Adding Experiment type to the sample metadata

bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

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Adding Experiment type to the sample metadata #50

Closed ypriverol closed 2 years ago

ypriverol commented 4 years ago

I think it would be a good idea to include the Proteomics Data Acquisition Method to explain the type of experiment, this term is in the NCI Thesaurus OBO Edition ontology and the terms are:

Data-Dependent Acquisition
Data-Independent Acquisition
Parallel Reaction Monitoring
Selected Reaction Monitoring

foellmelanie commented 4 years ago

Hi @ypriverol it seems that this was never implemented? Why not? I think it is good and would also help to clarify which experiments are "mass spectrometry imaging", even though MSI is not (yet) part of the suggested ontology.

ypriverol commented 4 years ago

Yes, I will push for this idea more.

foellmelanie commented 4 years ago

Cool. How can the ontology be updated to include MSI?

ypriverol commented 4 years ago

We need to request the term in that ontology.

levitsky commented 4 years ago

Would be a great enhancement.

Are there any other experiment types not mentioned?

Also, if we make it required, we'll need to go through the bulk of annotations and add them, although it's probably mostly DDA at this point, and DIA is marked in the file names, I think?