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opencobra / schema

xml/rdf schemas for annotating cobra models
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SBML -> Confidence Scores #9

Open tpfau opened 6 years ago

tpfau commented 6 years ago

This is a spin of from #6 for Confidence Scores.

Suggested: An additional (fbc or SBML) field "confidenceScore" associated with all model parts to indicate certainty of a specific model part.

ChristianLieven commented 6 years ago

I just want to point to @matthiaskoenig's most recent response in #4. I am not too sure if the, rather arbitrarily-defined, confidence scores from the Thiele&Palsson-Protocol can keep up with the evidence ontology system suggested by @matthiaskoenig. With this I don't want to discourage the effort of adding an additional field for this purpose, I'd just like us to be aware of potentially better options for the content of this field.

draeger commented 6 years ago

In the discussion of how to improve the output of https://github.com/SBRG/ModelPolisher (an application developed to ensure standard complience of BiGG models) @matthiaskoenig suggested Evidence Ontology (ECO) terms for the most common confidence scores used in COBRA models, see https://github.com/SBRG/ModelPolisher/issues/5.

tpfau commented 6 years ago

Fully agree on this. But as mentioned, We should have a translation scheme in both directions stored somewhere.