ELIXIR-UK and the ELIXIR Interoperability Platform
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Introduction to ELIXIR-UK and the ELIXIR Interoperability Platform presented by Carole Goble at the ELIXIR-UK Workshop during Genome Science 2016 in Liverpool on 31st August 2016
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ELIXIR-UK and the ELIXIR Interoperability Platform
- 1. ELIXIR-UK and the ELIXIR Interoperability Platform Helen Parkinson (EBI) Chris Evelo (NL) Carole Goble (UK)
- 3. ELIXIR Interoperating Services, Standards and Know-how 3 Publishing FAIR Data Interoperating frameworks Data Platform Interoperability Platform Use Cases Data Warehouse Workflows Integration Applications Federated search Link following LiteHeavy Experimental Data Archives Value-added Biological knowledge bases EGA, ENA, EuropePMC, BioSamples … UniProt , Ensembl, OrphaNet, Human Protein Atlas … Dynamic recordsStable record
- 4. Interoperability 101 4 Wrappers Common API BioSchema markup Application Userinterface Warehouse Search Workflows Dataset level Dataset Profiles and Operational Practices… Integrating Framework Harvesters, 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-boardingOn-boardingOn-boarding
- 5. Content level • Common Schemes • Self-describing metadata • Mappings • On-boarding 5
- 6. Interoperability Drivers: Global Co-operations 6
- 7. Interoperability Drivers: ELIXIR Use Cases 7 Marine metagenomics Access to a marine metagenomics databases and access to workflows Interoperability through workflows Crop and forest plants Infrastructure 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 repositories Interoperability through Linked DataWarehouses Secure transfer, storage and analysis of human biomedical data consented for research Interoperability through a DataWarehouse
- 8. 10 Standards(meta)data: File formats, minimum reporting guidelines, ontologies Search engine for datasets. Harmonisation between tools and pipelines Describing and sharing workflows between different systems Metadata 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 Rare Disease Human data
- 9. Pillars and Workstreams and ELIXIR-UK 11 Service management Catalogues Dataset profiles + on-boarding API profiles and service discovery Ontology services Identifier services and standards Workflow interoperability Knowledge Hub BYODs, Hackathons andWorkshops Services Standards Capacity
- 10. ELIXIR-UK: Standards Cataloguing, BioSharing.org Susanna Sansone, Oxford 12
- 11. ELIXIR-UK: Identifiers standards and services Manchester Standards Standards Identifier Resolution Services Service harmonisation Identifier Authorities Citation metadata Identifier Mapping Life cycle management
- 12. ELIXIR-UK: Dataset description, BioSchemas.org Manchester, Oxford 14 Google, Bing, Yahoo, Yandex Samples Experiments Citation Training materials Events Organizations DataSoftware Standards
- 13. ELIXIR-UK: Dataset Description, DATS & DataMED Oxford 15 https://biocaddie.org
- 14. ELIXIR-UK: Dataset Description: Discovery, Citation Depth DATS ReachDutch Node
- 15. ELIXIR-UK, Workflow description Manchester 17 • Common format for bioinformatics tool & workflow execution • Community based standards effort • Designed for clusters & clouds • Supports the use of containers (e.g. Docker)
- 16. ELIXIR-UK, metadata on-boarding services, templates 18 Goble, Manchester Sansone, Oxford
- 17. ELIXIR-UK A major contributor to Interoperability Activities and Services…. and more to come …? 19 Cambridge
Editor's Notes
- ENA (EBI) EGA (EBI and ELIXIR-Spain) PDBe (EBI) EuropePMC (EBI) Examples include: UniProt (EBI, SIB) Ensembl (EBI) OrphaNet (ELIXIR-France) Human Protein Atlas (ELIXIR-Sweden) MINT (ELIXIR-Italy) WikiPathways (ELIXIR-NL) LiceBase (ELIXIR-NO) CorkOakDB (ELIXIR-PT) IntOGen (ELIXIR Spain) ORCAE (ELIXIR-BE)
- Logo cloud…
- The Rare disease use case is developing an infrastructure to support the development of new therapies for rare diseases in humans. Core to this effort is the implementation of a technical framework for the comparison and standardisation of services. This includes a federated infrastructure for access to rare-disease repositories throughout Europe. These repositories contain different information on the illness, disease phenotype, treatments and outcomes, information on patient samples stored in biobanks and any omic information stored in the EGA (see Human data Use Case). 6.3.1 Key Interoperability Requirements: Standards for the representation of domain specific (meta)data. Including, Minimum Information reporting requirements, vocabularies, ontologies. Linking different resources and tools. Mapping services for identifiers. Support for federated meta-data harvesting 6.3.2 Aligned Technical Use Cases TUC ID TUC Name TUC Description 6.4 Use Case: Human data (WP9) The Human Genetic Data Use Case will use the ELIXIR framework for secure transfer, storage and analysis of human biomedical data consented for research. The interoperability requirements for this use case are largely in line with the Rare Disease Use Case. 6.4.1 Key Interoperability Requirements: 6.4.2 Aligned Technical Use Cases TUC ID TUC Name TUC Description
- Services: The EIP implements very few EIP services directly, rather it delivers a framework which aggregates existing and new services to deliver data discovery, data integration and data analysis for life sciences data and it determines the criteria for services which comprise the EIP (Section 4). Standards: The EIP supports and enables its drivers’ efforts and best practices on (i) standardised metadata for datasets and the APIs to access datasets; (ii) common formats, ontologies and reporting guidelines for the content of the datasets (both archives of experimental reports and biological knowledge bases); (iii) standardised metadata support tool and workflow interoperability; (v) standardised identifiers and identifier metadata; (v) common APIs for data types. Know how: the EIP gathers and channels its products, best practices, and know-how to its stakeholders through BYODs, hackathons, workshops and an online Knowledge Hub of guides and resources. 1 EIP service management Service framework, roadmapping of services, service elicitation from nodes, review of service delivery plans, service benchmarking, service sustainability 2 Catalogues Registration, curation and management of Standards Catalogue (BioSharing) and EIP services in bio.tools. 3 Dataset profiles, discovery and search and associated services 4 API profiles and service discovery Bioschemas for services, SWAGGER, common APIs (2 threads) 5 Ontology Services Data-ontology maps, ontologies 6 Identifier Services and Standards Resolution, authorities, id-id mappings, best practices, scheme harmonisation, service harmonisation, citation support 7 Workflow interoperability standards and services CWL 8 Knowledge Hub Best practices, guidelines, webinars, demonstrators 9 BYODs, Hackathons and Workshops
- It’s all about the metadata and knowledge graph 3rd of web pages Builds on a shared core and data structure Simple embedding in web pages and CMS Widespread tooling, harvesters and indexing Search engines and Integration tools
- BioCADDIE is the Rosetta Stone ELIXIR-NL FAIRifier DCAT+ coverage Indexing and harvesting: OAI-PMH COTS