[Psidev-pi-dev] Issue 45 in psi-pi: Number of peptides / proteins to be reported

[<cod...@go...>]

Status: Accepted
Owner: dcreasy
Labels: Type-Defect Priority-Medium

New issue 45 by dcreasy: Number of peptides / proteins to be reported
http://code.google.com/p/psi-pi/issues/detail?id=45

Writing documentation always brings a few problems to the surface...

Consider 2 separate use cases:
  - Import into a repository such as Pride
  - Import into an application such as Scaffold or Peptide Prophet

With the first, you probably only want to report and store proteins above a
certain threshold that for example gives an FDR described in the instance
document.
With the second, we need to give scores for all spectra. (See:
http://code.google.com/p/psi-pi/wiki/NotesForDocumentation#How_many_should__be_saved
for details).

One option is to insist that these two cases require two different instance
documents.

Another option is to 'encourage' people to save a larger number of results
and add (say) a boolean attribute to <SpectrumIdentificationItem> and
<ProteinDetectionHypothesis> that indicates that the result is above the
specified thresholds.
Without the boolean flag, if all results are saved (as in the current
Mascot examples), a repository such as Pride would need to understand the
relevant CV and only store results above a given score.

Any thoughts / preferences?



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