hardisty roberts tdwg_301013_min

Virtual BiodiversityViBRANT

-infrastructureSEVENTH FRAMEWORK PROGRAMME

A decadal view of biodiversity informatics: challenges and priorities Alex Hardisty, Dave Roberts, and the

biodiversity informatics community*

* 80 people took part in the open debate that led to this paper






“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)






“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”

Time to model all

life on Earth.

Purves et. al. (2013) Nature, 493: 295-297

E. O. Wilson, "Consilience: The Unity of Knowledge" (1998)



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




The Grand Challenge for Biodiversity Informatics

To achieve it we need:To build user confidenceIntegrative flexible e-Science environmentsPredictive models across multiple scales, coupled



1. Open Data should be normal practice;



1. Open Data should be normal practice;2. Data encoding should

allow analysis across multiple scales;



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;



Actinobacillus actimomycetemcomitansActinobacillus actimycetemcomitansActinobacillus actinmycetemcomitansActinobacillus actinomicetemcomitansActinobacillus actinomyActinobacillus actinomyceActinobacillus actinomycemcomitansActinobacillus actinomyceremcomitansActinobacillus actinomycetamActinobacillus actinomycetamcomitansActinobacillus actinomycetecomitansActinobacillus actinomycetemcmitansActinobacillus actinomycetemcomintansActinobacillus actinomycetemcomitanceActinobacillus actinomycetemcomitansActinobacillus actinomycetemcomitants

Actinobacillus actinomycetemcommitansActinobacillus actinomycetemocimitansActinobacillus actinomycetencomitansActinobacillus actinomycetumActinobacillus actinomyctemcomitansActinobacillus actinomyectomcomitansActinobacillus actinomyetemcomitansActinobacillus actinonmycetemcomitansActinobacillus actionomycetemcomitansActinobacillus actynomicetemcomitansActinobacillus antinomycetemcomitans

Difficulties with Latinized NamesTranscription errors

Nomenclator provides correct spelling. Indexing infrastructure resolves to it.

Names as strings of characters… 4. A list of taxon names

DOI: 10.4289/0013-8797.115.1.75

5. Persistent Identifiers



Actinobacillus actimomycetemcomitansActinobacillus actimycetemcomitansActinobacillus actinmycetemcomitansActinobacillus actinomicetemcomitansActinobacillus actinomyActinobacillus actinomyceActinobacillus actinomycemcomitansActinobacillus actinomyceremcomitansActinobacillus actinomycetamActinobacillus actinomycetamcomitansActinobacillus actinomycetecomitansActinobacillus actinomycetemcmitansActinobacillus actinomycetemcomintansActinobacillus actinomycetemcomitanceActinobacillus actinomycetemcomitansActinobacillus actinomycetemcomitants

Actinobacillus actinomycetemcommitansActinobacillus actinomycetemocimitansActinobacillus actinomycetencomitansActinobacillus actinomycetumActinobacillus actinomyctemcomitansActinobacillus actinomyectomcomitansActinobacillus actinomyetemcomitansActinobacillus actinonmycetemcomitansActinobacillus actionomycetemcomitansActinobacillus actynomicetemcomitansActinobacillus antinomycetemcomitans

Difficulties with Latinized NamesTranscription errors

Nomenclator provides correct spelling. Indexing infrastructure resolves to it.

Names as strings of characters… 4. A list of taxon names

DOI: 10.4289/0013-8797.115.1.75

5. Persistent Identifiers

6. Author identifiers



7. 3rd party authentication



8. Classification Bank

Embley & Stackebrandt (1994) Bergey’s Manual, 2nd Edition (2012)

Actinomycetes: the antibiotic factories

Atopobium minutumSphaerobacter thermophilus

strain TH3

Bifidobacteriaceae

Actinomycetaceae

Arthrobacteriaceae, Cellomonadaceae, Microbacteriaceae, Dermatophilaceae and realtives

Propionibacteriaceae

Nocardioidaceae

Frankiaceae

Corynebacteriaceae, Mycobacteriaceae, Nocardiaceae and realtives

Actinoplanaceae

Pseudonocardiaceae

Streptomycetaceae, Streptosporangiaceae and relatives

Insertion element in 23S rRNA



9. Accepted names

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10. Tools to make LOD

Implicit semantics“Compound 2a melted at 119oC”

Humans are good at interpreting this:

Explicit semantics CML Schema<cml:molecule ref=“2a”> <cml:property> <cml:scalar dictRef=“prop:mpt” units=“units:celsius” dataType=“xds:float” >119</cml:scalar> </cml:property></cml:molecule>

Molecules in CML/InChl

propertyDictionaryunitsDictionary

W3CSchema

4 namespaces, 3 dictionaries

Machines need this:



GBIF/GBIC – 2-4 Jul 2012 – Copenhagen, © 2012, R. J. Robbins

The generation of important new insights while handicapped with limited technology, indirect measurement, and fuzzy data is the mark of scientific greatness.



11. Data fit for purposeData are received at face-value, examined and tested. If the user is satisfied, then the data will be applied.



12. Observational data infrastructure

Agriculture Systems

Climate Change

Forest Management

Invasion Biology

Urban Ecosystems

http://www.teamnetwork.org

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

http://www.eubon.eu

http://www.neoninc.org

http://mooreabiocode.org/

Moorea Biocode Project

http://www.ilternet.edu

GBIO Document

Courtesy of Donald Hobern: http://tinyurl.com/BIH13-hobern

http://www.biodiversityinformatics.org/

RESEARCH INFRASTRUCTURE INVESTMENTS

OTHER INFORMATION

DOMAINS

ASSESSMENTS AND INDICATORS

GBIO Framework


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


http://tinyurl.com/oalvv8rStructuring the biodiversity informatics community at the European level and beyond

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..

The biodiversity informatics community needs :

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.



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



Integrative flexible e-Science environmentsUsing 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)



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

http://h2020.myspecies.info

ViBRANTVirtual Biodiversity

Structuring the biodiversity informatics community at the European level and beyond

Our goal, sine qua non, is to deliver predictive

modelling of the biosphere.

hardisty roberts tdwg_301013_min

Technology

open data

vibrant virtual biodiversity1

indexing infrastructure

infrastructure projects

vibrant names

open debate

multiple scalesinfrastructure

alex hardisty