Correct non-existent EFO code in example query#997
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Pull request opentargets#958 replaced some superseded EFO codes, but I noticed that at least this one was not replaced by the actual successor, but by a mix of the new prefix with the old number, leading to a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>
Author
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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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.
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: