Making your data work for you: Scratchpads, publishing & the Biodiversity Data Journal Vince Smith 1, Dave Roberts 1 & Lyubomir Penev 2 1. Natural History Museum, London 2. Pensoft Publishers, Sofia, Bulgaria Linnean Society, UK 20 September, 2012

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: /j.tree

Our informatics grand challenge… Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi: /j.tree 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”

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… Most of our output is not digital, open or linked Typically generated by small communities for “local” research projects Figures from 1) Zhang, Zootaxa , 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

Scratchpad Virtual Research Environments Making taxonomy digital, open & linked

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

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)

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

+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 +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 What can Scratchpads do?

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

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

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

Getting data in and out of Scratchpads 2

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 - Open Source Development -

Online community revision Freeloader flies 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

Publishing observations & taxon data Specimen records & species pages on Scratchpads Pushed to GBIF & EOL (requires site registration with GBIF & EOL) >19K specimen records > 122k species pages >377M specimen records GBIF > 1 M species pages in EOL > & Darwin Core Archive (DwCA)

Experiments with article publishing Paper assembled from Scratchpad database XML submission, peer review & marked-up publication by Pensoft 5-step workflow for selecting data, adding metadata & previewing Published in Zookeys & Phytokeys (worldwide coverage) PDF HTML XML > doi: /zookeys

Example papers via Scratchpads… Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: 79–90. doi: /zookeys Faulwetter S, Chatzigeorgiou G, Galil BS, Nicolaidou A, Arvanitidis C (2011. ZooKeys 150: 327–345. doi: /zookeys Brake I, von Tschirnhaus M (2010). ZooKeys 50: 91–96. doi: /zookeys Live (updated) versions of these papers

But… Limited uptake in 2 years -1 genus -6 n. spp -11 re-descriptions Software bugs -Pushing the boundaries of SP1 -Fixed in SP2 Focused on synthetic papers -Not suited to small papers -Less emphasis on data -Hard to properly link in the data More effort than MS Word -Especially for new SP users

BDJ The Biodiversity Data Journal Making small data big!

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… Why do we need another new journal!!! Taxonomy needs less fragmentation, not more!

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

BDJ publication & dissemination workflow

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

Testing screenshots of the writing tool ID Key preview Multi-figure platesPlate layout ID Key builder Manuscript preview

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!

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 Starting late 2012, early 2013 Recruiting editors now

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

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

Source: Wikipedia