[Psidev-pi-dev] examples for the discussion: attributes vs. elements vs. CV terms

[Martin E. <mar...@ru...>]

Hi psi-pi-devs!

(See
http://code.google.com/p/psi-pi/issues/d
etail?id=8)

In the following four possible layouts
of a SpectrumIdentificationRedultSet are
given
(use attached files to review in
XMLSpy).
To my knowledge in the "elements with
body" solution we cannot control the
type ("double" is "xs:decimal" in xsd).

 Bye
   Martin



	<!-- attributes: -->
	<SpectrumIdentificationResultSet
identifier="Peptides1">
	
<SpectrumIdentificationResult
identifier="ident_pep_1_1">
	
<SpectrumIdentificationHypothesis
identifier="SIH1" peptide_ref="1_1"
calculatedMassToCharge="670.86261"
chargeState="2"
experimentalMassToCharge="671.9">
	
<HypothesisValueProperty value="62.72"
valuePropertyTerm_ref="DP:1:mascot_ions_
score"/>
	
</SpectrumIdentificationHypothesis>
			<SpectrumElement
spectrumID="S1"
spectraDataInputRef_ref="file://F:/spect
ra_file_1.mzML"/>
	
</SpectrumIdentificationResult>
	
</SpectrumIdentificationResultSet>

	<!-- elements WITHOUT XML body
text (as commonly done at the moment):
-->
	<SpectrumIdentificationResultSet
identifier="Peptides1">
	
<SpectrumIdentificationResult
identifier="ident_pep_1_1">
	
<SpectrumIdentificationHypothesis
identifier="SIH1" peptide_ref="1_1">
	
<calculatedMassToCharge
value="670.86261"/>
	
<chargeState value="2"/>
	
<experimentalMassToCharge
value="671.9"/>
	
<HypothesisValueProperty value="62.72"
valuePropertyTerm_ref="DP:1:mascot_ions_
score"/>
	
</SpectrumIdentificationHypothesis>
			<SpectrumElement
spectrumID="S1"
spectraDataInputRef_ref="file://F:/spect
ra_file_1.mzML"/>
	
</SpectrumIdentificationResult>
	
</SpectrumIdentificationResultSet>

	<!-- elements WITH XML body
text: -->
	<SpectrumIdentificationResultSet
identifier="Peptides1">
	
<SpectrumIdentificationResult
identifier="ident_pep_1_1">
	
<SpectrumIdentificationHypothesis
identifier="SIH1" peptide_ref="1_1">
	
<calculatedMassToChargeALT>670.86261</ca
lculatedMassToChargeALT>
	
<chargeStateALT>2</chargeStateALT>
	
<experimentalMassToChargeALT>671.9</expe
rimentalMassToChargeALT>
	
<HypothesisValueProperty value="62.72"
valuePropertyTerm_ref="DP:1:mascot_ions_
score"/>
	
</SpectrumIdentificationHypothesis>
			<SpectrumElement
spectrumID="S1"
spectraDataInputRef_ref="file://F:/spect
ra_file_1.mzML"/>
	
</SpectrumIdentificationResult>
	
</SpectrumIdentificationResultSet>

	<!-- CV terms (NOT line-in yet):
-->
	<SpectrumIdentificationResultSet
identifier="Peptides1">
	
<SpectrumIdentificationResult
identifier="ident_pep_1_1">
	
<SpectrumIdentificationHypothesis
identifier="SIH1" peptide_ref="1_1">
	
<HypothesisValueProperty
value="670.86261"
valuePropertyTerm_ref="internal_ref:calc
ulatedMassToCharge"/> <!-- plus
OntologyCollection entry -->
	
<HypothesisValueProperty value="2"
valuePropertyTerm_ref="internal_ref:char
geState"/> <!-- plus OntologyCollection
entry -->
	
<HypothesisValueProperty value="671.9"
valuePropertyTerm_ref="internal_ref:expe
rimentalMassToCharge"/> <!-- plus
OntologyCollection entry -->
	
<HypothesisValueProperty value="62.72"
valuePropertyTerm_ref="DP:1:mascot_ions_
score"/>
	
</SpectrumIdentificationHypothesis>
			<SpectrumElement
spectrumID="S1"
spectraDataInputRef_ref="file://F:/spect
ra_file_1.mzML"/>
	
</SpectrumIdentificationResult>
	
</SpectrumIdentificationResultSet>