How to calculate the overall association score?

[charlie]

Hello Open Targets Platform,

I am interested in the overall association score between myeloproliferative disorder (EFO: EFO_0004251) and JAK2 (Ensembl: ENSG00000096968). The overall score shown on the web page is 0.87. How to calculate this score?

Step 1: Obtain source score

Step 2: Weight those data source score by Data source weights.
I have some problem with the mapping with “datasourceId” and the " Data source"
on the above website. For example, does “ot_genetics_portal” belong to “Others” on the web?
Do “eva” and “eva_somatic” belong to “Others” as well?

Step 3: Sort those weighted data source score in a descending order.

Step 4: Do the harmonic sum, that is, S = S1/1^2 + S2/2^2 + S3/3^2 + …

Step 5: Calculate the normalized factor: NS = 1/1^2 + … + 1/11^2 = 1.558

Step 6: Normalized score = S/NS is not equal to 0.87

My question is which steps are wrong for calculating the overall association score.

Best,
Charlie

[hcornu]

Hi @charlie,

Thanks for your question!

Your steps are correct. However, for the overall association score, the normalized factor (maximum theoretical harmonic sum) is approximated to 1.644 (see the Platform’s Association scoring documentation).

For the data source weights, all other data sources that are not listed in the table are included in ‘Others’ and scored as 1. So “ot_genetics_portal”, “eva”, and “eva_somatic” belong to “Others”.

If you’re unsure, you can check the default weightings in the new Associations on the Fly view (in Advanced Options, click Show data source controls):

Let me know if you have further questions!

[charlie]

Than you so much. The scores are consistent now.
Best,
Charlie