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

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
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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
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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
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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
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5. ViBRANT
Virtual Biodiversity
1. Open Data should be normal practice;
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6. ViBRANT
Virtual Biodiversity
1. Open Data should be normal practice;
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2. Data encoding should
allow analysis across
multiple scales;
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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;
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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
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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
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5. Persistent
Identifiers
DOI: 10.4289/0013-8797.115.1.75
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10. ViBRANT
Virtual Biodiversity
7. 3rd party authentication
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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)
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Bergey’s Manual, 2nd Edition (2012)
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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
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catalogueoflife Catalogue of Life,
11th March 2013 is now online at
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Design: Chris Turnbull
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Content: Simon Thornton-Wood
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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
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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
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15. ViBRANT
Virtual Biodiversity
11. Data fit for purpose
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Data are received at face-value,
examined and tested. If the
user is satisfied, then the data
will be applied.
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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
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http://www.ilternet.edu
Agriculture
Systems
Climate
Forest
Invasion
Urban
Change Management Biology Ecosystems
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17. GBIO Document
http://www.biodiversityinformatics.org/
Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern

18. GBIO Framework
ASSESSMENTS AND INDICATORS
OTHER
INFORMATION
DOMAINS
RESEARCH INFRASTRUCTURE INVESTMENTS
Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern

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. 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. 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
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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)
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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
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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.