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Issues with the spec doc #51

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Drop any issues with the spec doc in here

Original issue reported on code.google.com by andrewro...@googlemail.com on 21 Jul 2009 at 12:39

GoogleCodeExporter commented 8 years ago 
- Remove all intances of "pf:"

- Change "-" to optional for attributes as requested by a reviewer

Original comment by andrewro...@googlemail.com on 21 Jul 2009 at 12:41

GoogleCodeExporter commented 8 years ago 
After a first look, I would change the following:

- "Cosmetic change": the tables in the spec doc for elements 6.7
(SequenceCollection)and 6.15 (DBSequence) need to be resized in order to fit in 
the page.
- In point 7.3, the example must be updated in order to change the translation 
frames
to include now 1,2,3,-1,-2,-3.
- I would add Florian Reisinger from the PRIDE team, to the list of 
acknowledgements,
since he contributed to the new schema.

Original comment by javizca74@gmail.com on 22 Jul 2009 at 3:05

GoogleCodeExporter commented 8 years ago 
A section about the element <SpectrumIdentificationItem> is missing, as well as 
its
graphical context, which I have grabbed, but could not include.

Original comment by eisena...@googlemail.com on 23 Jul 2009 at 3:39

GoogleCodeExporter commented 8 years ago 
A "graphical context" paragraph is missing for element <mzIdentML>, for which I
grabbed an image, but not include

Original comment by eisena...@googlemail.com on 23 Jul 2009 at 3:45

GoogleCodeExporter commented 8 years ago 
It seems that there are some elements missing in the automatically generated 
part of
the schema desription, e.g.:

<Measure>
<SpectrumIdentificationItem>
<ProteinDetectionHypothesis>
<PeptideEvidence>
<Fragmentation>
<PeptideHypothesis>
<IonType>
<FragmentArray>

In the AnalysisXML spec doc these were listed after <Exclude>, which is here 
the last
described element.

Original comment by eisena...@googlemail.com on 23 Jul 2009 at 4:18

GoogleCodeExporter commented 8 years ago 
The example for Sample doesn't show the use of sub samples. The only one that 
does
this is the 15N example - could maybe swap it for that one?

7.6 Database Filter
Example needs updating from Mascot 15N example
The paragraph after the example is no longer correct. Can probably just be 
removed?

7.7 Do we still have any <ParamType>?

Original comment by dcre...@gmail.com on 23 Jul 2009 at 5:03

GoogleCodeExporter commented 8 years ago

Original comment by eisena...@googlemail.com on 20 Aug 2009 at 11:29