Harry Hochheiser

Expose db.index.fulltext index to Lucene API

5

The Lucene fulltext index capabilities are really great, but they're also limited. I'd love to get at the guts of the index, to pull out term frequency, document frequency, etc....

image is 404 and link does not resolve.

normalize documentation

2

Consider reviewing various documentation pages for consistency of tone and coverage. For example, the (https://github.com/phenopackets/phenopacket-format/wiki/Identifiers)[identifiers page] refers to a default JSON-LD context, which might or might not make sense for...

negation not handled in schema: ``` phenotype: type: not: id: HP:0001608 label: Abnormality of the voice ``` does not validate

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

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...

negation

1

assertions of the absence of a phenotype might be needed.

treatment histories

2

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

add annotation suffiicency score to analyze/phenotypes input

1

When providing a set of phenotypes to be analyzed, an annotation sufficiency meter would be helpful for showing users the quality of their annotations.

Is there some reason why these routines don't work for results of scan_bayes_negbin?