, L. 2014. Scratchpads introductory presentation. Slideshare. http://www.slideshare.net/vsmithuk/Scratchpad-2014-Introduction Where to find and how to cite this presentation:
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Publications based on countless specimens, images, maps, keys 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
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However… not publicly accessible lack sufficient 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datasets (i.a. local or regional Floras, Faunas) Published knowledge cannot easily be mobilised Vast amounts of unpublished taxonomic “knowledge”
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On the other hand: Estimates of 7.5 million species still undescribed 1 1 How Many Species Are There on Earth and in the Ocean? Mora C et al. doi:10.1371/journal.pbio.1001127
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Expected volume of taxonomic and biodiversity data Need of extracting, aggregating and linking data on a global level
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The four nodes of data cycle 1. We collect and generate data 2. We curate, link and structure data 3. We analyse data 4. We publish data
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Data curation Data curation Data publishing Data publishing The four nodes of data cycle Data collection & generation Data collection & generation What are the bottlenecks in the workflow ? Data analysis Data analysis
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Data curation Data curation Data publishing Data publishing What we need is… Data collection & generation Data collection & generation a seamless workflow Data analysis Data analysis
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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…
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Scratchpads Virtual Research Environments Making taxonomy digital, open & linked
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so… what are the Scratchpads ?
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What are Scratchpads? Hosted websites for biodiversity data Virtual research & publication platform Completely open access & open source Modular & flexible
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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
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A Scratchpad is a website that holds data for you and your community The Scratchpads concept Your data External data & services
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The Scratchpads concept
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Examples of use: Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation ProjectsRegionsSocieties
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Red List conservation assessments Examples of use:
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Bulbous monocot genera listed in CITES
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Global Invasive Alien Species Information Partnership Examples of use:
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Belgian Network for DNA Barcoding Examples of use:
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Major integrated projects Online resource for monocot plants Collaboration between Kew, Oxford University and NHM Data to be open and usable by other scientists
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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
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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/
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65,000 unique visitors/month Per month unique visitors to Scratchpads sites 665 Scratchpads Communities by 7,334 active registered users covering 162,432 taxa in 735,660 pages. Are Scratchpads sustainable? 81 paper citations in 2012 In total more than 1,300,000 visitors
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Are Scratchpads sustainable? 2007 2011 2014 ViBRANT Virtual Biodiversity Research & & Other grants in the pipeline New Proposals
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the main features
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Classification term oriented system Biological classifications Non-biological classifications Taxonomies Hierarchical controlled vocabularies The main features
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Dynamic Biological Classifications Manually entered or imported Auto generated The main features
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Taxon pages Overview of data related to taxon Generated from tagged content The main features
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Bibliography management Faceted browsing An inbuilt Bibliography manager Taxon tagging and free keywords Import from and export to all major formats The main features
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Specimen/Observation data Linked to images and georeferenced Annotated full specimen/observation records The main features Linked to GenBank accession numbers
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Distribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data The main features
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Example regional distribution The main features
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Create phylogenetic trees Based on Newick/NeXML Different views
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Character matrices – Key construction Quantitative or qualitative characters Auto generation of keys Taxon based matrices [Specimens based character matrices] The main features
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Media handling Bulk upload Metadata (EXIF & Aubudon core) Media galleries The main features
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Generation of custom pages Tagged or not External RSS Twitter feeds Media files The main features
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Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments Enhanced communication tools The main features
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analytical tools OBOE service i.a. Ecological informatics, Phylogenetics, Sequence alignment The main features
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MCMC methods to estimate the posterior distribution of model parameters Phylogenies Sequence alignment Multiple sequence alignment Microsatellite repeats finder
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data mobilisation more on the way… External services Integration
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IUCN data integration
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GBIF data integration
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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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Data curation Data curation Data publishing Data publishing Data collection & generation Data collection & generation a seamless workflow Data analysis Data analysis Data publishing
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Helping researchers take credit for all research products The vision
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Publication module
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The Publication module Open-access journal The main features
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What does the 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
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How do Scratchpads and the BDJ interact?
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Allow submission of datasets for publication without reformatting and restructuring Working in a single environment based on standardised XML schema
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Work on multiple manuscripts Allocate different people to different manuscripts Handle permissions Assembling a manuscript
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Author names and affiliations Data included in manuscript in a structured annotated format Assembling a manuscript
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Taxon descriptions Assembling a manuscript
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Specimen data Assembling a manuscript
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Figures and Tables
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Supplementary files Select from existing or upload new
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References Assembling a manuscript Easily cite bibliography Auto compile list of references
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Assembling a manuscript Texts
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XML Figures and Tables Keys References Texts The publication module Author names and affiliations Taxon descriptions Specimen data Supplementary files
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Previewing your manuscript
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Submission & enhanced peer review Manuscript data validation One-click submission to BDJ Traditional peer review and optional panel/public review
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The workflow MANUSCRIPT PUBLISHED (XML, PDF) MANUSCRIPT PUBLISHED (XML, PDF) PENSOFT JOURNAL SYSTEM (PJS 2.0) XML submission SCRATCHPADS Community Taxon namesOccurrence datadatasets Archive Taxon treatments Plazi Wiki
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Scratchpads are an integrated system to Enter, Curate, Mark-up, Link and Publish data taxonomic workflow in a single virtual environment
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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 Acknowledgements
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Thank you Data curation Data curation Data analysis Data analysis Data publishing Data publishing Data collection & generation Data collection & generation
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However… not publicly accessible lack sufficient 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”
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