HIPBI-RD: Harmonising phenomics information for a better interoperability in the rare disease field - Ana Rath
Rare disease (RD) research is a field of medicine increasingly reliant on information technology, with the advent of low-cost whole-genome sequencing revolutionising the discovery of genetic causes of disorders. Detailed phenotype data, combined with genomic data, have an enormous potential to accelerate the identification of clinically actionable prognostic or therapeutic implications and to improve our understanding of RD. The harmonisation of phenomics information, including disorders and phenotype traits that are stored in different contexts in a non-standardised way, is a cornerstone for producing sound data to foster research. HIPBI-RD («Harmonising phenomics information for a better interoperability in the rare disease field ») is a three-year project starting in 2016 funded via the E-Rare 3 ERA-NET. This project builds on three resources largely adopted by the RD community: Orphanet, its ontology ORDO (the Orphanet Rare Disease Ontology), HPO (the Human Phenotype Ontology) and PhenoTips, with the support of outstanding bio-ontologies players, the European Bioinformatics Institute and the Garvan Institute. The project aims to provide the community with an integrated, RD-specific bio-informatics ecosystem that will harmonse the way phenomics information is stored in databases and patient files worldwide, and thereby contribute to interoperability. This ecosystem will consist of a suite of tools and ontologies, optimised to work together, made available through commonly used software repositories. The HIPBI-RD ecosystem will contribute to the interpretation of variants identified through exome and full genome sequencing by harmonising the way phenotypic information is collected, thus improving diagnostics. The ultimate goal of HIPBI-RD is to provide a resource that will contribute to bridging genome-scale biology and a disease-centered view on human pathobiology. Acknowledgements: This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the ERA-NET Cofund action N° 643578, E-Rare3. The project is co-funded by the French National Research Agency (ANR), the German Federal Ministry of Education and Research (BMBF), German Research Foundation (DFG), and the Canadian Institutes for Health Research (CIHR)
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HIPBI-RD: Harmonising phenomics information for a better interoperability in the rare disease field - Ana Rath
- 1. www.orpha.net HIPBI-RD Harmonising phenomics information for a better interoperability in the RD field Ana Rath, Annie Olry, Marc Hanauer, Peter Robinson, Sebastian Köhler, Michael Brudno, Helen Parkinson, Simon Jupp,Tudor Groza ana.rath@inserm.fr Human Variome Project 6th Bienal meeting – UNESCO, Paris June 2016
- 2. HIPBI-RD • Aims: – Contribute to harmonisation of phenotype annotations – Contribute to interoperability between patient-centered resources and genetic-centered resources We aim to provide the community with an integrated, RD-specific informatics ecosystem that will harmonize the way phenomics information is stored in databases and in patient files worldwide, and thereby contribute to interoperability. This ecosystem will consist of a suite of tools and ontologies, optimized to work together, and available to clinicians and scientists through commonly used software repositories. Additionally, the ecosystem will contribute to the interpretation of variants identified through exome and full genome sequencing by harmonizing the way phenotypic information is collected, thus improving diagnostics.
- 3. Specific objectives • Integrate Human Phenotype Ontology (HPO) and Orphanet Rare Disease Ontology (ORDO). • Have ORDO & HPO translated in 7 languages. • Enrich rare disorder annotations via automated concept recognition (literature, records). • Enrich rare disorder annotations via Crowdsourcing. • Improve algorithms to allow clinical and genetic differential diagnosis. – Improve Phenomizer and Genomizer
- 4. Orphanet scientific content UniProt Reactome OMIM ICD10 ICD11 UMLS MedDRA SNOMED CT gene OMIM HGNC IUPHAR ensembl Genatlas ORPHA ICF-CY derived terms A. Rath, A. Olry, M. Hanauer, Inserm, US14, Paris France
- 5. Orphanet Rare Diseases Onntology (ORDO) Orphanet & European Bioinformatics Institute (EBI)
- 6. Helen Parkinson, Simon Jupp, EMBL-EBI, Hinxton, UK
- 7. Peter Robinson, Sebastian Köhler, La Charité, Berlin, Germany
- 8. HPO controlled vocabulary and the Phenomizer https://compbio.charite.de/phenomizer/
- 9. HPO annotations of Orphanet Rare Disorders Around 6,000 rare disorders HPO phenotypes Frequencies Diagnostic criteria Obligate (100%) Pathognomonic sign Very frequent (99-80%) Diagnostic criterion Frequent (79-30%) Occasional (29–5%) Very rare (1-4%) Absent 0% Annotated by Orphanet Disseminated by Orphanet and HPO 2,340 rare disorders 5,750 phenotypes 49,600 annotations
- 10. ORDO HPO Orphanet HPO Ontologies integrated Bio-named entity recognition Phenome Central Phenomizer Exomizer Hipbi-RD ecosystem Literature Re-use PhenoTips Crowdsourcing OKM Projet HIPBI-RD
- 11. Bio-named recognition Bio-LarK CR Tudor Groza , Garvan Institute, Australia
- 12. https://phenotips.org/ Michael Brudno, SickKids Hospital, Toronto, Canada
- 13. In conclusion… • Having structured data in databases (but also in the healthcare setting) is a cornerstone to foster research by allowing for agregation of interoperable data. • Providing an integrated, computable ontologies ecosystem will help to standardisation and harmonisation of phenotypic and clinical annotations. • The ecosystem will contribute to the interpretation of variants identified through exome and full genome sequencing by harmonizing the way phenotypic information is collected, thus improving diagnostics.
- 14. THANK YOU FOR YOUR ATTENTION!
Editor's Notes
- Application submitted; 2 succesful rounds of evaluation. Building a bioinformatics ecosystem allowing for refining phenotype-diseases annotations and curation, improvement of ontological resources via semantic interpretation of literature and crowdsourcing. Integration to genes in ORDO allowing for genotype-phenotype correlations. Re-use in the Exomizer, the Phenomizer and available for re-use in databases, matchmakers, etc The Hipbi-RD ecosystem will consist of a suite of tools and ontologies, optimized to work together, and available to clinicians and scientists through commonly used software repositories, such as GitHub. It builds on our two existing ontologies: ORDO and HPO, which are promoted as reference ontologies in the field of RD by the IRDiRC (International Rare Diseases Research Consortium), the broadly used PhenoTips tool used for collecting structured patient data and the PhenomeCentral matchmaker portal, and expands tools developed by Bio-Lark and the European Bioinformatics Institute (EBI). This proposal therefore aims to provide the community with an integrated, RD-specific informatics ecosystem that will harmonize the way phenomics information is stored in databases and in patient files worldwide, and thereby contributing to interoperability between databases, registries and biobanks.
- Application submitted; 2 succesful rounds of evaluation. Building a bioinformatics ecosystem allowing for refining phenotype-diseases annotations and curation, improvement of ontological resources via semantic interpretation of literature and crowdsourcing. Integration to genes in ORDO allowing for genotype-phenotype correlations. Re-use in the Exomizer, the Phenomizer and available for re-use in databases, matchmakers, etc