ELIXIR-UK and the ELIXIR Interoperability Platform

Helen Parkinson (EBI)Chris Evelo (NL)

Carole Goble (UK)

FAIRFindable

Accessible

Interoperable

ReusableIntelligible

Reproducible

Citable

Trackable & Countable

ELIXIR Interoperating Services, Standards and Know-how

3

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

Interoperability 101

4

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

Content level• Common

Schemes

• Self-describing metadata

• Mappings

• On-boarding

5

Interoperability Drivers: Global Co-operations

6

Interoperability Drivers: ELIXIR Use Cases

7

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

10

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

Pillars and Workstreams and ELIXIR-UK

11

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

ELIXIR-UK: Standards Cataloguing, BioSharing.orgSusanna Sansone, Oxford

12

ELIXIR-UK: Identifiers standards and servicesManchester

Standards

Standards

Identifier Resolution ServicesService harmonisation

Identifier Authorities

Citation metadata

Identifier Mapping

Life cycle management

ELIXIR-UK: Dataset description, BioSchemas.orgManchester, Oxford

14

Google, Bing, Yahoo, Yandex SamplesExperimentsCitation

Trainingmaterials

Events Organizations

DataSoftware

Standards

ELIXIR-UK: Dataset Description, DATS & DataMEDOxford

15

https://biocaddie.org

ELIXIR-UK: Dataset Description: Discovery, Citation

Depth

DATS

ReachDutch Node

ELIXIR-UK, Workflow descriptionManchester

17

• Common format for bioinformatics tool & workflow execution

• Community based standards effort

• Designed for clusters & clouds

• Supports the use of containers (e.g. Docker)

ELIXIR-UK, metadata on-boarding services, templates

18

Goble, Manchester

Sansone, Oxford

ELIXIR-UK

A major contributor to

Interoperabilit

y Activities and Services….

and more to come …?19

Cambridge