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mondo

The purpose of this app is to extract a list of phenopackets that have narrow and broad parents according to the ClintLR schema.

To run it, enter the following command

mondo
--allppkt allppkt0_1_15/
--clintlr DiseaseIntuitionGroupsTsv.tsv
  • allppkt0_1_16 is the path to the all_phenopackets directory that can be downloaded from the phenopacket-store Releases page. Note that you need to have at least version 0.1.16 of phenopacket-store.
  • DiseaseIntuitionGroupsTsv.tsv is the file with mappings to narrow and broad Mondo parents (see the ClintLR project for more details).

The result of this command is a new directory called "candidates" that contains a file called candidates.tsv as well as each of the references phenopackets.