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Correct non-existent EFO code in example query#997

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opentargets:mainfrom
thehyve:fix-evidence-example-query-efoid
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Correct non-existent EFO code in example query#997
fedde-s wants to merge 1 commit into
opentargets:mainfrom
thehyve:fix-evidence-example-query-efoid

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@fedde-s

@fedde-s fedde-s commented Jul 8, 2026

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Pull request #958 replaced some superseded EFO codes, but I noticed that at least this one was not replaced by the actual successor, but by a mix of the new prefix with the old number, leading to a zero-row response for a very different disease, that does not relate to the queried gene at all.

See the deprecation notice for EFO_0005952 on
https://www.ebi.ac.uk/ols4/ontologies/efo/classes/?short_form=EFO_0005952

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

I tried the query with the corrected ID on https://platform.opentargets.org/api, and no longer got a zero-row response but one that's identical, though with different disease IDs/names and sorting, to the equivalent as of 26.03.

Checklist:

  • I have commented my code, particularly in hard-to-understand areas
  • My changes generate no new warnings
  • I have made corresponding changes to the documentation

Pull request opentargets#958
replaced some superseded EFO codes, but I noticed that at least this one
was not replaced by the actual successor, but by a mix of the new prefix
with the old number, leading to a zero-row response for a very different
disease, that does not relate to the queried gene at all.

See the deprecation notice for EFO_0005952 on
<https://www.ebi.ac.uk/ols4/ontologies/efo/classes/?short_form=EFO_0005952>
@fedde-s

fedde-s commented Jul 8, 2026

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diff -u \
  <(jq '.data.disease.evidences.rows | sort_by(.cohortId)' <26.03-equivalent)  \
  <(jq '.data.disease.evidences.rows | sort_by(.cohortId)' <26.06-equivalent) | sed -n '3,$p'
@@ -1,8 +1,8 @@
 [
   {
     "disease": {
-      "id": "EFO_0000095",
-      "name": "chronic lymphocytic leukemia"
+      "id": "MONDO_0004948",
+      "name": "B-cell chronic lymphocytic leukemia"
     },
     "diseaseFromSource": "Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma",
     "target": {
@@ -35,8 +35,8 @@
   },
   {
     "disease": {
-      "id": "EFO_0000095",
-      "name": "chronic lymphocytic leukemia"
+      "id": "MONDO_0004948",
+      "name": "B-cell chronic lymphocytic leukemia"
     },
     "diseaseFromSource": "Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma",
     "target": {
@@ -69,7 +69,7 @@
   },
   {
     "disease": {
-      "id": "EFO_0000403",
+      "id": "MONDO_0018905",
       "name": "diffuse large B-cell lymphoma"
     },
     "diseaseFromSource": "Diffuse Large B-Cell Lymphoma, NOS",
@@ -103,7 +103,7 @@
   },
   {
     "disease": {
-      "id": "EFO_0000403",
+      "id": "MONDO_0018905",
       "name": "diffuse large B-cell lymphoma"
     },
     "diseaseFromSource": "Diffuse Large B-Cell Lymphoma, NOS",
@@ -135,8 +135,8 @@
   },
   {
     "disease": {
-      "id": "EFO_0000095",
-      "name": "chronic lymphocytic leukemia"
+      "id": "MONDO_0004948",
+      "name": "B-cell chronic lymphocytic leukemia"
     },
     "diseaseFromSource": "Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma",
     "target": {
@@ -163,7 +163,7 @@
   },
   {
     "disease": {
-      "id": "EFO_0000403",
+      "id": "MONDO_0018905",
       "name": "diffuse large B-cell lymphoma"
     },
     "diseaseFromSource": "Diffuse Large B-Cell Lymphoma, NOS",
@@ -197,8 +197,8 @@
   },
   {
     "disease": {
-      "id": "EFO_0005952",
-      "name": "non-Hodgkins lymphoma"
+      "id": "MONDO_0018908",
+      "name": "non-Hodgkin lymphoma"
     },
     "diseaseFromSource": "Non-Hodgkin Lymphoma",
     "target": {
@@ -230,8 +230,8 @@
   },
   {
     "disease": {
-      "id": "EFO_0000095",
-      "name": "chronic lymphocytic leukemia"
+      "id": "MONDO_0004948",
+      "name": "B-cell chronic lymphocytic leukemia"
     },
     "diseaseFromSource": "Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma",
     "target": {
@@ -259,7 +259,7 @@
   },
   {
     "disease": {
-      "id": "EFO_0000403",
+      "id": "MONDO_0018905",
       "name": "diffuse large B-cell lymphoma"
     },
     "diseaseFromSource": "Diffuse Large B-Cell Lymphoma, NOS",

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