ELIXIR Recommended Interoperability Resources Carole Goble, ELIXIR-UK Interoperability Platform ExCo ELIXIR Fifth Anniversary, 11 December 2018 www.elixir-europe.org www.elixir-europe.org ELIXIR-EXCELERATE is funded by the European Commission within the @ELIXIREurope Research Infrastructures programme of Horizon 2020, grant agreement number 676559.
Turning FAIR Data into reality: Final Report and Action Plan, European Commission, Nov 2018
Building a suitable FAIR infrastructure for finding , exchanging, comparing, aggregating and interlinking biological information across Europe
Rare Disease research Combine more of the same data type Link up different data types for a more complete picture Images courtesy of Marco Roos and RD-CONNECT
Rare Disease research Retrieval and analysis across resources Harmonise database formats and models Map between the terms used in the databases Link to reference knowledge bases Images courtesy of Marco Roos
Genotypic and Phenotypic data for Crop and Forest Plants 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 High throughput genomics
Maize Plant Height Arabidopsis Leaf Length ? Identifier Identifier CO_322: CO_322: 0000007 0000994 Thanks to Frederik Coppens
Common Agreements for IDs & Descriptions Standards, Link Points 700 224 types Is the same identifier Are the formats the being used for X? same? Can they be Can they be linked? mapped? 754 Are terms being used consistently? Are terms being used in common? Do (micro) Are the same things services have the being reported in the same or compatible same way? APIs? 122 Data from Bioportal.bioontology.org, FAIRsharing.org and Identifiers.org Icons courtesy of FAIRsharing.org
Cedar waxwing BOLD (Barcode of life) Taxon:9606 Arabian tea plant NCBI Taxonomy Mappings across Ontologies for NCIt Mappings across databases for the same entity** (Retinoblastoma)* GRIN plant taxonomy * Courtesy of Simon Jupp, ** Courtesy of openPHACTS
Making connections across fragmented resources
Hence…. FAIR Data Principles Registration and search Persistent and reused identifiers Common, structured, interlinked metadata Open access protocols Machine processing
Turning FAIR Data Principles into Reality Open Standards Machine processable Services & Resources
Interoperability Resources Validata
Genotypic and Phenotypic data for Crop and Forest Plants Interoperability Resources Registries for the standards and ontologies Look up services for the identifiers and concepts Map between different concepts and identifiers for same thing. Services to help annotate & validate databases and data submissions against to reporting guidelines & formats ELIXIR Plant Data Lookup Service Services to harvest, map, search metadata ..
What Interoperability Resources are needed? Marine Plants Rare Human Disease Data Standards : formats, reporting guidelines, ontologies Metadata Standards Resource Markup Registries Metadata Services Linked Data Services and Resources Framework FAIR Metrics Metadata services : ontology, annotation, validation, harvesting, Indexing Register services and datasets Search engine for datasets. Id Services Identifier resolution & management Identifiers Identifier mapping services Describing and sharing workflows Workflow between different systems Workflows Harmonisation of tools and pipeline s APIs Common Programmable Interfaces Knowledge BYODs Hub Best practice.
ELIXIR Interoperability Resources Framework Applications Identifiers Standards Ontologies Tools Workflows Registry Registry Registry Search Identifier Ontology Extract Harvesting Search minting Management Transform Load Citation Indexing Type Aggregators specific Metadata Ontology integration Annotation Identifier Type Lookup Markup resolution specific mapping Workflows Ontology Identifier Metadata and Mapping Mapping Validation resolution Resources Data type specific Identifier Tool & Workflows Standards (Bioschemas) Authorities Ontologies, formats, API (CWL) reporting guidelines, APIs
Interoperable ELIXIR Interoperability Resources Framework Applications Identifiers Standards Ontologies Tools Workflows Registry Registry Registry Search Identifier Ontology Extract Harvesting Search minting Management Transform Load Citation Indexing Type Harvesting Aggregators specific Metadata Ontology integration Annotation Identifier Type Lookup Markup resolution specific mapping Workflows Ontology Identifier Metadata and Mapping Mapping Validation resolution Resources Data type specific Identifier Tool & Workflows Standards (Bioschemas) Authorities Ontologies, formats, API (CWL) reporting guidelines, APIs
Example: Identifier Resolution of Data on the Web Multiple URLs for the same collection make object unification challenging Resolution Services keep track and handle the different locations and different identifier systems The Resolution Services themselves are harmonised http://purl.uniprot.org/taxonomy http://www.ebi.ac.uk/ena/data/view/Taxo /9606 n:9606 NCBITaxon:9606 http://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms? short_form=NCBITaxon_9606 Thanks to Nick Juty and Sarala Wimalaratne
International Interoperability Resources ELIXIR is part of a global ecosystem
What are Recommended Interoperability Resources? An ELIXIR Service supplied by one or more Nodes Are FAIR Plays important High quality and role in our of service interoperate interoperability and support in a resource framework ecosystem https://www.elixir-europe.org/platforms/interoperability/rir-selection
What are Recommended Interoperability Resources? An ELIXIR Service supplied by one or more Nodes establish connections between data (and other) resources Plays important acquire and expose metadata of data (and role in our other) resources helps interoperability framework create infrastructure needed to build integrable data collections use interoperability resources to support delivery of FAIR principles https://www.elixir-europe.org/platforms/interoperability/rir-selection
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
An Interoperability Resource for findability & metadata exchange for all of ELIXIR’s Resources aggregators Metadata about web based resources using a widely adopted web standard in registries a community agreed way search engines applications
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
Resources gap FAIR metadata first at source last “The first and last mile” Image courtesy of Sansone, McQuilton et al FAIRsharing.org
First round of Recommended Interoperability Resources completes process ….
First round of Recommended Interoperability Resources completes process …. tomorrow!
RIRs are ELIXIR added value to enable FAIR Core Data Resources (and other ELIXIR resources) Oversee quality and reliability RIR Develop an integrated portfolio Support sustainability
Acknowledgements Special Thanks: Marco Roos Michael Crusoe And many more! Rafael Jimenez Alasdair Gray Stian Soiland-Reyes Susanna Sansone Simon Jupp Tony Burdett Sira Sarntivijai Jerry Lanfear Nick Juty Sarala Wimalaratne Frederik Coppens Justin Clark-Casey Peter McQuilton Robert Finn
Thank you! www.elixir-europe.org www.elixir-europe.org ELIXIR-EXCELERATE is funded by the European Commission within the @ELIXIREurope Research Infrastructures programme of Horizon 2020, grant agreement number 676559.
ELIXIR Interoperability Resources Framework Applications Identifiers Standards Ontologies Tools Workflows Registry Registry Registry Search Identifier Ontology Extract Harvesting Search minting Management Transform Load Citation Indexing Type Aggregators specific Metadata Ontology integration Annotation Identifier Type Lookup Markup resolution specific mapping Workflows Ontology Identifier Metadata and Mapping Mapping Validation resolution Resources Data type specific Identifier Tool & Workflows Standards (Bioschemas) Authorities Ontologies, formats, API (CWL) reporting guidelines, APIs
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