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ELIXIR-UK and the ELIXIR Interoperability Platform
Helen Parkinson (EBI)Chris Evelo (NL)
Carole Goble (UK)
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FAIRFindable
Accessible
Interoperable
ReusableIntelligible
Reproducible
Citable
Trackable & Countable
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ELIXIR Interoperating Services, Standards and Know-how
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Publishing FAIR Data
Interoperating frameworks
Data Platform
InteroperabilityPlatform
Use Cases
Data Warehous
e Workflows
Integration Applications
Federated search
Link following
LiteHeavy
Experimental Data Archives
Value-addedBiological knowledge basesEGA, ENA,
EuropePMC, BioSamples …
UniProt , Ensembl, OrphaNet, Human Protein Atlas …
Dynamic records
Stable record
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Interoperability 101
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Wra
pper
sCo
mm
on
API
BioS
chem
am
arku
p
Appl
icatio
nUs
er in
terfa
ceWarehouse
Search
Workflows
Dataset level Dataset Profiles and Operational Practices…
Integrating FrameworkHarvesters, iindexers, integrators
Content level Standards, id mapping, data-concept mapping, identifier authority, ontology authority, standard formats, common ontology concepts…
Common APIs, standard practices…Interface level
On-b
oard
ing
On-b
oard
ing
On-b
oard
ing
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Content level• Common
Schemes
• Self-describing metadata
• Mappings
• On-boarding
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Interoperability Drivers: Global Co-operations
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Interoperability Drivers: ELIXIR Use Cases
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Marine metagenomicsAccess to a marine metagenomics databases and access to workflows Interoperability through workflows
Crop and forest plantsInfrastructure to facilitate genotype-phenotype analyses for crop and tree-species.Interoperability through federated metadata-driven Search using standard-compliant services.
Rare diseases
Human data – EGA
Federated infrastructure for access to heterogeneous rare-disease repositoriesInteroperability through Linked Data Warehouses
Secure transfer, storage and analysis of human biomedical data consented for researchInteroperability through a Data Warehouse
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Standards(meta)data:File formats, minimum reporting guidelines, ontologies
Search engine for datasets.Harmonisation between tools and pipelinesDescribing and sharing workflows between different systemsMetadata on-boarding: annotation, validation and harvesting services
Register/access services and datasets
Common APIs
Identifiers management
Dissemination of learned best practice.
Mapping services for identifiers
Marine Plants RareDisease
Human data
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Pillars and Workstreams and ELIXIR-UK
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Service managementCatalogues
Dataset profiles + on-boarding
API profiles and service discovery
Ontology services
Identifier services and standards
Workflow interoperability
Knowledge Hub
BYODs, Hackathons and Workshops
Services
Standards
Capacity
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ELIXIR-UK: Standards Cataloguing, BioSharing.orgSusanna Sansone, Oxford
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ELIXIR-UK: Identifiers standards and servicesManchester
Standards
Standards
Identifier Resolution ServicesService harmonisation
Identifier Authorities
Citation metadata
Identifier Mapping
Life cycle management
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ELIXIR-UK: Dataset description, BioSchemas.orgManchester, Oxford
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Google, Bing, Yahoo, Yandex SamplesExperimentsCitation
Trainingmaterials
Events Organizations
DataSoftware
Standards
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ELIXIR-UK: Dataset Description, DATS & DataMEDOxford
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https://biocaddie.org
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ELIXIR-UK: Dataset Description: Discovery, Citation
Depth
DATS
ReachDutch Node
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ELIXIR-UK, Workflow descriptionManchester
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• Common format for bioinformatics tool & workflow execution
• Community based standards effort
• Designed for clusters & clouds
• Supports the use of containers (e.g. Docker)
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ELIXIR-UK, metadata on-boarding services, templates
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Goble, Manchester
Sansone, Oxford
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ELIXIR-UK
A major contributor to
Interoperabilit
y Activities and Services….
and more to come …?19
Cambridge