ScratchpadsVirtual Research Environmentsfor taxonomic and biodiversity related data
Scratchpads introductory presentation. DimitriosKoureas, Laurence Livermore. figshare. 2013.doi:10.6084/m9.figshare.640101...
Publications based on countlessspecimens, images, maps, keys and datasetsCurrent taxonomic data productionTypically genera...
On the other hand:Estimates of7.5 million speciesstill undescribed11How Many Species Are There on Earth and in the Ocean? ...
Expected volumeof taxonomic andbiodiversity dataNeed ofextracting, aggregatingand linking data on a globallevel
The four nodes of data workflow1.We collect and generate data2.We curate, link and structure data3.We analyse data4.We pub...
DatacurationDataanalysisDatapublishingThe four nodes of data workflowDatacollection &generationWhat are thebottlenecksin t...
DatacurationDataanalysisDatapublishingWhat we need is…Datacollection &generationaseamlessworkflow
Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001This requires data, informatio...
ScratchpadsVirtual Research EnvironmentsMaking taxonomy digital, open & linked
so…what aretheScratchpads?
What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open acc...
What are Scratchpads?development of online research communitiesfacilitatestandardized environment of entering and curating...
A Scratchpad is a website that holds data for you and your communityThe Scratchpads conceptYour data External data & servi...
The Scratchpads concept
Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic& morphometric datasets, k...
Red List conservation assessmentsExamples of use:
Examples of use:Bulbous monocot genera listed in CITES
Global Invasive Alien Species Information PartnershipExamples of use:
Major integrated projects• Online resource formonocot plants• Collaboration betweenKew, Oxford Universityand NHM• Data to ...
Major integrated projects• 21+ open community sites andgrowing• Over 45 internationallycollaborating scientists• Site data...
Major integrated projects• Retrieve information onany Monocot plant• Rich downloadable data• Identification keys• Model ex...
65,000unique visitors/monthPer month unique visitors to Scratchpads sites580Scratchpads Communitiesby 8,185active register...
Are Scratchpads sustainable?2007 2011 2014ViBRANTVirtual Biodiversity Research& &Other grants in the pipelineProposals?
the mainfeatures
Classification termoriented systemBiologicalclassificationsNon-biologicalclassificationsTaxonomies Hierarchical controlled...
Dynamic Biological ClassificationsManually entered or importedAuto generatedThe main features
Taxon pagesOverview of data related to taxonGenerated from tagged contentThe main features
Bibliography managementFaceted browsingAn inbuilt Bibliography managerTaxon tagging and free keywordsImport from and expor...
Specimen/Observation dataLinked to images and georeferencedAnnotated full specimen/observation recordsThe main features
Distribution mapsGoogle maps basedData layersOccurrence dataDistribution dataTDWG regionsGBIF dataThe main features
Example regional distributionThe main features
Character matrices – Key constructionQuantitative or qualitative charactersAuto generation of keysTaxon based matrices[Spe...
Media handlingBulk uploadMetadata (incl. EXIF)Media galleriesThe main features
Generation of custom pagesTagged or notExternal RSSTwitter feedsMedia filesThe main features
Working groupsForumsBlog entriesWebformsNewslettersRSS syndicationInbuilt commentsEnhanced communication toolsThe main fea...
analyticaltoolsOBOE servicei.a.Ecological informatics,Phylogenetics,Sequence alignmentThe main features
datamobilisationmore on the way…External services Integration
IUCN data integration
GBIF data integration
BRAHMS data migration
ThePublicationmoduleOpen-accessjournalThe main features
How doScratchpadsandBDJinteract?
Allow submission ofdatasetsfor publicationwithoutreformatting and restructuringWorking in a single environmentbased on sta...
Assembling a manuscript
XMLFigures and TablesReferencesManuscript textSubmitting your dataAuthor names and affiliationsTaxon descriptionsSpecimen ...
Previewing your manuscript
Submission & enhanced peer review• Manuscript data validation• One-click submission to BDJ• Traditional peer review and op...
XMLFigures and TablesKeysReferencesTextsThe publication moduleAuthor names and affiliationsTaxon descriptionsSpecimen data
The data workflowMANUSCRIPT PUBLISHED(XML, PDF)PENSOFT JOURNAL SYSTEM(PJS 2.0)XMLsubmissionSCRATCHPADSCommunityTaxon names...
What will BDJ publish?• Single taxon treatments andnomenclatural acts• Local or regional checklists• Sampling reports and ...
Scratchpads are an integrated system toEnter, Curate, Mark-up, Link and Publish datataxonomic workflowin a single virtual ...
Scratchpads technical development- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine BoutonScratchpads outreach...
Help & Support• In-site Support• Wiki• Training Courses (12 in 2012)• Ambassadors Programme• Embedded Issues Queue• Sandbo...
Thank youDatacurationDataanalysisDatapublishingDatacollection &generation
Authors and ContributorsLead authorContributors(mentor, linguis c editor, copy editor,poten al reviewer, colleague/friend)...
• 15-20k new spp. described annually (2M total)1• 30k nomenclatural acts (12M total) 1• 20k phylogenies (750k total)2• 31k...
Scratchpads introductory presentation   45mins
Scratchpads introductory presentation   45mins
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Scratchpads introductory presentation 45mins

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  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • Scratchpads introductory presentation 45mins

    1. 1. ScratchpadsVirtual Research Environmentsfor taxonomic and biodiversity related data
    2. 2. Scratchpads introductory presentation. DimitriosKoureas, Laurence Livermore. figshare. 2013.doi:10.6084/m9.figshare.640101Where to find and how to cite this presentation
    3. 3. Publications based on countlessspecimens, images, maps, keys and datasetsCurrent taxonomic data productionTypically generated bysmall communitiesfor “local” research projectsFigure from Costello M.J et al, 2013. doi: 10.1126/science.1230318
    4. 4. On the other hand:Estimates of7.5 million speciesstill undescribed11How Many Species Are There on Earth and in the Ocean? Mora C et al.doi:10.1371/journal.pbio.1001127
    5. 5. Expected volumeof taxonomic andbiodiversity dataNeed ofextracting, aggregatingand linking data on a globallevel
    6. 6. The four nodes of data workflow1.We collect and generate data2.We curate, link and structure data3.We analyse data4.We publish data
    7. 7. DatacurationDataanalysisDatapublishingThe four nodes of data workflowDatacollection &generationWhat are thebottlenecksin the workflow?
    8. 8. DatacurationDataanalysisDatapublishingWhat we need is…Datacollection &generationaseamlessworkflow
    9. 9. Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001This requires data, information & knowledgeto be…• DigitalNot printed paper• Openly accessibleNot behind barriers (e.g. paywalls)• Linked-upNot in silos“Link togetherevolutionarydata… by developinganalytical tools andproperdocumentation andthen use this framework toconduct comparativeanalyses, studies ofevolutionary process andbiodiversity analyses”To achieve this…
    10. 10. ScratchpadsVirtual Research EnvironmentsMaking taxonomy digital, open & linked
    11. 11. so…what aretheScratchpads?
    12. 12. What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open access & open source• Modular & flexible
    13. 13. What are Scratchpads?development of online research communitiesfacilitatestandardized environment of entering and curating datathroughsharing and interlinkingthat allowdissemination of research productsand
    14. 14. A Scratchpad is a website that holds data for you and your communityThe Scratchpads conceptYour data External data & services
    15. 15. The Scratchpads concept
    16. 16. Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic& morphometric datasets, keys, phylogenies)ProjectsConservation Regions SocietiesExamples of use:
    17. 17. Red List conservation assessmentsExamples of use:
    18. 18. Examples of use:Bulbous monocot genera listed in CITES
    19. 19. Global Invasive Alien Species Information PartnershipExamples of use:
    20. 20. Major integrated projects• Online resource formonocot plants• Collaboration betweenKew, Oxford Universityand NHM• Data to be open andusable by other scientists
    21. 21. Major integrated projects• 21+ open community sites andgrowing• Over 45 internationallycollaborating scientists• Site data feeds into a “Portal”Site List: http://about.e-monocot.org/list-emonocot-scratchpads
    22. 22. Major integrated projects• Retrieve information onany Monocot plant• Rich downloadable data• Identification keys• Model example of linkedattributed dataeMonocot Portal: http://e-monocot.org/
    23. 23. 65,000unique visitors/monthPer month unique visitors to Scratchpads sites580Scratchpads Communitiesby 8,185active registered userscovering 155,607taxain 653,274 pages.Are Scratchpads sustainable?In total more than1,200,000 visitors
    24. 24. Are Scratchpads sustainable?2007 2011 2014ViBRANTVirtual Biodiversity Research& &Other grants in the pipelineProposals?
    25. 25. the mainfeatures
    26. 26. Classification termoriented systemBiologicalclassificationsNon-biologicalclassificationsTaxonomies Hierarchical controlledvocabulariesThe main features
    27. 27. Dynamic Biological ClassificationsManually entered or importedAuto generatedThe main features
    28. 28. Taxon pagesOverview of data related to taxonGenerated from tagged contentThe main features
    29. 29. Bibliography managementFaceted browsingAn inbuilt Bibliography managerTaxon tagging and free keywordsImport from and export to all major formatsThe main features
    30. 30. Specimen/Observation dataLinked to images and georeferencedAnnotated full specimen/observation recordsThe main features
    31. 31. Distribution mapsGoogle maps basedData layersOccurrence dataDistribution dataTDWG regionsGBIF dataThe main features
    32. 32. Example regional distributionThe main features
    33. 33. Character matrices – Key constructionQuantitative or qualitative charactersAuto generation of keysTaxon based matrices[Specimens based character matrices]The main features
    34. 34. Media handlingBulk uploadMetadata (incl. EXIF)Media galleriesThe main features
    35. 35. Generation of custom pagesTagged or notExternal RSSTwitter feedsMedia filesThe main features
    36. 36. Working groupsForumsBlog entriesWebformsNewslettersRSS syndicationInbuilt commentsEnhanced communication toolsThe main features
    37. 37. analyticaltoolsOBOE servicei.a.Ecological informatics,Phylogenetics,Sequence alignmentThe main features
    38. 38. datamobilisationmore on the way…External services Integration
    39. 39. IUCN data integration
    40. 40. GBIF data integration
    41. 41. BRAHMS data migration
    42. 42. ThePublicationmoduleOpen-accessjournalThe main features
    43. 43. How doScratchpadsandBDJinteract?
    44. 44. Allow submission ofdatasetsfor publicationwithoutreformatting and restructuringWorking in a single environmentbased on standardised XML schema
    45. 45. Assembling a manuscript
    46. 46. XMLFigures and TablesReferencesManuscript textSubmitting your dataAuthor names and affiliationsTaxon descriptionsSpecimen data
    47. 47. Previewing your manuscript
    48. 48. Submission & enhanced peer review• Manuscript data validation• One-click submission to BDJ• Traditional peer review and optional panel/public review
    49. 49. XMLFigures and TablesKeysReferencesTextsThe publication moduleAuthor names and affiliationsTaxon descriptionsSpecimen data
    50. 50. The data workflowMANUSCRIPT PUBLISHED(XML, PDF)PENSOFT JOURNAL SYSTEM(PJS 2.0)XMLsubmissionSCRATCHPADSCommunityTaxon namesOccurrence datadatasetsArchive Taxon treatmentsPlazi Wiki
    51. 51. What will BDJ publish?• Single taxon treatments andnomenclatural acts• Local or regional checklists• Sampling reports and occasionalinventories• Habitat-based checklists and inventories• Ecological and biological observations ofspecies and communities?• Single identification keys• biodiversity-related databases, includinggenomic, ecological and environmentaldata (data papers)• Biodiversity-related software tools
    52. 52. Scratchpads are an integrated system toEnter, Curate, Mark-up, Link and Publish datataxonomic workflowin a single virtual environment
    53. 53. Scratchpads technical development- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine BoutonScratchpads outreach- Laurence Livermore, Isa van deVelde & Dimitris Kourease-Monocot- Paul Wilkin & the Kew team, Charles Godfray & the Oxford teamViBRANT- Vince Smith, Dave Roberts & Lucy ReevePensoft- Lyobomir Penev and the Pensoft teamOur 8000 usersAcknowledgements
    54. 54. Help & Support• In-site Support• Wiki• Training Courses (12 in 2012)• Ambassadors Programme• Embedded Issues Queue• Sandbox Sitehttp://help.scratchpad.eu
    55. 55. Thank youDatacurationDataanalysisDatapublishingDatacollection &generation
    56. 56. Authors and ContributorsLead authorContributors(mentor, linguis c editor, copy editor,poten al reviewer, colleague/friend)Co-authorsInviteInviteTemplate-basedmanuscriptcrea onTaxon treatmentInterac ve keyChecklistData paperAuthoringAuthoringContribungManuscript ready to submit
    57. 57. • 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 datasetsOur current taxonomic data productionTypically generated by small communities for“local” research projectsFigures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

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