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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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Add term allelic_frequency #357

Closed gafiore closed 7 years ago

keilbeck commented 8 years ago

HI

I'm not sure what kind of thing an allelic frequency is? I can see it being the property, but it is not a sequence feature. Any thoughts, suggestions for a definition? It is always going to be dependent on a particular population right?

--Karen

thefferon commented 8 years ago

@gafiore, please follow up with an explanation, definition, and an example of how you would use allelic_frequency.

bheale commented 8 years ago

Given the presence of allelic state as a separate issue, I'd suggest that allelic frequency is similar to variant frequency. http://www.sequenceontology.org/browser/current_svn/term/SO:0001763 Under sequence attribute/variant quality. Variant frequency's definition is "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population."
I'm not sure allelic frequency is really different from variant frequency. Or is Allelic frequency more about the occurrence of an allelic state....I'll have to double check the resource to look for implied meaning.

from the CG HL7 current proposed FHIR/observation-genetics: Allelic Frequency is "A physical quality which inheres to the allele by virtue of the number of instances of the allele within a population."

Again, I'm not sure there is a difference between Allelic Frequency or Variant frequency, unless an Allele and variant have a meaningful difference. To me the way we are using them in the FHIR observation profile implies an isosemantic relationship.

keilbeck commented 8 years ago

Hi Bret thanks, It looks like HL7 copied the definition from SO :o) Does allele frequency need to be a separate entity from allele frequency or should it be a synonym.

--K

keilbeck commented 8 years ago

I have added this terms as a child of variant frequency. The ID is: SO:0002119 The definition is: A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population.

keilbeck commented 8 years ago

This is checked into the latest revision. I'll keep this open for comments for a couple of days.

gafiore commented 8 years ago

Thank you! I'm including the HL7 Clinical Genomics Work Group for feedback.

On Thu, Jul 21, 2016 at 2:14 PM Karen EIlbeck notifications@github.com wrote:

I have added this terms as a child of variant frequency. The ID is: SO:0002119 The definition is: A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population.

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