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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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Wrong formulas/calculations of memote scores #730

Closed mckohnen closed 2 years ago

mckohnen commented 2 years ago

Hi,

When I calculated the results according to the formulas provided in the html report I noticed that the score of "Annotation - Metabolites" (63.23%) does not match the displayed results (81.83%) (see screenshot1). Same goes for "Annotation - Genes" and "Annotation - Reactions". Unlike in the formula, where every single value is weighted equally, I figured that memote first calculates normalized scores for the parameters "Annotations Per Database" and "Annotation Conformity Per Database" and then uses these summarized scores to calculate the metabolites/genes/reactions annotation scores. Thus, the displayed formulas need be corrected. In this case for example, the formula would be as follows:

memote_metabolic_annotation_corrected_formula

Furthermore I also noticed that total score (69.94%) (see screenshot2) does not match the calculations according to the displayed formula (66.94%). However, here I really have no idea what is going wrong... Could you maybe have a look at this?

Best regards Max

P.S.: I installed the latest stable version of memote using pip.

memote_metabolic_annotation_result

memote_total_score

Midnighter commented 2 years ago

Duplicate of #716. If you have the time to fix it, any help is appreciated.