Where to find the harmonic sum calculations in the code?

Hello Open Targets Community,

I’d like to know where to find the calculations of harmonic sums and more generally, where to find the scores calculation in the code ? In which module can I find these informations ?

Thanks in advance,

Best regards,
Nathalie

Hi @njeanray!

The harmonic sum calculations for the overall, datasource, and datatype association scores can be found in the Association.scala module.

Individual pieces of evidence are scored in the evidence_datasource_parsers module or ETL configuration.

For example, the PhenoDigm evidence is scored in the PhenoDigm.py module. The resulting resource_score field is then used in the ETL configuration to calculate the association scores.

However, for a datasource like ClinGen, the individual pieces of evidence are scored in the ETL configuration file. The confidence string generated by the ClinGen module is used and mapped to a score.

Also, note that the ETL configuration also sets the default weights and datasource-specific weights.

Cheers,

Andrew :slight_smile: