# Duplicated diseases in 22.06

**URL:** <https://community.opentargets.org/t/duplicated-diseases-in-22-06/702>\
**Category:** Data issue\
**Created:** [12 July 2022 09:51 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702 "2022-07-12T09:51:56Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![ochoa](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/ochoa/32/189_2.png) [@ochoa](https://community.opentargets.org/u/ochoa)\
**Post date:** [12 July 2022 09:51 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/1 "2022-07-12T09:51:57Z")

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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.

 ![Screenshot 2022-07-12 at 10.48.41](https://europe1.discourse-cdn.com/flex017/uploads/opentargets/original/1X/045e1b8fb7af64dbd5de7fd1101d95c54179816a.png)

We are working with EFO to resolve this issue ASAP:

> <https://github.com/EBISPOT/efo/issues/1645>
>
> 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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**Author:** ![hcornu](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/hcornu/32/716_2.png) [@hcornu](https://community.opentargets.org/u/hcornu)\
**Post date:** [3 October 2022 11:49 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/2 "2022-10-03T11:49:38Z")

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Update: This issue has been resolved in our latest update — 22.09.

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**Author:** ![vcatterson](https://avatars.discourse-cdn.com/v4/letter/v/edb3f5/32.png) [@vcatterson](https://community.opentargets.org/u/vcatterson)\
**Post date:** [31 October 2022 18:30 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/3 "2022-10-31T18:30:39Z")

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Hi team! I wanted to thank you for the v22.09 update; it’s really great to see the additions and the clean-up of these duplicate terms!

However, it seems that while the `diseases` dataset has had the duplicate entries removed, the `diseaseToPhenotype` dataset has had entries with the retired IDs removed entirely, instead of updating/remapping to the new term.

For example, “Familial dilated cardiomyopathy” was one of those rare diseases with a duplicate entry of Orphanet\_217607 and MONDO\_0016333. Now only the MONDO ID is contained in the `diseases` data. But `diseaseToPhenotype` previously had over 60 phenotypes associated with the Orphanet ID. Now there are no phenotypes associated with either the MONDO or the (retired) Orphanet ID.

The related rare disease of “Familial dilated cardiomyopathy with conduction defect due to LMNA mutation” only ever had a single Orphanet ID (Orphanet\_300751). This still exists in both the `diseases` and the `diseaseToPhenotype` datasets.

Please let me know if you want any more information about this issue!

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**Author:** ![ochoa](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/ochoa/32/189_2.png) [@ochoa](https://community.opentargets.org/u/ochoa)\
**Post date:** [1 November 2022 12:54 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/4 "2022-11-01T12:54:19Z")

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This is definitely a bug derived from the obsoletion of the Orphanet\_217607 term in EFO.

We are investigating:

> <https://github.com/opentargets/issues/issues/2778>
>
> As reported in a recent \[community post\](https://community.opentargets.org/t/dup…licated-diseases-in-22-06/702/2), some diseases that used to have \`disease2phenotype\` relationships (\[ETL code\](https://github.com/opentargets/platform-etl-backend/blob/0de07d193816ef8790bfb820597f9c9adf3a9843/src/test/scala/io/opentargets/etl/backend/target/HpoTest.scala)) don't have it anymore.
> 
> In the \`hpo-phenotypes.jsonl\` 22.09 input file we can find entries linked to an obsoleted ID ("ORPHA:217607") that the user has reported.
> 
> \`\`\`
> \> gsutil cat gs://open-targets-data-releases/22.09/input/ontology-inputs/hpo-phenotypes.jsonl | grep '"Familial dilated cardiomyopathy"'
> 
> {"databaseId": "ORPHA:217607", "diseaseName": "Familial dilated cardiomyopathy", "qualifier": null, "HPOId": "HP:0001712", "references": \["ORPHA:217607"\], "evidenceType": "TAS", "onset": null, "frequency": "HP\_0040281", "sex": null, "modifiers": null, "aspect": "P", "biocuration": "ORPHA:orphadata\[2022-06-11\]", "resource": "HPO"}
> {"databaseId": "ORPHA:217607", "diseaseName": "Familial dilated cardiomyopathy", "qualifier": null, "HPOId": "HP:0025169", "references": \["ORPHA:217607"\], "evidenceType": "TAS", "onset": null, "frequency": "HP\_0040281", "sex": null, "modifiers": null, "aspect": "P", "biocuration": "ORPHA:orphadata\[2022-06-11\]", "resource": "HPO"}
> ...
> \`\`\`
> 
> Because the \`ORPHA:217607\` ID has been obsoleted in EFO, my impression is that we are dropping all the records. 
> 
> Using the disease index we can rescue the obsoleted IDs in the same way that we rescue them for the purpose of evidence. An example of how the relevant ID is found in our disease index linked to \`MONDO\_0016333\` (with the annoying ORPHA == Orphanet conversion).
> 
> \`\`\`
> ❯ gsutil cat 'gs://open-targets-data-releases/22.09/output/etl/json/diseases/\*.json' | jq 'select(.id == "MONDO\_0016333") | \[{id:.id, obsoleteTerms:.obsoleteTerms}\]'
> 
> \[
> {
> "id": "MONDO\_0016333",
> "obsoleteTerms": \[
> "Orphanet\_217607"
> \]
> }
> \]
> \`\`\`
> 
> Half-baked feature, bug or enhancement, depending on how you see it ;)

Thanks for reporting!

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**Author:** ![vcatterson](https://avatars.discourse-cdn.com/v4/letter/v/edb3f5/32.png) [@vcatterson](https://community.opentargets.org/u/vcatterson)\
**Post date:** [1 November 2022 13:14 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/5 "2022-11-01T13:14:42Z")

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Thank you! Much appreciated 😃 🙏

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**Author:** ![vcatterson](https://avatars.discourse-cdn.com/v4/letter/v/edb3f5/32.png) [@vcatterson](https://community.opentargets.org/u/vcatterson)\
**Post date:** [9 March 2023 19:17 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/6 "2023-03-09T19:17:58Z")

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Hi team,

I noticed that this bug has been closed, as it relates to an older version of Open Targets now:

[https://github.com/opentargets/issues/issues/2778](https://github.com/opentargets/issues/issues/2778)

But the underlying problem has not been fixed. There are still no phenotypes associated with all the rare diseases which were previously duplicated. As a test case, the ID for Familial Dilated Cardiomyopathy `MONDO_0016333` has no phenotypes associated with it, when the previous ID of `Orphanet_217607` did have phenotypes.

Hoping this bug can be reopened, and the rare disease phenotypes recaptured!

Thanks 🙏

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<div class="post-metadata">

**Author:** ![ochoa](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/ochoa/32/189_2.png) [@ochoa](https://community.opentargets.org/u/ochoa)\
**Post date:** [13 March 2023 11:18 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/7 "2023-03-13T11:18:33Z")

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Thanks for raising. Re-opened. Apologies

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<div class="post-metadata">

**Author:** ![vcatterson](https://avatars.discourse-cdn.com/v4/letter/v/edb3f5/32.png) [@vcatterson](https://community.opentargets.org/u/vcatterson)\
**Post date:** [13 March 2023 13:40 UTC](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/8 "2023-03-13T13:40:42Z")

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Thank you! I appreciate it 😄