Delivering biodiversity
knowledge in the
information age
Vince Smith

Hellenic Botanical Society
Thessaloniki, Greece, 3-6...
Overview

1. Background – biodiversity data diversity
•
•

An introduction to me (lice to data infrastructures)
The proble...
1. Background
Lice to data infrastructures (1997-2004)

Systematics (circa 1998)
- No high level keys
- Poor high level taxonomy
- Just ...
Lousy data infrastructures (circa 2004)

Images

Specimens

(SID)

LouseBASE

Glasgow version at:
http://darwin.zoology.gl...
The problem – integrating biodiversity research (2004>)
How to we join up these activities?
What infrastructures do we nee...
2. Biodiversity data tools
- Scratchpads
- Biodiversity Data Journal
- eMonocot
Scratchpads – a space for your data

• Hosted websites for
biodiversity data
• Virtual research
environments

• Completely...
Scratchpads– a space for your data

Taxa

Projects

544 Scratchpad Communities
by

6,644 active registered users

covering...
Biodiversity Data Journal – incentivising data publishing
• New, Open Access data journal
• Linked to Scratchpads via Publ...
Biodiversity Data Journal – easy manuscript assembly

Structured data

Select, describ
e & annotate
data

Publication modu...
eMonocot – aggregating data across communities

• Online resource for monocot
plants
• Collaboration between
Kew, Oxford U...
eMonocot – aggregating data across communities
• Linking monocot
communities
• Identification, checklist
& taxonomic data ...
3. Example challenges
- Social issues (openness)
- Data issues (mobalising existing data)
- Synthetic issues (modelling)
Social challenges: openness
“A piece of data or content is open if anyone is free to use, reuse, and redistribute it subje...
Data challenges: mobilising existing data
Collections, literature & metadata
How can we quickly, efficiently and cost
effe...
Synthetic challenges: Modeling the biosphere
Reasoning across large, linked biodiversity datasets
A clear, singular, long-...
4. Next steps
- Further reading
- H2020 Opportunities
A strategic view: community informatics challenges

Biodiv. Inf. Challenges
(April, 2013)

GBIF GBIC Report
(Sept. 2013)

...
QUESTIONS
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Vince smith-delivering biodiversity knowledge in the information age-notext

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Smith, V.S. 2013. Delivering biodiversity knowledge in the information age. Hellenic Botanical Society, Thessaloniki, Greece, 3-6 Oct. 2013. [Delivered via video link through Google Hangouts]

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Vince smith-delivering biodiversity knowledge in the information age-notext

  1. 1. Delivering biodiversity knowledge in the information age Vince Smith Hellenic Botanical Society Thessaloniki, Greece, 3-6 Oct. 2013
  2. 2. Overview 1. Background – biodiversity data diversity • • An introduction to me (lice to data infrastructures) The problem (integrating biodiversity research) 2. Example tools to manage biodiversity data • • • Scratchpads (a platform to manage data) Biodiversity Data Journal (incentives to work digitally) eMonocot (aggregating data across communities) 3. Big community challenges – three examples • • • Social issues (openness) Data issues (mobilizing existing data) Synthetic issues (modeling data) 4. Next steps • Toward an integrated view for H2020 (strategy)
  3. 3. 1. Background
  4. 4. Lice to data infrastructures (1997-2004) Systematics (circa 1998) - No high level keys - Poor high level taxonomy - Just one phylogeny - Few living experts! Circa 5,000 spp. Mammals & birds 12,000 associations 15,000 potential hosts
  5. 5. Lousy data infrastructures (circa 2004) Images Specimens (SID) LouseBASE Glasgow version at: http://darwin.zoology.gla.ac.uk/~rpage/LouseBase/2/ Lab Notebook Literature http://darwin.zoology.gla.ac.uk/~SID/ Host-Parasite Checklists PHPBib http://www2.flmnh.ufl.edu/pdb/ http://myphpbib.sourceforge.net/ http://www2.flmnh.ufl.edu/adb/
  6. 6. The problem – integrating biodiversity research (2004>) How to we join up these activities? What infrastructures do we need? (technologies, tools, standards…) What processes do we need? (Modelling, workflows…) What data do we need? (Genes, localities…) How do we use this as a tool? Species conservation & protected areas Impacts of human development Biodiversity & human health Impacts of climate change Food, farming & biofuels Invasive alien species
  7. 7. 2. Biodiversity data tools - Scratchpads - Biodiversity Data Journal - eMonocot
  8. 8. Scratchpads – a space for your data • Hosted websites for biodiversity data • Virtual research environments • Completely open access & open source • Modular & flexible • Running since 2007 • Making taxonomy digital, open & linked http://scratchpads.eu
  9. 9. Scratchpads– a space for your data Taxa Projects 544 Scratchpad Communities by 6,644 active registered users covering 91,631 taxa in 535,317 pages. http://scratchpads.eu Regions Societies In total more than 1,300,000 visitors 81 paper citations in 2012
  10. 10. Biodiversity Data Journal – incentivising data publishing • New, Open Access data journal • Linked to Scratchpads via Publication Module • Supports the life cycle of a manuscript • Writing, submission, review, publication & dissemination, all in one place • Structured, reusable, standardised data • Launched in Sept 2013 with 24 articles http://biodiversitydatajournal.com
  11. 11. Biodiversity Data Journal – easy manuscript assembly Structured data Select, describ e & annotate data Publication module Review, Publish , cite & disseminate http://biodiversitydatajournal.com EOL Dryad GBIF Wiki Species-Id PubMed Plazi
  12. 12. eMonocot – aggregating data across communities • Online resource for monocot plants • Collaboration between Kew, Oxford University and NHM • Data to be open and usable by other scientists http://e-monocot.org
  13. 13. eMonocot – aggregating data across communities • Linking monocot communities • Identification, checklist & taxonomic data for: - 275,000 taxa 8,300 images 15 identification keys 3 phylogenies • A sustainable digital portal • A source of data for analysis http://e-monocot.org
  14. 14. 3. Example challenges - Social issues (openness) - Data issues (mobalising existing data) - Synthetic issues (modelling)
  15. 15. Social challenges: openness “A piece of data or content is open if anyone is free to use, reuse, and redistribute it subject, at most, to the requirement to attribute and/or share-alike.” http://opendefinition.org/ • Sharing data is a foundation for our activities • Normal practice in some communities (molecular) • Mandated by some funders & governments Many kinds of openness: • Open Access • Open Data • Open Science • Open Source E. Archambault et. al., Proportion of Open Access Peer-Reviewed Papers at the European and World Levels--2004-2011, June 2013, Science-Metrix Inc. “One-half of all papers are now freely available within a year or two of publication” Need to continue to incentivise openness
  16. 16. Data challenges: mobilising existing data Collections, literature & metadata How can we quickly, efficiently and cost effectively mobilise biological data at scale? Collections • 1.5-3B specimens in collections worldwide • Fragments efforts / need coordination Biodiversity literature • >300M pages, BHL scanned 41M to date • Copyright post-1923 & article metadata NHM Digitisation BHL literature Informatics challenges • Automation & annotation • Storage & persistence • Business models to sustain activity Bibliography of Life (RefFinder & RefBank)
  17. 17. Synthetic challenges: Modeling the biosphere Reasoning across large, linked biodiversity datasets A clear, singular, long-term vision, which biodiversity data can contribute too Conceptually has many potential uses • Identifying trends • Explaining patterns • Making predictions • Real time alerts - when data contradicts current knowledge • The ultimate policy tool Major informatics challenges • Technical very difficult (many years off) • Needs effective prototypes & platforms • Some first steps e.g. Local Ecological Footprint Tool Nature 2013, doi:10.1038/493295a
  18. 18. 4. Next steps - Further reading - H2020 Opportunities
  19. 19. A strategic view: community informatics challenges Biodiv. Inf. Challenges (April, 2013) GBIF GBIC Report (Sept. 2013) Grand Challenges for Biodiversity Informatics (integrating activities for H2020)
  20. 20. QUESTIONS
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