SlideShare a Scribd company logo
Don’t make me think
Biodiversity data publishing made easy
Vince Smith, Alice Heaton, Laurence Livermore,
Simon Rycroft, Ben Scott & Lyubomir Penev*
The Natural History Museum London
Pensoft Publishing*, Bulgaria
Data
curation
Data
publishing
What we need is…
Data
collection &
generation
a
seamless
workflow
Data
analysis
• Hosted websites for
biodiversity data
• Virtual research
environments
• Completely open
access & open source
• Modular & flexible
• Running since 2007
• Making taxonomy
digital, open & linked
Scratchpads (http://Scratchpads.eu)
65,000
unique visitors/month
Per month unique visitors to Scratchpad sites
512Scratchpad Communities
by 6,500active registered users
covering 73,444taxa
in 515,189 pages.
Scratchpad usage metrics
81 paper citations in 2012
In total more than
1,300,000 visitors

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The document discusses best practices and considerations for developing workflows for ingesting digital objects into repositories and digital libraries. It covers key aspects of ingest workflows including standards, quality assurance procedures, metadata, tools and software. Example ingest workflows are provided using systems like Archivematica, DSpace and DataVerse to illustrate the ingest process.

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Antica Culina talks about open science for Ecology | OSFair2017 Workshop Workshop title: Open Science as a service: tools for research communities Workshop overview: The aim of this workshop is to work with research communities especially interested/relevant to open science publishing paradigms: publishing of literature, datasets, methods, and experiments for reproducibility and transparent assessment of science. This will be an interactive session with communities presenting their requirements and current tooling to identify overlaps, better and cost-effective solutions. When: DAY 2 - PARALLEL SESSION 3

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Presentation by Costis Dallas Digital Curation Unit-IMIS, Athena Research Centre Department of Communication, Media and Culture, Panteion University Faculty of Information, University of Toronto and Dimitris Gavrilis Digital Curation Unit-IMIS, Athena Research Centre Full-day session on archaeological infrastructures and services at the 18th Cultural Heritage and New Technologies (CHNT) conference Vienna, Austria 11th -13th November 2013

ariadneinteroperabilityresearch data
Taxa
(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic
& morphometric datasets, keys, phylogenies)
ProjectsConservation Regions Societies
Examples of Scratchpad use
Data
curation
Data publishing via Scratchpads
Data
collection &
generation
Data
analysis
Data
publishing
No kudos, credit
or citation of data
in Scratchpads
Structured data
Publish, cite,
disseminate &
archive data
EOL
Dryad
GBIF
Wiki Species-Id
PubMed
Plazi
Select,
describe &
annotate data
Publication module
Biodiversity Data Journal
• New, Open Access data journal
• Launches Mid-2013
• Supports the full life cycle of a
manuscript
• Writing, submission, review,
publication & dissemination
• Structured, reusable,
standardized data
• Linked to Scratchpads via
publishing module
http://biodiversitydatajournal.com/

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Labman is a research information system developed by DeustoTech at the University of Deusto to help researchers effectively manage research data. It deals with issues related to data collection, storage, linking and presentation for entities like projects, publications, people, events and organizations. More than 100 entities are involved in Labman's data model. Labman publishes research data as linked open data and allows importing publication metadata from Zotero. It also provides visualizations of the research data through interactive charts and networks. Future work will include providing a JSON-LD API and tagging pages with schema.org definitions.

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The publication module
Scratchpad templates for publishing...
• Taxon treatments
• Nomenclatural acts
• Checklists / inventories
• Identification keys and trees
• Metadata descriptions of databases
• Descriptions of software tools
Easy & intuitive
• Draws on data from your site
• Pre-submission validation
• Submitted as structured XML
• No reformatting
Assembling a manuscript
1. Add article level metadata...
• Choose authors, select template
• Add context (title, abstract)
2. Select data
• Taxon descriptions
• Specimens
• Datasets
• Figures & tables
• Keys & trees
3. Describe data
• Intro., methods, conclusions
• Auto-compile references
4. Submit
• Preview manuscript
• Validate
After submission
More information
Scratchpads (GPLv2 License)
• http://scratchpads.eu/ (Scratchpad project)
• http://scratchpads.eu/develop/repository (Developer resources)
• https://git.scratchpads.eu/v/scratchpads-2.0.git/tree (Git repository)
Scratchpad Publication Module (also GPLv2)
• https://git.scratchpads.eu/v/scratchpads-2.0.git/tree/
HEAD:/sites/all/modules/custom/publication
Biodiversity Data Journal
• http://biodiversitydatajournal.com/
Credits
• Alice Heaton, Simon Rycroft, Ben Scott (programming)
• Laurence Livermore (user testing & support)
• Lyubomir Penev & the Pensoft team (Biodiversity Data Journal)
Funding
• EU FP7 Infrastrastructures (ViBRANT), UK NERC (e-Monocot)

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Don’t make me think: biodiversity data publishing made easy

  • 1. Don’t make me think Biodiversity data publishing made easy Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev* The Natural History Museum London Pensoft Publishing*, Bulgaria
  • 2. Data curation Data publishing What we need is… Data collection & generation a seamless workflow Data analysis
  • 3. • Hosted websites for biodiversity data • Virtual research environments • Completely open access & open source • Modular & flexible • Running since 2007 • Making taxonomy digital, open & linked Scratchpads (http://Scratchpads.eu)
  • 4. 65,000 unique visitors/month Per month unique visitors to Scratchpad sites 512Scratchpad Communities by 6,500active registered users covering 73,444taxa in 515,189 pages. Scratchpad usage metrics 81 paper citations in 2012 In total more than 1,300,000 visitors
  • 5. Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) ProjectsConservation Regions Societies Examples of Scratchpad use
  • 6. Data curation Data publishing via Scratchpads Data collection & generation Data analysis Data publishing No kudos, credit or citation of data in Scratchpads
  • 7. Structured data Publish, cite, disseminate & archive data EOL Dryad GBIF Wiki Species-Id PubMed Plazi Select, describe & annotate data Publication module
  • 8. Biodiversity Data Journal • New, Open Access data journal • Launches Mid-2013 • Supports the full life cycle of a manuscript • Writing, submission, review, publication & dissemination • Structured, reusable, standardized data • Linked to Scratchpads via publishing module http://biodiversitydatajournal.com/
  • 9. The publication module Scratchpad templates for publishing... • Taxon treatments • Nomenclatural acts • Checklists / inventories • Identification keys and trees • Metadata descriptions of databases • Descriptions of software tools Easy & intuitive • Draws on data from your site • Pre-submission validation • Submitted as structured XML • No reformatting
  • 10. Assembling a manuscript 1. Add article level metadata... • Choose authors, select template • Add context (title, abstract) 2. Select data • Taxon descriptions • Specimens • Datasets • Figures & tables • Keys & trees 3. Describe data • Intro., methods, conclusions • Auto-compile references 4. Submit • Preview manuscript • Validate
  • 12. More information Scratchpads (GPLv2 License) • http://scratchpads.eu/ (Scratchpad project) • http://scratchpads.eu/develop/repository (Developer resources) • https://git.scratchpads.eu/v/scratchpads-2.0.git/tree (Git repository) Scratchpad Publication Module (also GPLv2) • https://git.scratchpads.eu/v/scratchpads-2.0.git/tree/ HEAD:/sites/all/modules/custom/publication Biodiversity Data Journal • http://biodiversitydatajournal.com/ Credits • Alice Heaton, Simon Rycroft, Ben Scott (programming) • Laurence Livermore (user testing & support) • Lyubomir Penev & the Pensoft team (Biodiversity Data Journal) Funding • EU FP7 Infrastrastructures (ViBRANT), UK NERC (e-Monocot)