Phenio toolkit

[souzadevinicius]

We want to build a simple tool that allows us to construct specific pathways through the Phenio KG. Pathways components include:

• cross-species exact matches
• cross-species semantic similarity threshold matches
• genetic orthologs
• anatomical homologs
• gene to phenotype associations
• phenotype trait generalisation
• trait to measurement
• etc

As a first basic pass, we want to:

• create a package called phenio-toolkit with a simple CLI using Monarch cookiecutter
• create a class to represent paths with methods to add specific associations
• create at least one implementation of a conflict pathway (Monarch Default cross-species gene confirm pipeline )

For the basic method to work for IMPC gene use case, we need the following data:

• MP HP Mappings
• IMPC Gene HGNC Mappings
• MP OBA Mappings
• OBA EFO Mappings
• EFO HGNC (GWAS)