USEFULNESS OF ONTOLOGIES FOR RARE DISEASES

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1 USEFULNESS OF ONTOLOGIES FOR RARE DISEASES M a n u e l P o s a d a, Ve r ó n i c a A l o n s o a n d E s t r e l l a L ó p e z M a r t í n I n s t i t u t e o f R a r e D i s e a s e s R e s e a r c h ( I I E R - I S C I I I ) M a d r i d, S p a i n RD-Connect Workshop Data Linkage and Ontologies ISS, Rome, th September 2015

2 2 No conflict of interest is linked to this presentation 11 November 2015

3 INTERNATIONAL DATA SHARING Research enhancement Better knowledge of RD New therapies Improvement of patients life s quality

4 INTEROPERABILITY Capability of two or more systems or components to exchange information and to use the exchanged information

5 BIOBANKS (Sample data) GUID ONTOLOGIES CDEs SOPs ELSI PATIENTS REGISTRIES (Clinical data) INTEROPERABILITY TOOLS DATA FLOW REPOSITORIES FOR OMICS DATA (Genomic & other -omics data)

6 EUROPEAN RESOURCES GUID ONTOLOGIES CDEs SOPs ELSI USA RESOURCES INTEROPERABILITY TOOLS AUSTRALIAN RESOURCES DATA FLOW

7 WHAT ARE THE ONTOLOGIES?

8 ONTOLOGY An ontology describes the concepts in some knowledge domain, some of their properties and how the concepts relate to each other. Each concept (theoretical item) is represented by one unique reference (URI, real item), which is computerreadable. The references are associated to humanreadable terms, definitions and synonyms.

9 HUMAN READABLE MULTIPLE POSSIBILITIES Protein HDAC1 interacts with gene Parvb or La proteína HDAC1 interacciona con el gen Parvb or (different synonyms, languages, etc) COMPUTER READABLE UNIQUE REFERENCES

10 W H AT I S T H E U S E F U L N E S S O F O N T O L O G I E S I N T H E R A R E D I S E A S E S F I E L D?

11 CLASSIFICATION OF BIOMEDICAL ONTOLOGIES USEFUL IN THE RD FIELD

12 CLASSIFICATION OF BIOMEDICAL ONTOLOGIES USEFUL IN THE RD FIELD PHENOTYPE CLINIC CLASSIFICATIONS AND NOMENCLATURES DISORDER/DISEASE-SPECIFIC ONTOLOGIES ANATOMY PATIENTS-RELATED DATA PHARMACY EPIDEMIOLOGY HEALTH INDICATORS OTHER

13 PHENOTYPE ONTOLOGIES USEFUL IN THE RD FIELD Human Phenotype Ontology (HPO): The HPO contains more than 10,000 terms and provides a structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other diseases. The HPO itself does not describe individual disease entities but, rather, the phenotypic abnormalities associated with them. Orphanet Ontology (ORDO): The ORDO is an ontology of rare diseases whose content attempts disorders, subtypes, clinical signs and genes. It also includes epidemiology data related to rare diseases in Europe. In practical terms, HPO and ORDO cover different aspects and their use is perfectly complementary.

14 EXAMPLE 1 ATAXIA_USE_CASE_ISCIII Woman, 49 years old (age at diagnosis). Diagnosis: Spinocerebellar Ataxia Type 3 (SCA3), also known as Machado-Joseph Disease. Patient case registered in the Spanish National Rare Diseases Registry.

15 EXAMPLE 1 ATAXIA & FAMILIAL SPASTIC PARAPARESIS PATIENT REGISTRY Personal Information Family History Diagnosis-related Issues Phenotypic Traits Genetic Data

16 EXAMPLE 1 PHENOTYPIC TERMS (REGISTRY) HPO CODE PHENOTYPIC TERMS (HPO) Cerebellar system affected HP: Abnormality of the cerebellum Pyramidal system affected HP: Abnormality of pyramidal motor function Brain stem affected HP: Abnormality of brainstem morphology Sensory central system affected HP: Abnormality of central sensory function Polyneuropathy HP: Polyneuropathy Demyelinating polyneuropathy HP: Demyelinating sensory neuropathy HP: Demyelinating motor neuropathy Axonal polyneuropathy HP: Sensory axonal neuropathy HP: Motor axonal neuropathy Mixed polyneuropathy HP: Mixed demyelinating and axonal polyneuropathy Second motor neuron signs HP: Abnormality of the lower motor neuron Extrapyramidal system affected HP: Abnormality of extrapyramidal motor function Visual system affected HP: Abnormality of vision Hearing system affected HP: Hearing abnormality Cognitive/Behavioural impairment HP: Cognitive impairment HP: Behavioural abnormality Epilepsia HP: Epileptic spasms Walk HP: Difficulty walking Autonomous walk Not found Not found Use of walking stick Not found Not found Use of wheelchair Not found Not found Bedridden Not found Not found Oculomotor signs HP: Abnormality of eye movements Other signs (free text) - -

17 EXAMPLE 2 Five years old child (non diagnosed case) with the following phenotype: o o o o o o o o o o o o Hypothyroidism Hyperpigmentation Intellectual disability Delayed speech and language development Delayed motor development Short stature Microcephaly Microretrognathia Trigonocephaly Macrotia Low IGF-1 blood levels Low Fe 2+ blood levels

18 SpainRDR: Issues regarding the use of ontologies in registry data curation 18 HPO: HPO: HPO: HPO: HPO: HPO: HPO:

19 SpainRDR: Issues regarding the use of ontologies in registry data curation 19 Limiting factors for the integration of phenotype ontologies into the RD registries architecture: Practical examples extracted from a real case of the IIER Undiagnosed Disease Program (IIER-UDP) Five years old child with the following phenotype: Hypothyroidism Intellectual disability Delayed speech and language development Delayed motor development Short stature Hyperpigmentation Microcephaly Temporal evolution of a phenotype (limiting factor) EXAMPLE 1 Microretrognathia Trigonocephaly Macrotia Low IGF-1 blood levels Low Fe 2+ blood levels Accuracy in descriptions of phenotypic features (limiting factor) EXAMPLE 2

20 Useful Resources

21 Undiagnosed Cases Program SpainUDP, IIER: Software to help to the diagnosis Others

22 Undiagnosed Cases Program SpainUDP - IIER EQUIPO MULTIDISCIPLINAR - Clínica - Genética - Biología celular y molecular - Anomalías congénitas - Bioinformática SOFTWARES DE AYUDA AL DIAGNÓSTICO

23 Present vs Absent Features

24

25 SOPs ELSI

26 Thank you for your attention

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