elixir recommended interoperability resources · standards and ontologies look up services for the...
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www.elixir-europe.org
@ELIXIREurope
www.elixir-europe.org
ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.
ELIXIR Recommended Interoperability Resources
Carole Goble, ELIXIR-UKInteroperability Platform ExCo
ELIXIR Fifth Anniversary, 11 December 2018
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Turning FAIR Data into reality: Final Report and Action Plan, European Commission, Nov 2018
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Building a suitable FAIR infrastructure for
finding, exchanging, comparing, aggregating and interlinking biological information across
Europe
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Rare Disease research
Combine more of the same data typeLink up different data types for a more complete picture
Images courtesy of Marco Roos and RD-CONNECT
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Rare Disease research
Harmonise database formats and modelsMap between the terms used in the databasesLink to reference knowledge bases
Images courtesy of Marco Roos
Retrieval and analysis across resources
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Genotypic and Phenotypic data for Crop and Forest Plants
High throughput genomics
Large scale automated phenotyping
Standards for representation of genotypic and phenotypic data
Make data discoverable and interoperable by common APIs
Annotate datasets to deposit into public archives
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Arabidopsis Leaf Length
?IdentifierCO_322:0000994
Maize Plant Height
Identifier CO_322:0000007
Thanks to Frederik Coppens
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Icons courtesy of FAIRsharing.org
Is the same identifier being used for X?Can they be linked?
Are terms being used consistently?Are terms being used in common?
Are the formats the same? Can they be mapped?
Are the same things being reported in the same way?
Do (micro) services have the same or compatible APIs?
Common Agreements for IDs & Descriptions Standards, Link Points
700types 224
754
122
Data from Bioportal.bioontology.org, FAIRsharing.org and Identifiers.org
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BOLD (Barcode of life)
NCBI Taxonomy
Arabian tea plant
Cedar waxwing
GRIN plant taxonomy
Taxon:9606
Mappings across Ontologies for NCIt (Retinoblastoma)*
* Courtesy of Simon Jupp, ** Courtesy of openPHACTS
Mappings across databases for the same entity**
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Making connections across fragmented resources
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Hence…. FAIR Data Principles
Registration and search
Persistent and reused identifiers
Common, structured, interlinked metadata
Open access protocols
Machine processing
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Turning FAIR Data Principles into Reality
Open Standards
Services &Resources
Machine processable
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Interoperability Resources
Validata
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Genotypic and Phenotypic data for Crop and Forest PlantsInteroperability Resources
ELIXIR Plant Data Lookup Service
Registries for the standards and ontologies
Look up services for the identifiers and concepts
Services to help annotate & validate databases and data submissions against to reporting guidelines & formats
Services to harvest, map, search metadata ..
Map between different concepts and identifiers for same thing.
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Standards: formats, reporting guidelines, ontologies
Search engine for datasets.
Metadata services: ontology, annotation, validation, harvesting, Indexing
Register services and datasets
Best practice.
Harmonisation of tools and pipelines
Describing and sharing workflows between different systems
Common Programmable Interfaces
Identifier resolution & management
Identifier mapping services
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What Interoperability Resources are needed?
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ELIXIR Interoperability Resources Framework
Workflows
Aggregators
Applications
Search
Tool & API
Resources(Bioschemas)
Workflows(CWL)
Data type specific Ontologies, formats, reporting guidelines,
APIs
AuthoritiesIdentifier
Metadata Annotation
Markup
Citation
Harvesting
MetadataValidation
OntologyMapping
IdentifierMapping
Indexing
Search
OntologyLookup
Identifierresolution
OntologyManagement
Identifier minting
ExtractTransformLoad
Type specific mapping
and resolution
Type specific
integration
Standards
StandardsRegistry
OntologiesRegistry
Tools WorkflowsIdentifiersRegistry
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StandardsRegistry
OntologiesRegistry
IdentifiersRegistry
Interoperable ELIXIR Interoperability Resources Framework
Workflows
Aggregators
Applications
Search
Tool & API
Resources(Bioschemas)
Workflows(CWL)
Data type specific Ontologies, formats, reporting guidelines,
APIs
Standards AuthoritiesIdentifier
Tools Workflows
Metadata Annotation
Markup
Citation
MetadataValidation
OntologyMapping
IdentifierMapping
OntologyLookup
Identifierresolution
OntologyManagement
Identifier minting
ExtractTransformLoad
Harvesting
Harvesting
Indexing
Search
Type specific mapping
and resolution
Type specific
integration
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Example: Identifier Resolution of Data on the WebMultiple URLs for the same collection make object unification challenging
NCBITaxon:9606
http://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?short_form=NCBITaxon_9606
http://www.ebi.ac.uk/ena/data/view/Taxon:9606
http://purl.uniprot.org/taxonomy/9606
Resolution Services keep track and handle the different locations and different identifier systemsThe Resolution Services themselves are harmonised
Thanks to Nick Juty and Sarala Wimalaratne
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International Interoperability Resources
ELIXIR is part of a global ecosystem
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What are Recommended Interoperability Resources?An ELIXIR Service supplied by one or more Nodes
High quality of service
and support
Plays important role in our
interoperability framework
Are FAIR and
interoperate in a resource ecosystem
https://www.elixir-europe.org/platforms/interoperability/rir-selection
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What are Recommended Interoperability Resources?An ELIXIR Service supplied by one or more Nodes
https://www.elixir-europe.org/platforms/interoperability/rir-selection
establish connections between data (and other) resources
helpsacquire and expose metadata of data (and other) resources
create infrastructure needed to build integrabledata collections
use interoperability resources to support delivery of FAIR principles
Plays important role in our
interoperability framework
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An Interoperability Resource for findability & metadata exchange for all of ELIXIR’s Resources
Metadata about web based resources using a widely adopted web standard in a community agreed way
MarRef Database
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An Interoperability Resource for findability & metadata exchange for all of ELIXIR’s Resources
Metadata about web based resources using a widely adopted web standard in a community agreed way
aggregators
registries
search engines
applications
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An Interoperability Resource for findability and exchange of ELIXIR’s workflows and pipelines
Pioneered by Marine Metagenomics
Courtesy Rob Finn, Nils P. Willassen and Michael Crusoe
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Resources gap
FAIR metadata at source
“The first and last mile”
Image courtesy of Sansone, McQuilton et al FAIRsharing.org
first
last
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First round of Recommended Interoperability Resources
completes process ….
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First round of Recommended Interoperability Resources
completes process ….
tomorrow!
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RIRs are ELIXIR added value to enableFAIR Core Data Resources (and other ELIXIR resources)
Oversee quality and reliability
Develop an integrated portfolio
Support sustainability
RIR
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Acknowledgements
Special Thanks:Michael CrusoeRafael JimenezAlasdair Gray Stian Soiland-ReyesSusanna Sansone Simon JuppTony Burdett Sira SarntivijaiJerry LanfearNick JutySarala WimalaratneFrederik CoppensJustin Clark-CaseyPeter McQuiltonRobert Finn
Marco RoosAnd many more!
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www.elixir-europe.org
@ELIXIREurope
www.elixir-europe.org
ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.
Thank you!
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ELIXIR Interoperability Resources Framework
Workflows
Aggregators
Applications
Search
Tool & API
Resources(Bioschemas)
Workflows(CWL)
Data type specific Ontologies, formats, reporting guidelines,
APIs
AuthoritiesIdentifier
Metadata Annotation
Markup
Citation
Harvesting
MetadataValidation
OntologyMapping
IdentifierMapping
Indexing
Search
OntologyLookup
Identifierresolution
OntologyManagement
Identifier minting
ExtractTransformLoad
Type specific mapping
and resolution
Type specific
integration
Standards
StandardsRegistry
OntologiesRegistry
Tools WorkflowsIdentifiersRegistry
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The 2018 Recommendations of RIRs
Resource Description
FAIRsharing Registry of curated metadata of DBs, Policies, Standards
g:Profiler Gene-centric data integrator - Web UI, and API services
Identifiers.org Persistent URL provider & identifier resolver
Intermine DIY database portal builder for model organism of choice
ISA Framework Curation for metadata of experiments (Project -> Study -> Assay)
Ontology Lookup Service (OLS) Google-like ontology term search
3DBIONOTES API* API aiding protein annotation by calling info from ref. resources
BridgeDb Identifier mapping for cheminformatics domain
DisGeNET API* API SPARQL Endpoint for genetic variant - human disease data
MOLGENIS Bioinformatics data integrator suite - explore/annotate/exchange