ochoa
12 July 2022 09:51
#1
Due to a problem in the ontology, a number of rare diseases are duplicated in the 22.06. EFO is currently undergoing a cleanup of the Orphanet terms to assign them to their corresponding MONDO id when appropriate. As part of this process, a large number of terms have been duplicated in the ontology.
We are working with EFO to resolve this issue ASAP:
opened 04:32PM - 26 Jun 22 UTC
Open Targets
At least in 3.42 and 3.43, there are a large number of duplicated terms in EFO m… ostly affecting rare diseases.
Just by lower-casing the names and looking for exact matches, there are 3036 duplicated terms (v3.42). Some of them are explained by disease vs phenotype conondrum, but the vast majority correspond to a MONDO vs Orphanet duplication.
Some examples:
[Hemophilia](https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_448) Orphanet:448 - [hemophilia](https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0018660) MONDO:0018660
[Fragile X syndrome](https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_908) Orphanet:908 - [fragile X syndrome](https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0010383) MONDO:0010383
[Apert syndrome](https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_87) Orphanet:87 - [apert syndrome](https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0007041) MONDO:0007041
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