Peter Robinson

get_weighted_triads_number

3

For consistency with other methods, this should be named ``` get_number_of_weighted_triads() ```

Add explanation and reference to this issue https://github.com/protocolbuffers/protobuf/issues/2679

We need to provide more values for the documentation. At present, there are just unspecified_molecule_context https://phenopacket-schema.readthedocs.io/en/latest/variant.html#moleculecontext I cannot seem to find where this is coming from in the protobuf code.

A question is if there is a best practice for representing knowledge about parental consanguinity in phenopackets. In principle this could be infered from the pedigree or later the GA4GH...

Check examples for validitty

1

While developing https://github.com/phenopackets/phenopacket-validator, I am noticing that several of the examples in this repository are not valid. For instance, the AML example shows this error ``` $.metaData.resources[0].iriPrefix: is missing but...

Terms for temporal patterns

1

check that the terms in PATO are sufficient to cover the terms in the Human Phenotype Ontology Clinical Course subontology.

This PATO term, as well as its children, do not seem like valid qualities. The definition of radiation exposure tries to make it into a quality but does not really...

BindingDB

2

https://www.bindingdb.org/bind/index.jsp especially antivirals

NCBI GEO

5

There are lots of relevant datasets. Many of them appear to be good old fashioned microarrays. This can be processed semiautomatically, and so we could try to download "lots" of...

DNA sequences and protein sequences for corona virus

2

Collection of all available sequences for pathogenic and non pathogenic HCovs