What happened?
When we run the gget opentargets -r diseases we get a score but if you go to the opentargets view for the same ensemble ID you get a table with a number of scores -- it is not clear two things:
- it isn't your fault it seems but OpenTargets reports an EFO measurement as a disease -- for example if you use LILRA4 you will see there is an score of 0.34 which appears to be the association score
gget opentargets ENSG00000239961 -r diseases | grep -B6 -A1 '\"score\":0.3'
returns
{
"id":"EFO_0007937",
"name":"blood protein measurement",
"description":"quantification of the levels of some protein in a blood sample",
"score":0.3370941177
}EFO is not the OBO foundry's ontology for disease -- but a measurement - which it confirms - which if you dig you see is the measurement of the LILRA4 protein in the blood and if you look at the table you see in (opentargets disease associations)[https://platform.opentargets.org/target/ENSG00000239961/associations] there are animal model evidence for mondo diseases that have a weak association score but a pretty good (0.48) score on the animal model for a MONDO termed disease.
but the issue is that though opentargets returns this - should you as the creator of this tool prevent non Mondo terms from presenting themselves as a disease?
- Looking at the webpage it seems we should adjust this call to allow a user to choose which of the 23 terms to choose evidence for -- so I guess this becomes a feature request.
gget version
gget version: 0.29.0
Operating System (OS)
macOS
User interface
Command-line
Are you using a computer with an Apple M1 chip?
Not applicable
What is the exact command that was run?
gget opentargets ENSG00000239961 -r diseases | grep -B6 '\"score\":0.3'
Which output/error did you get?
{
"id":"EFO_0007937",
"name":"blood protein measurement",
"description":"quantification of the levels of some protein in a blood sample",
"score":0.3370941177
},
What happened?
When we run the gget opentargets -r diseases we get a score but if you go to the opentargets view for the same ensemble ID you get a table with a number of scores -- it is not clear two things:
returns
{ "id":"EFO_0007937", "name":"blood protein measurement", "description":"quantification of the levels of some protein in a blood sample", "score":0.3370941177 }EFO is not the OBO foundry's ontology for disease -- but a measurement - which it confirms - which if you dig you see is the measurement of the LILRA4 protein in the blood and if you look at the table you see in (opentargets disease associations)[https://platform.opentargets.org/target/ENSG00000239961/associations] there are animal model evidence for mondo diseases that have a weak association score but a pretty good (0.48) score on the animal model for a MONDO termed disease.
but the issue is that though opentargets returns this - should you as the creator of this tool prevent non Mondo terms from presenting themselves as a disease?
gget version
gget version: 0.29.0
Operating System (OS)
macOS
User interface
Command-line
Are you using a computer with an Apple M1 chip?
Not applicable
What is the exact command that was run?
Which output/error did you get?
{ "id":"EFO_0007937", "name":"blood protein measurement", "description":"quantification of the levels of some protein in a blood sample", "score":0.3370941177 },