Presentation given at Biodiversity Informatics Horizons 2013 (BIH2013) on 5th September 2013. 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 for biodiversity science 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?

1. Structuring the biodiversity informatics community at the European level and beyond
Service Networks, Service Sets and
Biodiversity Catalogue
Alex Hardisty
Cardiff University

2. 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?

3. 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 WS2
WS4
WS5
WS3

4. 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

5. 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-BGC
monte 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 and
population modelling
Ecosystem functioning
and valuation
?
Genes-Species-Specimens
(multi-scale linkages)
Citizen Science &
Observations
Mapping, visualization and
transformation services

6. 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

7. 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
Modelling
ecosystem services
Modelling
CO2 sequestration
Calculating
measures of genetic diversity
Assessing adaptation
to changing conditions
Supporting processes
of conservation
Assisting invasive
species management

8. • 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
InformationTechnologists’
perspectives
Biodiversity studies & experiments
Services for biodiversity science
compose to support
ICT Technical Capabilities
ICT Technical Elements
combine to deliver
combine to support

9. How to build Service Networks and Service Sets?
Discipline
Scientists
Scientific PAL
Technical PAL
Scientific and Technical Service Providers
Scientific
Requirements
Translation
Technical
Requirements
Technical
Capabilities
Scientific
Capabilities
Application
Services Team
Prioritisation
Support Centre
Training &
Issue Resolution
Service Level
Requirements
Sustainability
Community
Community
Source: M.Obst

10. 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

11. Services MUST be secure, scalable,
reliable, and well-documented
Users’ workflows and
applications
Sustained Service and
Data Providers
GBIF, CoL, ITIS, OBIS, WoRMS,
EBI, BGBM, CRIA, EoL, BHL,
ALA, etc. + many many more
Recognised and stable
Resource Providers
National, EGI.eu, PRACE,
commercial, etc.

12. 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
?

13. 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.
?

14. Services MUST be discoverable
www.biodiversitycatalogue.org
A fully curated, well-founded catalogue of
Web services for biodiversity science

15. • 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?

16. • 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

17. 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

18. 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!