Towards integrated measures of biodiversity, ecosystem function and ecosystem service
Service Networks, Service Sets and Biodiversity Catalogue
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Transcript of Service Networks, Service Sets and Biodiversity Catalogue
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Structuring the biodiversity informatics community at the European level and beyond
Service Networks, Service Sets and Biodiversity Catalogue
Alex HardistyCardiff University
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Outline
Provision of data and processing of information are both “services”. How can we establish a landscape in which services are both discoverable and interoperable?
• What is a Service Network and what are Service Sets?
• Why do we need them and how do we build them?
• What is the role of the Biodiversity Catalogue?
• Where is this all going?
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What is a Service Network?
• A set of Web service (WS) instances that interact together to perform an application objective– In our case: multiple objectives, varying over time and
from one user to another
• Usage and hence composition needs to be dynamic
• In a Service Network:– Instances may join and leave– Instances are discoverable– Managed to a greater or lesser extent
WS1 WS2WS4
WS5
WS3
Biodiversity Service Network
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Workflow and experiments to study the ecological niche of the Horseshoe crab (Limulus polyphemus)
Workflows, pipelines and other applications are built from “services”
• Workflows allow to run studies and experiments to process vast amounts of data, repeatedly– Select and apply successive “services”
(data analysis and processing steps)– Import data from own research and/or
from existing public sources– Choose input parameters
• Service nesting– Services can themselves be made up
of combinations of other services or of workflow fragments
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A grouping of Web services having related functionality is called a ‘Service Set’
Taxonomy Metagenomics and metagenetics
Ecological niche and population modelling
Ecosystem functioning and valuation
Mapping, visualization, transformation
Catalogue of Life name lookup
QIIME ENM (openModeller)
Get meteor-ological data
Spatio-temporal visualization
GBIF occurrence data retrieval
BOLD PopBio Weather to Biome-BGC data
GeoServer WMS/WFS/WCS
GBIF ChecklistBank
BlastX Biome-BGCmonte carlo
Raster Diff
WoRMS aphia name
Sequence (OTU) clustering
Biome-BGC sensitivity anal.
ISO Country Code
PESI name Functional diversity
Data-Model harmonization
DwC-A to JSON shim
Checklist Cross-mapping
Taxonomic diversity
Biome-BGC CARBON
DwC-A to CSV shim
?
Taxonomy &Systematics
Ecological niche andpopulation modelling
Ecosystem functioningand valuation
?
Genes-Species-Specimens(multi-scale linkages)
Citizen Science &Observations
Mapping, visualization andtransformation services
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Service sets driven by science and policy needs
• CO2 emissions continuously increasing– 10 GtC in 2010; Sequestration is the sustainable
process to mitigate the effects
• Over the past 50 years, humans have changed ecosystems– resulting in a substantial and largely irreversible loss
of biodiversity
• Invasions of alien species– A leading cause of biodiversity loss and related
economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation.
“transportation with ships is a high risk to
spread the species to these spots”
Stelzer et al 2013
Source: NOAA
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Service sets driven by science and policy needs
• CO2 emissions continuously increasing– 10 GtC in 2010; Sequestration is the sustainable
process to mitigate the effects
• Over the past 50 years, humans have changed ecosystems– resulting in a substantial and largely irreversible loss
of biodiversity
• Invasions of alien species– A leading cause of biodiversity loss and related
economic damages. They degrade ecosystem services, generate human health problems and impact outdoor recreation.
“transportation with ships is a high risk to
spread the species to these spots”
Stelzer et al 2013
Source: NOAA
Modellingecosystem services
ModellingCO2 sequestration
Calculating measures of genetic diversity
Assessing adaptationto changing conditions
Supporting processesof conservation
Assisting invasivespecies management
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• Connecting biology and IT communities– Distinct languages, different understandings– Service Network approach connects them
• Supporting use cases we know today ...– … and use cases in the future that we cannot
yet imagine
• Different Service Providers are good (competent) at different things
• Deals with multiple jurisdictions and supports a business model– Leading to sustainability
Why do we need them?
Scientists’ perspectives
Info
rmati
on T
echn
olog
ists
’pe
rspe
ctive
s
Biodiversity studies & experiments
Services for biodiversity science
compose to support
ICT Technical Capabilities
ICT Technical Elements
combine to deliver
combine to support
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How to build Service Networks and Service Sets?Discipline
Scientists
Scientific PAL
Technical PAL
Scientific and Technical Service Providers
ScientificRequirements
Translation
TechnicalRequirements
TechnicalCapabilities
ScientificCapabilities
ApplicationServices Team
Prioritisation
Support Centre
Training &Issue Resolution
Service LevelRequirements
Sustainability
Community
CommunitySource: M.Obst
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Objectives in building Service Networks
1. Services MUST be secure, scalable, reliable, and well-documented
2. Services CAN be deployed on standard cloud configurations
3. Services SHOULD be implemented according to recognised ‘best practices’
4. Services MUST be discoverable
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Services MUST be secure, scalable, reliable, and well-documented
Users’ workflows and applications
Sustained Service and Data ProvidersGBIF, CoL, ITIS, OBIS, WoRMS,EBI, BGBM, CRIA, EoL, BHL, ALA, etc. + many many more
Recognised and stable Resource ProvidersNational, EGI.eu, PRACE, commercial, etc.
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Services CAN be deployed on standard cloud configurations
• Deployment on standard cloud platforms for better availability and scalability
– 2-tier trust relations
• Pilot service for ‘e-Infrastructure Commons’– Private / public collaboration– Builds in 2014
?
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Services SHOULD be implemented according to recognised ‘best practices’
• Best practices for improving ease of use and scalability– “The perfect API” : What would be its characteristics?– Wider adoption of standard data and parameter formats to promote
interoperability
• Classes of “shims”– Utility, Format handling, Data from sources
• Founded on standard infrastructure– Use of standard approaches
• to e.g., authentication, authorization– For data storage and staging– For persistent identifiers– For metadata generation– Etc.
?
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Services MUST be discoverable
www.biodiversitycatalogue.orgA fully curated, well-founded catalogue of
Web services for biodiversity science
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• GEO BON– Biodiversity Observation
Network– By 2015
• Functional infrastructure“from observations to Essential
Biodiversity Variables (EBV) and derived indicators”
• Using a plug-and-play, service-oriented approach
• Coordinated through a registry system
• Linked to the GEOSS Common Infrastructure
Where’s this all going?
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• ALA• SiBBr• SpeciesLink• GBoWS• DataONE• GBIF• GEOSS• LifeWatch• SANBI
Towards interoperability guidelines for an Integrated Virtual Environment (IVE) for Biodiversity Science at the
international level
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What’s trending?
• Software is a key enabling technology– In a distributed and mobile world, this means Web apps
• Web apps means APIs. APIs give access to services– How to create connections between APIs that don’t usually
talk to each other?
• WebApp automation like:– IFTTT – “IF this THEN that”– Zapier
• API / service management & monetization like:– 3Scale
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Take home messages
• Separate:– Services from underlying infrastructure– Applications, workflows and VREs from the services
• Ensure Service Networks are built using standard Web 2.0 technologies
• BiodiversityCatalogue is the well-founded place to register and discover services
• There’s much more to do!