Protein coverage CV term

[mwalzer]

Name:
Protein coverage

Definition:
The coverage of protein sequences from the peptide sequences identified. The table records the coverage itself (in percent), the protein accession (SHOULD correspond to the accession used in fasta document used for Sequence DB based identification), Length of the protein(, and optionally if it is 'target' or 'decoy' entry.)

Comment: The protein coverage can provide insight into the sensitivity of the instrument/identification/protocols used.

Proposed value type:

• table
  {'coverage':[...], 'accession':[...], 'length':[...], *'TD':[...]}
  *optional

[mwalzer]

[julianu]

Please add comments (i.e. descriptions on how to interpret the values) for the metrics.

As we also have "table" as type, this would be a better suggestion in my opinion.

[julianu]

@mwalzer please add comment (explanation for interpretation)

[mwalzer]

Indeed, and I refined the definition a little.

Name:
Protein coverage

Definition:
The coverage of protein sequences from the peptide sequences identified. The table records the coverage itself (percentage), the protein accession (SHOULD correspond to the accession used in the document used for Sequence DB based identification), Length of the protein(, and optionally if it is a decoy entry.)

Comment:
Higher is better. Gives insight into how much of the target search space is covered. Low coverage can be caused by the absence of proteins, because of the used acquisition methods insensitivity to certain peptide species or shortcomings of the identification method.

Proposed value type:

• single value
• n-tuple
• table
• corresponding lists
• matrix

{'coverage':[...], 'accession':[...], 'length':[...], *'TD':[...]}
*optional

[mwalzer]

@julianu Where would we put something like relationship: has_order MS:1002108 ! higher score better? As text in the comments is suboptimal. And how do we designate which column is primary/affected by has_order? And units.

[mwalzer]

@julianu Maybe we can use this one as an example during PSI2020 to formalise the cv term value situation.