Hello OT team!
In the same line of “clarifying scores of evidence”. But I write it here because it is defined “Evidence Count”.
Basically I extracted the “score” and the “evidenceCount” from “diseaseId”=EFO_0000565 & “targetId”=ENSG00000157764 (leukemia and BRAF).
The information comes from "Associations - direct (overall score) " and "Associations - direct (by data source) " json files.
And the evidenceCount of both json files is the same for this association (4) .
the results is just one dictionary for each json file.
“associationByDatasourceDirect”:
“score”: 0.16253705352810702,
“datasourceId”: “chembl”,
“evidenceCount”: 4,
“diseaseId”: “EFO_0000565”,
associationByOverallDirect_view
“score”: 0.09881128059278485,
“targetId”: “ENSG00000157764”,
“diseaseId”: “EFO_0000565”,
“evidenceCount”: 4
In which part of the documentation do they say how is calculated the evidenceCount? I understand is the ontology evidence ? Should I assume evidenceCount means that the ontological association between “TargetID” and “DiseaseID” appears in ONLY 1 datasource from the total of 23 (in OT_24.06), which is on the order 4 ? or the string appears 4 times in the ontology association calculation algorithm (that I guess is somewhere related with the data_processing?)
Each unique target-disease pair in the Open Targets Platform is defined as an association . For example, while there might be several pieces of evidence referring to CFTR and Cystic fibrosis from multiple sources, one single association contextualises all this information within the Platform. [1]
Just to be sure I understand the numbers behind and when to use them.
Many thanks again!
UPDATE:
I Think I found part of my answer in this piece of text.
" Target - disease evidence
Every event or set of events pinpointing a target as a potential causal gene or protein for a disease, represents the unit of information, most often referred as evidence. Within Open Targets, a series of pipelines ensure information is retrieved from their sources and standardised in a way that can be immediately applied to answer drug development queries."
I was able to establish the comparison between the score and evidenceCount in the platform and the downloaded JSON files. Many thanks!