phenopacket-format

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Modifiers

1

Consider allowing modifiers such as bilateral, unilateral. For instance these modifiers could be taken from the HPO subontology for clinical modifiers. For instance, we might want *\* bilataral *\* iris...

pnrobinson

such as "is causal for", "has been associated with", "is protective for" etc. Need to define these. see also https://github.com/monarch-initiative/dipper/issues/195

mellybelly

temporal onset

2

relative temporal ordering of phenotype onset may be important for diagnosis. I think @mellybelly has some examples where a before b vs. b before a is a vital difference

harryhoch

consider VCF format specification

2

in comparison to what we will do with with phenopackets: https://github.com/samtools/hts-specs/blob/master/VCFv4.3.tex @jmcmurry @drseb @pnrobinson

mellybelly

we need to think about this in the context of journal associated data. make a table that has examples, reference GENO @probinson

mellybelly

consider scope.

3

"The format is intended for rare and undiagnosed disease patients. It is not intended for cancer patients (although presence of cancer may be a feature of the disease). It is...

harryhoch

If there is a tool to be developed, it should be possible to enter pedigree information in that tool as well. the output of the tool should then be **two**...

drseb

negation

1

assertions of the absence of a phenotype might be needed.

harryhoch

treatment histories

2

" For example, it would not record any history of treatment". Certain treatments may be important for discussions of medication sensitivities, etc.

harryhoch