Why are the evidences in Animal Models and Genetic associations not mentionned ?
ALso, I checked in the database, in table associationByDataTypeIndirect, and these evidences are also mentionned :
A particularity of the Platformâs interface is that it will display direct or indirect evidence depending on which page you are looking at.
In this case, when you look at the associations page for diseases and phenotypes associated with MKS1, the Platform displays only direct evidence for the association between MKS1 and neoplasm, i.e. where each of these entities is specifically referred to.
However, when you click on the cell, the evidence page you land on displays both direct and indirect evidence for the association. The Platform uses the properties of our disease ontology (EFO) to gather evidence for MKS1 in neoplasm and any of its ontological descendants. In the evidence page, the evidence from GEL PanelApp is for renal fibrosis, and the evidence from PhenoDigm refers to CHILD Syndrome, rather than the more general term âneoplasmâ.
Since these are indirect pieces of evidence, they will appear in the associationByDataTypeIndirect table.
Thanks for your fast answer, I got it !
So if I undersand well, is the assumption telling that âall the direct evidences for a given disease-target association are included in indirect evidences for this disease-target associationâ correct ?
Does it mean that, somewhere, the score for the direct association is included in the indirect association score ?
Yes, that is correct. Each piece of evidence we have is given a single score, and the switch between âdirectâ and âindirectâ only affects the evidence which is selected to be included in the aggregated scores (e.g. overall score or Data Type score).
When you view diseases associated with a target (for example, diseases associated with MKS1), the Platform will display a score which aggregates only direct pieces of evidence. In this example, the association between MKS1 and neoplasm has an overall score of 0.00 because the only direct evidence is from text mining.
However, when you search for targets associated with a disease (for example, targets associated with neoplasm), the Platform will display a score which aggregates both direct and indirect pieces of evidence. In this example, the association between neoplasm and MKS1 has an overall score of 0.53, because the score includes indirect evidence, e.g. from the Genomics England PanelApp.
However, I downloaded the .tsv files of both diseases and found that there exists several targets of the T-cell non-Hodgkin lymphoma that are not the targets of the umbrella disease:
{âAPLP1â,
âAPOBEC2â,
âASPHâ,
âECSITâ,
âGAS1â,
âGGTLC3â,
âH4C13â,
âIGHV4-4â,
âMIR135Bâ,
âPARD6Aâ,
âRPL17-C18orf32â,
âSAP18â,
âSLC16A4â,
âSNORD25â,
âTRBV7-9â,
âUPK1Bâ}.
Could you help me check if this is indeed the case, or is my understanding incorrect?
That is correct. When looking at targets associated with a disease, the Platform will also display indirect associations; that is, targets associated with diseases that are child terms of the disease in question.
Ah I think I got why. I downloaded the .tsv of hematopoietic and lymphoid system neoplasm (umbrella disease) from the exact same disease association page in March 2022 (two months ago), and the .tsv of T-cell non-Hodgkin lymphoma yesterday. It seems there has been a version update between this two time points, and the number of targets of the umbrella disease decreased from 10679 to 10350.
Sorry for bothering you⌠I just canât download the large table of the umbrella disease now (because of an issue), but weirdly, I can download the T-cell non-Hodgkin lymphoma one (perhaps because itâs small), so I wanted to use these two datasets together. But it looks like there are indeed some inconsistencies (update) between the two versions.
No worries! Weâre not entirely sure why the issue is happening for some diseases and not others, which is why I could only check by searching the table in the web app.