- make AnalysisSummary semantic rule clearer in terms of SRM

Former-commit-id: d785d413a04b8c2dce8aa7cc2a8da145ecae944d

schema/Schema_rules_absolute_quant_under_review.txt

@@ -13,11 +13,11 @@ The following term MAY also be used if an SRM analysis has been performed in lab
 
 MS:1001838 - name: SRM quantitation analysis
 
-The following MUST both be present in AnalysisSummary with values of true of false :
+The following MUST both be present in AnalysisSummary with values of true or false :
 
 MS:XXXXXXX: "peptide internal reference used" (if true, an AssayQuantLayer of "internal reference abundance" MUST be present in PeptideConsensusList) 
 MS:XXXXXXX: "protein internal reference used" (if true, an AssayQuantLayer of "internal reference abundance" MUST be present in ProteinList)
 
-- If either value of CV term "peptide internal reference used" or "protein internal reference used" is true, there MUST be a AssayQuantLayer in PeptideConsensusList or ProteinList respectively, of data type -- "internal reference abundance", with appropriate unit.
+- If either value of CV term "peptide internal reference used" or "protein internal reference used" is true, there MUST be an AssayQuantLayer in PeptideConsensusList or ProteinList respectively, of data type -- "internal reference abundance", with appropriate unit.
 
 - There SHOULD be at least one peptide-level, protein-level or protein group-level AssayQuantLayer containing absolute abundance values for all peptides or proteins.

schema/Schema_rules_general.txt

@@ -19,11 +19,16 @@ Failure of a rule with a SHOULD causes a WARNING to be produced
 
 Mapping file additions and associated rules
 *********************************************
-- There MUST be ONE or MORE cvParams in AnalysisSummary for the general type of technique. We support four techniques in level 1 release (add following cvParams where they do not already exist): 
-"MS2 Tag-based analysis"  (General term needed? Otherwise we could just use specific terms for iTRAQ / TMT etc?)
-"MS1 Label-based analysis" (General term needed? Otherwise we could just use specific terms for SILAC / N15 etc?)
+- There MUST be ONE or MORE cvParams in AnalysisSummary for the general type of technique. We support five techniques in level 1 release: 
+id: MS:1002023 - name: MS2 Tag-based analysis
+id: MS:1002018 - name: MS1 Label-based analysis
 id: MS:1001834 - name: LC-MS label-free quantitation analysis
 id: MS:1001836 - name: spectral counting quantitation analysis
+id: MS:1001838 - name: SRM quantitation analysis
+
+- If "SRM quantitation analysis" is present in <AnlaysisSummary>, either "LC-MS label-free quantitation analysis" or "MS1 Label-based analysis" MUST be present in <AnlaysisSummary>.
+
+- If "SRM quantitation analysis" is not present in <AnlaysisSummary>, EXACTLY ONE of the other four CV terms MUST be present in <AnalysisSummary>
 
 
 Additional notes or discussed rules not currently to implement