Create a basic Phenotype profile

[ljgarcia]

We mentioned this during the Samples meeting last week. @ficolo was pointed as the one to lead this profile. Maybe @CarlosHorro could help as well?

[ficolo]

For our particular use case at the IMPC we need a PhenotypeCall type, that is a Gene Phenotype association. We could use the work of http://phenopackets.org/ as a starting point.

They have already defined some type and relations using proto files:

https://github.com/phenopackets/phenopacket-schema/blob/master/src/main/proto/org/phenopackets/schema/v1/phenopackets.proto

The fields they have consider so far for the Phenopacket are:

• id: An identifier specific for the phenopacket
• patient: The individual representing the focus of the packet - e.g. the proband in rare disease cases or cancer patient
• individuals: Individuals genetically related to the patient - e.g. mother, father, siblings or members of a cohort
• pedigree: The pedigree defining the relations between the patient and their relatives
• biosamples: Biosample(s) derived from the patient or a collection of biosamples in isolation
• genes: Placeholder for gene concepts - could be used for either describing candidate genes or causative genes. The resources using these fields should define what this represents in their context
• variants: Placeholder for genetic variants - could be used for either describing candidate variants or diagnosed causative variants. The resources using these fields should define what this represents in their context.
• diseases: Placeholder for disease concepts - could be used for either describing diagnosed or suspect conditions. The resources using these fields should define what this represents in their context
• genome_assembly: Reference genome assembly against which the sample was called. This is required as the VCF specification does not mandate this
• vcf: Pointer to the relevant VCF file for the patient
• metaData: Structured definitions of the resources and ontologies used within the phenopacket
• relationships: Relationships between entities described in the phenopacket

I took this information from here and here.

[AlasdairGray]

First draft Phenotype profile was created in November 2018 at the Biohackathon.