chore: consistent names and terminology #229
Description
With the intense development work over the last months, there is not always consistency on what kind of terminology is used. It is helpful to be consistent, and it is good to enforce this from the first GECKO3 release onwards.
Note that the example function names indicated below are after changing them to their new name.
| Term | Meaning / use | Example |
|---|---|---|
| ecModel | abbreviation of enzyme-constrained model | |
| empty ecModel | ecModel after makeEcModel, without kcat values |
|
| modelAdapter | a model-specific version of ModelAdapter.m |
ecYeastGEMAdapter.m |
kcatList |
structure that contains kcat information, can have multiple entries per reaction / enzyme / source | output of fuzzyMatching, loadDLKcatOutput() |
load...() |
function that reads a datafile into MATLAB | loadEcModel() |
save...() |
function that writes a datafile from MATLAB | saveEcModel() |
gather...() |
function that downloads data or places API calls to an online resource. The output of this might be a data file, data structure in MATLAB, or directly in an ecModel |
gatherMetSMILES() |
fill...() |
function that downloads data or places API calls to an online resource | fillKcat() |
apply...() |
function that modifies an ecModel with information that it already contains. For instance: applyKcatConstraints takes the information from ecModel.ec.mw and ecModel.ec.kcat to modify ecModel.S. |
Not all function names will be covered by this scheme. For instance fuzzyKcatMatching does not fit any of the categories. Or should we have dofuzzyKcatMatching? Or specify get...() to indicate a function that applies some analysis on the model and gives an output that is outside the model (in this case a kcatList)? Edit: Or should we just accept that for instance fuzzyKcatMatching is not covered by the scheme and keep it unchanged?
This list is not complete yet, feel free to add suggestions below.