www.orpha.net Phenotype terminologies in use for genotype- phenotype databases: A common core for standardisation and interoperability HVP5 – UNESCO, Paris – 22 May 2014 Aymé S., Rath A., Chanas L., Hamosh A., Robinson P.N. & The International Consortium for Human Phenotype Terminologies
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Phenotype terminologies in use for genotype-phenotype databases: a common core for standardisation and interoperability - Ana Rath
The community needs to be provided with terminology standards in order to achieve interoperability between databases intended for clinical research and including description of phenotypes. This is crucial to interpret genomic rearrangements as well as future high-throughput sequence data. The aim of our work was to promote a core terminology of phenotypes interoperable with all the terminologies in use. Relevant terminologies in use by different communities to describe phenomes were cross–referenced: PhenoDB (2846 terms), London Dysmorphology Database (LDDB; 1318 terms), Orphanet (1243 terms), Human Phenotype Ontology (9895 terms, 22/08/2012), Elements of Morphology (AJMG; 423 terms), ICD10 (1230 terms), as well as medical terminologies in use: UMLS (7,957,179 distinct concept terms), SNOMED CT (>311,000 concepts), MeSH (26,853 concepts) and MedDRA (69,389 concepts). We established a strategy to compare them to find commonalities and differences, using ONAGUI as a tool to pick-up exact matches. The non-exact matches were verified manually by an expert. A core-terminology of 2,300 terms was derived and analysed by a panel of experts (International Consortium for Human Phenotype Terminologies – ICHPT). The resulting consensual terminology will be freely available in a dedicated website (www.ichpt.org) and mappings with other terminologies will be given in order to ease the interoperability between databases without disturbing the habits of the different groups of users.
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www.orpha.net
Phenotype terminologies in use for genotype-phenotype
databases:
A common core for standardisation and interoperability
HVP5 – UNESCO, Paris – 22 May 2014
Aymé S., Rath A., Chanas L., Hamosh A., Robinson P.N. &The International Consortium for Human Phenotype Terminologies
www.orpha.net
Do you mean?
elementsofmorphology.nih.gov
Long narrow head dolichocephaly
scaphocephaly
www.orpha.net
Different resources, different terminologies
(e)HR:SNOMED CT
Others?
Free text
Mutation/patient registries,databases:
HPOLDDB
PhenoDBElements of morphology
Others? Free text?
Tools for diagnosis:
HPOLDDB
Orphanet
www.orpha.net
Levels of granularity
Disorders• Purpose: coding diagnoses (i.e. medical records)
Work with file in owl format I-Sub algorithm: detect syntaxic
similarity Graphical interface to check
automatic mappings and manually add ones
Metamap (National Library of Medicine): a tool to map biomedical text to the UMLS Metathesaurus
Perl scripts: format conversion, launching Metamap, comparison of results…
www.orpha.net
Comparison of mappings and deductionPerl script to compare all the mappings and infer mappings of non-Orphanet terminologiesEg: Orphanet ID XX mapped to YY in HPO and ZZ in LDDB -> deduction: YY and ZZ should probably map
Retrieve HPO mappings versus UMLS, MeSH
First figures:LDDB El. Morpho PhenoDB HPO UMLS…
Orphanet E: 1062 E: 416 E: 978 E: 2228 E: 6948
LDDB D: 275 D: 533 D: 1123 D:2678
El. Morpho D: 177 D: 716 D: 409
PhenoDB D: 1045 D:3268
HPO D: 6307+4800
UMLS…
www.orpha.net
Mapping of non-Orphanet terminologiesAutomatic and infered mappings were checked by experts• Using OnaGUI for all, except UMLS