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SD2E / opil

The Open Protocol Interface Language (OPIL) is intended as a standard language for protocol interfaces
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How to encode temperatures for a measurement? #165

Open tramyn opened 3 years ago

tramyn commented 3 years ago

Moved issue from pysbol to here.

To recap: I have a list of temperature values with units used in a measurement. Intent Parser will need to encode this information using opil.SampleSet objects. @jakebeal and I discussed that the values for temperatures are represented using opil.Measure and added to an opil.SampleSet as a VariableFeature. The template of a opil.SampleSet, however, points to a media template. Is this solution still the best way of encoding temperatures ?

jakebeal commented 3 years ago

Are the temperatures being determined on a per-sample basis, or per-experiment?

If you have to have all samples at the same temperature, then it should be an opil:Parameter.

If different samples can have different temperatures, however, then we do need to put it as variantMeasure values on a VariableFeature in an opil:SampleSet. The problem is where to point the variable property, since SBOL needs that to go to a Feature of the template rather than the full template.

We don't really have a good answer for that, but I believe that pointing it at the media is an appropriate stopgap.

tramyn commented 3 years ago

From what I have seen in an ER document, a sample can have varying temperature values. Will Intent Parser have to check in the case that if a list of temperature values are the same per sample, then the temperatures must be encoded as an opil.Parameter ?

jakebeal commented 3 years ago

No, you can just trust what the document tells you.