Jules Jacobsen

Can we defer this to the pedigree working group? They already had a spirited discussion about this and have some guidance in their document https://docs.google.com/document/d/1UAtSLBEQ_7ePRLvDPRpoFpiXnl6VQEJXL2eQByEmfGY > Several REA ontologies exist,...

@heikkil I'm going to close this request for now as having discussed this with the group this evening we agreed that there are too many issues around this to know...

Re-opening given discussion with Pedigree group on 2022-03-03. This field is useful/required for many test ordering systems. The codes used will likely be national-specific codes and not necessarily universally applicable.

@lindsmith Did you manage to get hold of 2 and 3?

The ISO 11239:2012(E) `codeTermPair` `code` and `term` fields are directly comparable to the Phenopacket `OntologyClass` `id` and `label`, but other fields are not present in the `OntologyClass` although these are...

Hi @xiaofengleo did you pull in the git sub-modules before building? https://github.com/phenopackets/phenopacket-schema#git-submodules

what is the contents of the file phenopacket-schema/src/main/proto/ga4gh/vrs/v1/vrs.proto does it exist at all? It should look like this: ```proto syntax = "proto3"; package org.ga4gh.vrs.v1; option java_multiple_files = true; option java_package...

Did you add the first line yourself? It's failing to compile the protobuf because the vrs.proto file isn't protobuf, it's a symbolic link to a separate GitHub repository which needs...

Also using IntelliJ 2018.3 or above cloning the repository as a `New -> Project from Version Control` and then building it in the IDE also works without an issue on...

OK, it must be a symbolic link problem. **You don't need to add `syntax = "proto3";` to the phenopacket-schema\src\main\proto\ga4gh\vrs\v1\vrs.proto file. it should look like this without any intervention on your...