search

mwalzer / psi-pi

Automatically exported from code.google.com/p/psi-pi
0 stars 0 forks source link

Remove PolypeptideSearch and ProteinDetermination in the _analysisCollection #10

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Remove PolypeptideSearch and ProteinDetermination in the
_analysisCollection and just use the more general: AnalysisProtocolApplication

There doesn't seem to be much advantage in having these specific cases? 
Also, AnalysisProtocolApplication should be required?

From discussion in Toledo with dcreasy, jensiepen, Andreas Bertsch

Original issue reported on code.google.com by dcre...@gmail.com on 28 Apr 2008 at 1:34

GoogleCodeExporter commented 9 years ago 
I agree, that there is no advantage of having "special" analyses types to be
schema-valid. There are no important attributes or elements, which cannot be 
replaced
by "generics" or "generals".
BUT if we think about a later sematic validation it would be quite useful to 
know the
type of analysis to be able to check the type of result set (e.g. whether the 
refs
and scores are to peptide or proteins).
So IF we decide to have a general "AnalysisProtocolApplication" we should add a 
type
to it. I personally would prefer to have special elements at least for the CORE
analyses analysisXML was designed for (i.e. "SpectrumIdentification",
"ProteinDetermination" like dicussed in Toledo with Sean, Alexandre and others; 
and
"QualityAssessment", too).

Original comment by eisena...@googlemail.com on 29 Apr 2008 at 11:45

GoogleCodeExporter commented 9 years ago 
Closely related to this issue is the one, which “special” result types we 
need
(see http://code.google.com/p/psi-pi/issues/detail?id=22).
If we make both sections (analyses and results) “generic”, we need a special
“AnalysisType“ attribute (or CV), to be able to validate semantically or to 
parse
meaningful information.

Original comment by eisena...@googlemail.com on 2 May 2008 at 11:57

GoogleCodeExporter commented 9 years ago 
For the AnalysisProtocol and the Results sections we decided to model "special"
elements, i.e. <SpectrumIdentification> or <ProteinDetection>, because these 
can have
suitable attributes and sub-elements.

Original comment by eisena...@googlemail.com on 17 Jun 2008 at 11:52