Looking really good. Two quick questions on a skim— 1) Are you not going to include point mutations/replacements along with insertions/deletions (given the increasing use of MAGE, etc), 2) In the data file info on media would seem to need to be quantitative— so the amount of glucose, etc. should be noted. If there is a time series this might be measured in time. This would seem to be important to the analysis… where will that data be kept?
Hello all,
Attached is the proposal for phenotype data in KBase that was discussed in the developers call today. This is geared towards microbes, but probably works for other cases as well.
This is a draft, so modification can certainly be made.
Also, after discussing this with Paramvir and Ben, it’s been decided that we will also introduce a data format for “growth phenotypes”, which Ben is in charge of formulating. “Growth Phenotypes” will be highly derived datasets (basically knockouts/fitness pairs). “Growth Phenotypes” will ultimately be computed from the experimental data-structure described in the attached file, and “Growth phenotypes” will be used as direct inputs into FBA and Growmatch algorithms.
Chris