ViBRANT
Virtual Biodiversity

A decadal view of biodiversity informatics:
Alex Hardisty, Dave Roberts, and the
challenges ...
ViBRANT
Virtual Biodiversity

A decadal view of biodiversity informatics:
Alex Hardisty, Dave Roberts, and the
challenges ...
ViBRANT
Virtual Biodiversity

A decadal view of biodiversity informatics:
Alex Hardisty, Dave Roberts, and the
challenges ...
ViBRANT
Virtual Biodiversity

A decadal view of biodiversity informatics:
Alex Hardisty, Dave Roberts, and the
challenges ...
ViBRANT
Virtual Biodiversity

1. Open Data should be normal practice;

SEVENTH FRAMEWORK
PROGRAMME

-infrastructure
ViBRANT
Virtual Biodiversity

1. Open Data should be normal practice;

SEVENTH FRAMEWORK
PROGRAMME

2. Data encoding shoul...
ViBRANT
Virtual Biodiversity

1. Open Data should be normal practice;

2. Data encoding should
allow analysis across
multi...
ViBRANT
Names as strings of characters…

Virtual Biodiversity

4. A list of taxon names

Difficulties with Latinized Names...
ViBRANT
Names as strings of characters…

Virtual Biodiversity

4. A list of taxon names

Difficulties with Latinized Names...
ViBRANT
Virtual Biodiversity

7. 3rd party authentication

SEVENTH FRAMEWORK
PROGRAMME

-infrastructure
ViBRANT
Virtual Biodiversity

Atopobium minutum
Sphaerobacter
thermophilus
strain TH3

8. Classification Bank
Actinomycete...
ViBRANT
Virtual Biodiversity

9. Accepted names
Home

Overview
About the Catalogue of Life

Dynamic
Edition

Annual
Checkl...
ViBRANT
Virtual Biodiversity

10. Tools to make LOD
Humans are good at interpreting this:
Implicit semantics

o

“Compound...
ViBRANT
Virtual Biodiversity

The generation of
important new
insights while
handicapped with
limited technology,
indirect...
ViBRANT
Virtual Biodiversity

11. Data fit for purpose

SEVENTH FRAMEWORK
PROGRAMME

Data are received at face-value,
exam...
ViBRANT
Virtual Biodiversity

12. Observational data infrastructure

http://www.earthobservations.org/geobon.shtml

http:/...
GBIO Document

http://www.biodiversityinformatics.org/
Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern
GBIO Framework
ASSESSMENTS AND INDICATORS

OTHER
INFORMATION
DOMAINS

RESEARCH INFRASTRUCTURE INVESTMENTS
Courtesy of Dona...
Focus Area: Evidence

• Organised views of biodiversity data
–
–
–
–
–

Consistent assessment of quality and fitness-for-us...
http://tinyurl.com/oalvv8r
Structuring the biodiversity informatics community at the European level and beyond

The biodiv...
ViBRANT
Virtual Biodiversity

To build user confidence
Thus far, all projects share a common problem of keeping services
r...
ViBRANT
Virtual Biodiversity

Integrative flexible e-Science environments
Using standardised building blocks and workflows...
ViBRANT
Virtual Biodiversity

Predictive models across multiple scales
A new framework of methods, techniques, standards t...
http://h2020.myspecies.info
Structuring the biodiversity informatics community at the European level and beyond
ViBRANT

V...
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Hardisty roberts tdwg_301013_min

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TDWG (Firenze, 30 Oct 2013). Description of community view of priorities for future work in biodiversity informatics.

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Hardisty roberts tdwg_301013_min

  1. 1. ViBRANT Virtual Biodiversity A decadal view of biodiversity informatics: Alex Hardisty, Dave Roberts, and the challenges and priorities biodiversity informatics community* * 80 people took part in the open debate that led to this paper SEVENTH FRAMEWORK PROGRAMME -infrastructure
  2. 2. ViBRANT Virtual Biodiversity A decadal view of biodiversity informatics: Alex Hardisty, Dave Roberts, and the challenges and priorities biodiversity informatics community* “We are drowning in information, while starving for wisdom. The world henceforth will be run by synthesizers, people able to put together the right information at the right time, think critically about it, and make important choices” E. O. Wilson, "Consilience: The Unity of Knowledge" (1998) * 80 people took part in the open debate that led to this paper SEVENTH FRAMEWORK PROGRAMME -infrastructure
  3. 3. ViBRANT Virtual Biodiversity A decadal view of biodiversity informatics: Alex Hardisty, Dave Roberts, and the challenges and priorities biodiversity informatics community* “We are drowning in information, while starving for wisdom. The world henceforth will be run by synthesizers, people able to put together the right information at the right time, think critically about it, and make important choices” E. O. Wilson, "Consilience: The Unity of Knowledge" (1998) Time to model all life on Earth. Purves et. al. (2013) Nature, 493: 295-297 * 80 people took part in the open debate that led to this paper SEVENTH FRAMEWORK PROGRAMME -infrastructure
  4. 4. ViBRANT Virtual Biodiversity A decadal view of biodiversity informatics: Alex Hardisty, Dave Roberts, and the challenges and priorities biodiversity informatics community* The Grand Challenge for Biodiversity Informatics An infrastructure to allow the available data to be brought into a coordinated coupled modelling environment, capable of addressing questions relating to our use of the natural environment, that captures the variety, distinctiveness and complexity of all life on Earth To achieve it we need: To build user confidence Integrative flexible e-Science environments Predictive models across multiple scales, coupled * 80 people took part in the open debate that led to this paper SEVENTH FRAMEWORK PROGRAMME -infrastructure
  5. 5. ViBRANT Virtual Biodiversity 1. Open Data should be normal practice; SEVENTH FRAMEWORK PROGRAMME -infrastructure
  6. 6. ViBRANT Virtual Biodiversity 1. Open Data should be normal practice; SEVENTH FRAMEWORK PROGRAMME 2. Data encoding should allow analysis across multiple scales; -infrastructure
  7. 7. ViBRANT Virtual Biodiversity 1. Open Data should be normal practice; 2. Data encoding should allow analysis across multiple scales; 3. Infrastructure projects should devote significant resources to market the service they develop; SEVENTH FRAMEWORK PROGRAMME -infrastructure
  8. 8. ViBRANT Names as strings of characters… Virtual Biodiversity 4. A list of taxon names Difficulties with Latinized Names Actinobacillus actimomycetemcomitans Actinobacillus actimycetemcomitans Actinobacillus actinmycetemcomitans Actinobacillus actinomicetemcomitans Actinobacillus actinomy Actinobacillus actinomyce Actinobacillus actinomycemcomitans Actinobacillus actinomyceremcomitans Actinobacillus actinomycetam Actinobacillus actinomycetamcomitans Actinobacillus actinomycetecomitans Actinobacillus actinomycetemcmitans Actinobacillus actinomycetemcomintans Actinobacillus actinomycetemcomitance Actinobacillus actinomycetemcomitans Actinobacillus actinomycetemcomitants Actinobacillus actinomycetemcommitans Actinobacillus actinomycetemocimitans Actinobacillus actinomycetencomitans Actinobacillus actinomycetum Actinobacillus actinomyctemcomitans Actinobacillus actinomyectomcomitans Actinobacillus actinomyetemcomitans Actinobacillus actinonmycetemcomitans Actinobacillus actionomycetemcomitans Actinobacillus actynomicetemcomitans Actinobacillus antinomycetemcomitans Nomenclator provides correct spelling. Indexing infrastructure resolves to it. Transcription errors 5. Persistent Identifiers DOI: 10.4289/0013-8797.115.1.75 SEVENTH FRAMEWORK PROGRAMME -infrastructure
  9. 9. ViBRANT Names as strings of characters… Virtual Biodiversity 4. A list of taxon names Difficulties with Latinized Names Actinobacillus actimomycetemcomitans Actinobacillus actimycetemcomitans Actinobacillus actinmycetemcomitans Actinobacillus actinomicetemcomitans Actinobacillus actinomy Actinobacillus actinomyce Actinobacillus actinomycemcomitans Actinobacillus actinomyceremcomitans Actinobacillus actinomycetam Actinobacillus actinomycetamcomitans Actinobacillus actinomycetecomitans Actinobacillus actinomycetemcmitans Actinobacillus actinomycetemcomintans Actinobacillus actinomycetemcomitance Actinobacillus actinomycetemcomitans Actinobacillus actinomycetemcomitants Actinobacillus actinomycetemcommitans Actinobacillus actinomycetemocimitans Actinobacillus actinomycetencomitans Actinobacillus actinomycetum Actinobacillus actinomyctemcomitans Actinobacillus actinomyectomcomitans Actinobacillus actinomyetemcomitans Actinobacillus actinonmycetemcomitans Actinobacillus actionomycetemcomitans Actinobacillus actynomicetemcomitans Actinobacillus antinomycetemcomitans Nomenclator provides correct spelling. Indexing infrastructure resolves to it. Transcription errors 6. Author identifiers SEVENTH FRAMEWORK PROGRAMME 5. Persistent Identifiers DOI: 10.4289/0013-8797.115.1.75 -infrastructure
  10. 10. ViBRANT Virtual Biodiversity 7. 3rd party authentication SEVENTH FRAMEWORK PROGRAMME -infrastructure
  11. 11. ViBRANT Virtual Biodiversity Atopobium minutum Sphaerobacter thermophilus strain TH3 8. Classification Bank Actinomycetes: the antibiotic factories Bifidobacteriaceae Actinomycetaceae Insertion element in 23S rRNA Arthrobacteriaceae, Cellomonadaceae, Microbacteriaceae, Dermatophilaceae and realtives Propionibacteriaceae Nocardioidaceae Frankiaceae Corynebacteriaceae, Mycobacteriaceae, Nocardiaceae and realtives Actinoplanaceae Pseudonocardiaceae Streptomycetaceae, Streptosporangiaceae and relatives Embley & Stackebrandt (1994) SEVENTH FRAMEWORK PROGRAMME Bergey’s Manual, 2nd Edition (2012) -infrastructure
  12. 12. ViBRANT Virtual Biodiversity 9. Accepted names Home Overview About the Catalogue of Life Dynamic Edition Annual Checklist Welcome to the Catalogue of Life website: gateway to our database of the world's known species of animals, plants, fungi and micro-organisms Contributors & partners Contact us I . P . N . I User Guide Getting started Versions of the Catalogue Contributing your data Glossary Additional Services Downloads Advanced services » Explore This Dynamic Edition is a constantly evolving version of the Catalogue of Life. Now tracking 70% of species known to science 1,315,754 species Latest on Twitter 'The most comprehensive and authoritative global index of species currently available, the Catalogue of Life consists of a single integrated checklist and taxonomic hierarchy for all the world's species.' Catalogue of Life catalogueoflife catalogueoflife Catalogue of Life, 11th March 2013 is now online at catalogueoflife.org/col 6 days ago · reply · retweet · favorite catalogueoflife Catalogue of Life, 08th February 2013 is now online at catalogueoflife.org/col Annual Checklist » The Annual Checklist is a snapshot of the entire Catalogue of Life: a fixed imprint. 37 days ago· reply · retweet · favorite Why two versions? Join the conversation © 2013, Species 2000 at University of Reading | Disclaimer SEVENTH FRAMEWORK PROGRAMME Design: Chris Turnbull | Content: Simon Thornton-Wood -infrastructure
  13. 13. ViBRANT Virtual Biodiversity 10. Tools to make LOD Humans are good at interpreting this: Implicit semantics o “Compound 2a melted at 119 C” Machines need this: Explicit semantics CML Schema <cml:molecule ref=“2a”> <cml:property> Molecules in CML/InChl <cml:scalar dictRef=“prop:mpt” units=“units:celsius” propertyDictionary dataType=“xds:float” unitsDictionary >119</cml:scalar> W3CSchema </cml:property> </cml:molecule> 4 namespaces, 3 dictionaries SEVENTH FRAMEWORK PROGRAMME -infrastructure
  14. 14. ViBRANT Virtual Biodiversity The generation of important new insights while handicapped with limited technology, indirect measurement, and fuzzy data is the mark of scientific greatness. GBIF/GBIC – 2-4 Jul 2012 – Copenhagen, © 2012, R. J. Robbins SEVENTH FRAMEWORK PROGRAMME -infrastructure
  15. 15. ViBRANT Virtual Biodiversity 11. Data fit for purpose SEVENTH FRAMEWORK PROGRAMME Data are received at face-value, examined and tested. If the user is satisfied, then the data will be applied. -infrastructure
  16. 16. ViBRANT Virtual Biodiversity 12. Observational data infrastructure http://www.earthobservations.org/geobon.shtml http://www.eubon.eu http://www.teamnetwork.org http://mooreabiocode.org/ Moorea Biocode Project http://www.neoninc.org SEVENTH FRAMEWORK PROGRAMME http://www.ilternet.edu Agriculture Systems Climate Forest Invasion Urban Change Management Biology Ecosystems -infrastructure
  17. 17. GBIO Document http://www.biodiversityinformatics.org/ Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern
  18. 18. GBIO Framework ASSESSMENTS AND INDICATORS OTHER INFORMATION DOMAINS RESEARCH INFRASTRUCTURE INVESTMENTS Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern
  19. 19. Focus Area: Evidence • Organised views of biodiversity data – – – – – Consistent assessment of quality and fitness-for-use Comprehensive digital nomenclature and taxonomy Access to all evidence for recorded species occurrence Access to species traits, measurements and interactions Services and interfaces to access data as needed • Provide comprehensive organised views of all relevant data • Act as a “lens” into primary data Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern
  20. 20. http://tinyurl.com/oalvv8r Structuring the biodiversity informatics community at the European level and beyond The biodiversity informatics community needs : Clarity of vision, greater focus on end-goals; Good, simple tools with syntactic operability; Community identity; Better links within our community and with other disciplines ecology, agriculture, socioeconomics, remote sensing, etc.. We have a lot of data. Now we need to show that those data are actually useful. What questions can these data address? Stop mobilising just any data. Invert the system and direct what data are to be recovered by the question that is being addressed. This will also dictate the quality level.
  21. 21. ViBRANT Virtual Biodiversity To build user confidence Thus far, all projects share a common problem of keeping services running after project funding ended New models are needed To create translational pipelines to industry adoption To encourage institutional adoption for care and maintenance For recognition of contribution other than through publication of academic papers Stronger marketing and outreach Invest more in up-skilling and hand-holding SEVENTH FRAMEWORK PROGRAMME -infrastructure
  22. 22. ViBRANT Virtual Biodiversity Integrative flexible e-Science environments Using standardised building blocks and workflows Interoperable components With access to data from multiple sources Recognise different kinds of VRE General-purpose / specialised / single scientific objective - cf. chemistry laboratory vs forensics lab vs HIV vaccine lab - Scratchpads & BioVeL / AquaMaps and iMarine / CarbonWaterCloud Must generate immediate benefit for users Science driven, with scientists as active participants in creation of infrastructure Functions people find useful: simple and intuitive Technology invisible (disappears into background) SEVENTH FRAMEWORK PROGRAMME -infrastructure
  23. 23. ViBRANT Virtual Biodiversity Predictive models across multiple scales A new framework of methods, techniques, standards to bring about interoperability of data and models across different biological scales From Genetic through species and ecosystem to landscape Learn from Virtual Physiological Human and from Numerical weather prediction and climatology Edwards (2010). A Vast Machine “General Ecological Models” Purves et al. (2013). doi:10.1038/493295a Evolvable to incorporate new scientific insights Re-analysis models Making data we have global Implies ‘inversion’ of existing infrastructure ‘inversion’ of existing infrastructure is about re-examining every element of data we have to re-construct the past biodiversity, as a guide and calibrator of models that can predict the future SEVENTH FRAMEWORK PROGRAMME -infrastructure
  24. 24. http://h2020.myspecies.info Structuring the biodiversity informatics community at the European level and beyond ViBRANT Virtual Biodiversity Our goal, sine qua non, is to deliver predictive modelling of the biosphere.
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