Making your data work for you: Scratchpads, publishing & the Biodiversity Data Journal

1. Making your data work for you:Scratchpads, publishing & theBiodiversity Data Journal EBI, UK 25 September, 2012 Vince Smith1, Dave Roberts1 & Lyubomir Penev2 1.Natural History Museum, London 2. Pensoft Publishers, Sofia, Bulgaria vince@vsmith.info

2. Our informatics grand challenge… “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” 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… 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. Most of our output is not digital, open or linked • 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… 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.

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

6. 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

7. 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

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

9. 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 (bulk import) • 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

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. Getting data in and out of Scratchpads 2

13. Online community revision • Taxonomy is in perpetual beta • Constantly evolving • Changing contributors • Small granular contributions • Sustainability • A permanent space to work • Guaranteed access (2016) • 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

14. 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

15. Experiments with 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)

16. Example papers via Scratchpads… Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: 79–90. doi: 10.3897/zookeys.50.506 Faulwetter S, Chatzigeorgiou G, Galil BS, Nicolaidou A, Arvanitidis C (2011. ZooKeys 150: 327–345. doi: 10.3897/zookeys.150.1877 Brake I, von Tschirnhaus M (2010). ZooKeys 50: 91–96. doi: 10.3897/zookeys.50.505 http://sciaroidea.info/node/44428 http://polychaetes.marbigen.org/node/35 http://milichiidae.info/node/14995 Live (updated) versions of these papers

17. BDJThe Biodiversity Data Journal Making small data big!

18. Why do we need another new journal!!! Taxonomy needs less fragmentation, not more! • BUT… • We need to encourage taxonomists to mobilize & describe their data • This takes considerable effort (e.g. Scratchpads) • “Arguably” this is best rewarded through credit • This means papers and citations • Process must be very easy for authors • Process must facilitate data reuse • Meet “Open Data” policy commitments • The Biodiversity Data Journal is very different…

19. Biodiversity Data Journal (BDJ) • All data matters: No lower or upper limit of manuscript size! • Multiple publishing routes (not just Scratchpads) • ALL within a single online collaborative platform, including the writing of the manuscript! • New collaborative article authoring tool • Community peer review with “open” &“public” options • This is in addition to conventional peer-review • Online editorial process and version control • Standards-compliant (Darwin Core, Dublin Core, NLM etc.) • Pre-defined Code-compliant article templates

20. BDJ publication & dissemination workflow

21. Pensoft manuscript writing tool • Collaborative online editing • Rich text capabilities • Various templates for taxon treatments • Identification keys builder • Assembling plates from single figures • References import • (CrossRef, PubMed Central, etc.) • Species occurrence data import (Darwin Core compliant) • Smart citation for figures, tables, references & automated positioning

22. Testing screenshots of the writing tool Manuscript preview Multi-figure plates Plate layout ID Key preview ID Key builder

23. Why publish in the BDJ? • Joining (small) data into a large data pool • Open-access, archiving and re-using your data through data aggregators • Providing citation record and creditability for data in the form of peer-reviewed publications • Facilitating online article authoring and editorial process for authors, reviewers and editors • Using a truly innovative dissemination of atomized content • Very low-cost. Free in the launch phase, thereafter at fee that anyone can afford!

24. 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 • ANY KIND of biodiversity-related database, including genomic, ecological and environmental data (data papers) • Biodiversity-related software tools Recruiting editors now Starting late 2012, early 2013

25. BDJBarcoding, genomic & environmental sequence papers Making small data big!

26. Mammal taxa added to Genbank annually Aus sp. = dark taxa", taxa (specimens) that aren't identified to a known species Proper Linnaean names

27. Proportion of mammal dark taxa in Genbank Aus sp. Proper Linnaean names

28. Proportion of invert. dark taxa in Genbank BOLD

29. Dark taxa are the norm for bacteria

30. A lesson in principles for dealing with dark taxa Roth v. Wikipedia http://www.newyorker.com/online/blogs/books/2012/09/an-open-letter-to-wikipedia.html

31. But Wikipedia said “no” “I understand your point that the author is the greatest authority on their own work,” writes the Wikipedia Administrator—“but we require secondary sources.”

32. But Wikipedia said “no” One of Wikipedia’s core principles, along with things like neutrality, is verifiability: a reader must be able to look at a statement in a Wikipedia article and find out where it comes from. http://quominus.org/archives/981

33. Lessons for taxonomy & dark taxa… Taxonomic statements should be verifiable Literature is the evidence base for taxonomy Literature should be the evidence base for dark taxa http://quominus.org/archives/981

34. Example templates & dissemination Any other data “Dark” taxon data Occurrence data Biodiversity manuscript Genome descriptions Morphometric data Image galleries Environmental sequence data XML MARK UP Structured text (data!) Taxon names Taxon treatments Occurr-ence data ARTICLES Biblio-graphies COL Plazi Wiki BHL

35. Example template & data fields

36. Workflow describing “Dark Taxa” PWT– COLLABORATIVE ARTICLE AUTHORING TOOL Dark taxon sequenced MANUSCRIPT FINALISATION & SUBMISSION Automated submission to Pensoft Writing Tool BDJ– PEER-REVIEW Metadata: voucher specimen, images, locality, etc. MANUSCRIPT PUBLISHED Automated update of bibliographic metadata, taxon name, Zoobank record, etc.

37. Data published Nomenclature Literature Descriptions Images Occurrences Plazi

38. “Dark Taxon” papers • Should contain… • The scope of the taxonomic, ecological & geographic coverage • The sources of voucher specimens • The sampling & lab. protocols used • The process used to ID taxa to which vouchers belong • Possible data fields include… • Average no. of records per taxon • Range of records per taxon (Min-Max) • Average, min. and max. sequence length • Range of intraspecific variation • Median variation with in taxon X% • Range of divergence to closed know taxon pairs (min & max?) • Median divergence between closest taxon pair

39. Possible discussion points… • The concept… • Is it a good approach to incentivize data publishing & good metadata practices? • The suitability for “Dark Taxa”, new genomes and env. sequence data • Is this more suitable for some data papers (e.g. dark taxa) than others? • The practicalities… • The fit to existing systems (both for data collection and dissemination) • The data fields (Dark Taxa”, new genomes and env. sequence data) • Next steps in developing this concept

40. Acknowledgements • Scratchpad technical development • Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton, Katherine Boulton, • Scratchpad outreach • Irina Brake, Laurence Livermore, Dimitris Koureas • E-Monocot • Paul Wilkin &the Kew team, Charles Godfray & the Oxford team • ViBRANT • Dave Roberts, Lucy Reeve & many many more • Pensoft • Lyubomir Penev, Teodor Georgiev & colleagues • Our 7,000+ users

44. Why we need new methods of publishing… RE-USE of CONTENT Publishing and sharing of primary data Primary data Drawings: Slavena Peneva

45. Source: Wikipedia