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Service Networks, Service Sets and Biodiversity Catalogue
 

Service Networks, Service Sets and Biodiversity Catalogue

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Presentation given at Biodiversity Informatics Horizons 2013 (BIH2013) on 5th September 2013. ...

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?

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    Service Networks, Service Sets and Biodiversity Catalogue Service Networks, Service Sets and Biodiversity Catalogue Presentation Transcript

    • Structuring the biodiversity informatics community at the European level and beyond Service Networks, Service Sets and Biodiversity Catalogue Alex Hardisty Cardiff University
    • 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?
    • 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
    • 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
    • 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
    • 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
    • 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
    • • 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
    • 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
    • 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
    • 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.
    • 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 ?
    • 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. ?
    • Services MUST be discoverable www.biodiversitycatalogue.org A fully curated, well-founded catalogue of Web services for biodiversity science
    • • 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?
    • • 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
    • 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
    • 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!