The ELIXIR of Linked Data

Transcription

1 The ELIXIR of Linked Data Professor Carole Goble (UK node) Barend Mons (NL node), Helen Parkinson (EMBL-EBI node) The Interoperability Services Backbone Team European Life Sciences Infrastructure for Biological Information

2 What is ELIXIR? An international distributed infrastructure for life-science information orchestrate the collection, quality control and archiving of biological data produced by life science experiments. integrate research data ensure a seamless service provision that is easily accessible to all.

3 ELIXIR: An international distributed infrastructure for biological data major bioinformatics service providers (~130) Hub 16 ELIXIR members 4 observers

4 Drivers: Infrastructure Providers Crop and forest plants Marine metagenomics Human data COordinated Research Infrastructures Building Enduring Life-science Services Rare diseases

5 Rare diseases Sample data (biobank databases) Clinical data (registries, and phenotypic databases) 1000 exomes Genomic data (WES, WGS) 1000 exomes + > 2500 from other projects Other omics data (transcriptomics, metabolomics, proteomics )

6 Drug prioritization for Huntington s Disease Katerina Nosikova, Elizaveta Besedina, Eelke van der Horst, Peter-Bram t Hoen, Marco Roos, Eleni Mina, Human Genetics department, LUMC, NL Select drug compounds in Open PHACTS Select genes by phenotype matching in Monarch Filter on feasibility for treating HD Prioritized drug compounds 8

7 What is ELIXIR?

8 Technical platforms Data Secure and deliver core data resources Standards Tools Data management, reuse and integration Findable Accessible Interoperable Reusable Discoverable tools, services and connectors for data access and exploitation Compute Training Robust technical platforms and clouds for secure data access, data exchange and compute Training programme for professionals, bridging the computational biology skills gap

9 Training: BYODs, data wrangling, governance and quality assurance Linked Data experts, data experts from MycoBase and Human Protein Atlas Tomato genome, phenotypic observations, variants

10 Data: Basket of indicators, reflecting the multiple facets of bioinformatics resources Scientifi Quality c impact Legal & funding infrastructure Scientific focus Indicators Community Impact Mandatory and optional 1) Scientific focus and quality of science e.g. curational effort, benchmarking 2) Community served by the resource e.g. web statistics 3) Quality of service e.g. uptime, user support and training 4) Legal and funding infrastructure e.g. institutional support, use policy 5) Impact and translational stories

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12 Compute Platform: Authentication, Archiving and Movement

13 Tools Interoperability and APIs Describing Workflows Describing APIs Common format for bioinformatics tool execution Rich: Linked Data allows for infinite metadata annotations and reasoning SWAGGER.json API changes Semantic versioning Getting resources to have APIs Describing Tools EDAM Ontology

14 [Luiz Olavo Bonino, DTL] RD-CONNECT, ODEXA4ALL A FAIRifying Architecture

15 FAIR Interoperability Backbone Services Prepare for interop Access from Integrating Frameworks Warehouses API Interoperability Services: Identifiers, Ontologies, Schemas. Preparing Sources On boarding Datasets, Content, API

16 Paul Kersey Crop and forest plants Various species: maize, pine, potato Various data types: from genomes (sequences and annotations) to phenomes (traits) Various ontologies: Crop Ontology, Plant Ontology Emerging standards: MIAPPE (Minimum Information on Plant Phenotyping Experiment) Need for infrastructure o Manage identifiers o Register/access services and data sets o Metadata driven search

17 Ontology Services Ontology mapping Data-Ontology Tools OLS3

18 Identifiers the pivot of everything! Identifier Resolution Service (IRS2) Identifier Mapping Service (IMS)

19 FAIR Metadata at many levels Tool that provisioned the dataset Interface API and Access Tool using the dataset Data record content Dataset Collection mappings between datasets mappings between entities Dataset Profile

20 What is ELIXIR?

21 Metadata Profiles and Dataset Registration Governance, Compliance, Release Protocols Dataset Profile

22 Search, Index and Linked Data BioSolr Data Diabetic nephropathy (EFO_ ) (and Elasticsearch) Data

23 Two tiers of data repository Biological knowledge bases Curated and annotated biological entities and their relationships Uniprot, Ensembl, ChEMBL, Orphanet

24 Two tiers of data repository data records are dynamic and incomplete records update, diverge, merge over time, interpretation changes Biological knowledge bases Curated and annotated biological entities and their relationships Uniprot, Ensembl, ChEMBL, Orphanet identifier resolution varies over time relationships between records are unstable reproducibility potentially compromised a novel gene-rare disease relationship is reported consequences of a single nucleotide change in a regulatory genomic region is better understood.

25 linksets Legacy of Open PHACTS. Mappings are first class. mappings between entities provenance, versioning, mapping linksets Data record content

26 VoID Vocabulary of Interlinked Datasets Create description of a Linkset that connects two datasets. Select datasets from existing descriptions. Capture link predicate and justification

27 Legacy of Open PHACTS. Releasing Data Sets: Software-Like Research Objects Linked Data Manifests Publishing data the software way Controlled data Distribution Containers Builds Dependencies Versioning Verification data-maven-plugin Docker

28 Genotype-Phenotype Mapping terms Cross linking datasets Tracking provenance Linked Data Services Genotype-Phenotype Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, et al. (2015) Finding Our Way through Phenotypes. PLoS Biol 13(1): e doi: /journal.pbio

29 Interoperating Applications Interoperability Services Backbone Interoperability Backbone Publishing FAIR Data

30 Linked Data Big Picture lower the barriers to linking data connect related data that wasn't previously linked self-describe and annotate data in a common, machine readable form expose linking as a first class information element a term used to describe a recommended best practice for exposing, sharing, and connecting pieces of data, information, and knowledge on the Semantic Web using URIs and RDF. Wikipedia

31 Impact of Open PHACTS on ELIXIR Linked Data Components & Know-how Identifiers & Links Annotation & Ontologies Dataset Containers Integrate into off the shelf apps Publishing and Consuming Metadata & Mappings On boarding & Release pipelines APIs, Search Data.when it supports interoperability.retain native forms.preparation and maintenance.data governance..

32 Challenges of Linked Data Getting data providers to generate LOD Getting agreement on URIs Choosing ontologies and relations Modelling challenges (data vs biological reality) Appropriate Extract/Load/Transform pipelines Appropriate representation for datatypes Getting machine readable dataset descriptions Provide an API Link resources to ontology terms SPARQL fetish Expertise in the community to effectively produce/consume LD Services for finding and reusing URIs & ontologies Data annotation services (mapping data to ontologies)

33 [Mons]

34 What is ELIXIR?

35 Human data: The European Genomephenome Archive EGA