Participants

The participants were derived from 28 Terra projects assigned to AnVIL.

The attribute sets for participant were very consistent across projects. Only 1 project had two extra fields.

Mapping

Our intial mapping to a GDC-like graph is as follows:

• Added Diagnosis and Observation to differentiate phenotype links

Discussion points

• Should the Family entity should be added to the gen3 graph?
• Is the Affected/Unaffected edges to Phenotype synonymous with gen3's Diagnosis?
• What is the best way to model the present/absent edges to Phenotype? Perhaps an Observation type?
• What is the best way to lable the edge between participant and Gene (expressed is a placeholder)?
• Interestingly, the participant record in terra has a variant like set of fields [pos,ref,alt,hgvs,...] none of them have content. What is the intent of these fields?
• Temporal data:
• Do we have dob, age_at_diagnosis or age_at_enrollment to base timeseries data (PMI)
• Ontologies: Phenotype seems to be fairly uniform (HPO)
• ontology term on edge type: Is there a standard way to represent [Affected, Unaffected, present, absent]
• same-as : are subjects and samples shared between projects?

Samples

The properties associated with sample diverged widely, consisting mainly of CRAM summary statistics

Mapping

• Added Sample node
• Added CramFile CraiFile nodes

Discussion points

• Should we move the bulk of these attributes to the CramFile node?
• Should we reprocess the CRAM files to create an agreed upon set of attributes?