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

Vince Smith

Delivering biodiversity knowledge in the information age

Hellenic Botanical SocietyThessaloniki, Greece, 3-6 Oct. 2013

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)

1. Background

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

http://darwin.zoology.gla.ac.uk/~rpage/LouseBase/2/

LouseBASE

Specimens Images

(SID)

http://darwin.zoology.gla.ac.uk/~SID/

Literature

PHPBibhttp://myphpbib.sourceforge.net/

Lab Notebook

http://www2.flmnh.ufl.edu/pdb/

Host-Parasite Checklists

http://www2.flmnh.ufl.edu/adb/

Glasgow version at:

Lousy data infrastructures (circa 2004)

The problem – integrating biodiversity research (2004>)

How to we join up these activities? How do we use this as a tool? Species conservation & protected areas

Impacts of human developmentBiodiversity & human health

Impacts of climate changeFood, farming & biofuels

Invasive alien species

What infrastructures do we need?(technologies, tools, standards…)What processes do we need?(Modelling, workflows…)What data do we need?(Genes, localities…)

2. Biodiversity data tools- Scratchpads- Biodiversity Data Journal- eMonocot

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

Scratchpads– a space for your data

Taxa Projects Regions Societies

544 Scratchpad Communities

by 6,644 active registered users

covering 91,631 taxa

in 535,317 pages. 81 paper citations in 2012

In total more than

1,300,000 visitors

http://scratchpads.eu

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

Biodiversity Data Journal – easy manuscript assembly

Structured data

Review, Publish, cite &

disseminate

EOLDryad GBIFWiki Species-IdPubMed Plazi

Select, describe & annotate

dataPublication module

http://biodiversitydatajournal.com

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

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

3. Example challenges- Social issues (openness)

- Data issues (mobalising existing data)

- Synthetic issues (modelling)

Social challenges: openness

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”

“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/

Many kinds of openness:• Open Access• Open Data• Open Science• Open Source

• Sharing data is a foundation for our activities

• Normal practice in some communities (molecular)

• Mandated by some funders & governments

Need to continue to incentivise openness

Data challenges: mobilising existing data

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

Informatics challenges• Automation & annotation• Storage & persistence• Business models to sustain activity

Collections, literature & metadata

How can we quickly, efficiently and cost effectively mobilise biological data at scale?

Bibliography of Life (RefFinder & RefBank)

BHL literature

NHM Digitisation

Synthetic challenges: Modeling the biosphere

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

Reasoning across large, linked biodiversity datasets

A clear, singular, long-term vision, which biodiversity data can contribute too

4. Next steps- Further reading- H2020 Opportunities

A strategic view: community informatics challenges

GBIF GBIC Report(Sept. 2013)

Biodiv. Inf. Challenges(April, 2013)

Grand Challenges for Biodiversity Informatics(integrating activities for H2020)

QUESTIONS