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germagerma
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Added missing CV terms to AuditCollectionPerson_should_rule and AuditCollectionOrganization_should_rule
1 parent 493a6b5 commit 5f328c4

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8 files changed

+10
-28
lines changed

8 files changed

+10
-28
lines changed

‎validator/resources/miape-msi-rules.1.1.0.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
<!-- mzIdentML 1.1.0 mapping file derived by ME from mzIdentML 1.0.0 mapping file -->
55
<!-- mzIdentML 1.1.0 MIAPE MSI mapping file derived by SMB from mzIdentML 1.1.0 mapping file -->
66
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
7-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
7+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
88

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<CvReferenceList>
1010
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>

‎validator/resources/miape-msi-rules.1.2.0.xml‎

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<!-- mzIdentML 1.1.1 mapping file derived by SMDB from mzIdentML 1.1.0 mapping file -->
66
<!-- mzIdentML 1.2.0 MIAPE MSI mapping file derived by SMB from mzIdentML 1.1.0 mapping file -->
77
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
8-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.2.0.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd" modelVersion="1.2.0">
8+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.2.0.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd" modelVersion="1.2.0">
99

1010
<CvReferenceList>
1111
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>
@@ -27,7 +27,6 @@
2727
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2828
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2929
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
30-
<Description>Terms describing the contact information for a Person.</Description>
3130
</CvMappingRule>
3231

3332
<CvMappingRule id="AuditCollectionOrganization_should_rule" cvElementPath="/MzIdentML/AuditCollection/organization/cvParam/@accession" requirementLevel="SHOULD" scopePath="/MzIdentML/AuditCollection/organization" cvTermsCombinationLogic="OR">
@@ -38,7 +37,6 @@
3837
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
3938
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
4039
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
41-
<Description>Terms describing the contact information for an Organization.</Description>
4240
</CvMappingRule>
4341

4442
<CvMappingRule id="AnalysisSoftwareContactRole_must_rule" cvElementPath="/MzIdentML/AnalysisSoftwareList/AnalysisSoftware/contactRole/role/cvParam/@accession" requirementLevel="MUST" scopePath="/MzIdentML/AnalysisSoftwareList/AnalysisSoftware/contactRole/role" cvTermsCombinationLogic="OR">
@@ -350,7 +348,6 @@
350348
<CvTerm termAccession="MS:1002538" useTermName="false" useTerm="false" termName="PTM localization confidence metric" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
351349
<CvTerm termAccession="MS:1002549" useTermName="false" useTerm="false" termName="PTM localization distinct peptide-level statistic" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
352350
<CvTerm termAccession="MS:1002555" useTermName="false" useTerm="false" termName="PTM localization score threshold" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
353-
<Description>PTM location scores and thresholds.</Description>
354351
</CvMappingRule>
355352

356353
<!-- addition for mzIdentML 1.2 validation: -->
@@ -388,9 +385,8 @@
388385
<CvTerm termAccession="MS:1002549" useTermName="false" useTerm="false" termName="PTM localization distinct peptide-level statistic" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
389386
<CvTerm termAccession="MS:1002555" useTermName="false" useTerm="false" termName="PTM localization score threshold" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
390387
<!--
391-
<CvTerm termAccession="MS:1002505" useTermName="false" useTerm="false" termName="regular expression for modification localization scoring" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
388+
<CvTerm termAccession="MS:1002505" useTermName="false" useTerm="false" termName="regular expression for modification localization scoring" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"/>
392389
-->
393-
<Description>Term that must be present under SpectrumIdentificationItem in case of modification location scoring.</Description>
394390
</CvMappingRule>
395391

396392
<!-- addition for mzIdentML 1.2 validation: -->

‎validator/resources/mzIdentML-mapping_1.1.0.xml‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
<!-- mzIdentML 1.0.0 mapping file created by ARJ and AB and the whole PSI-PI group -->
44
<!-- mzIdentML 1.1.0 mapping file derived by ME from mzIdentML 1.0.0 mapping file -->
55
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
6-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
6+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
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<CvReferenceList>
99
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>
@@ -24,7 +24,6 @@
2424
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2525
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2626
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
27-
<Description>some text to describe this rule</Description>
2827
</CvMappingRule>
2928

3029
<CvMappingRule id="AuditCollectionOrganization_should_rule" cvElementPath="/MzIdentML/AuditCollection/organization/cvParam/@accession" requirementLevel="SHOULD" scopePath="/MzIdentML/AuditCollection/organization" cvTermsCombinationLogic="OR">

‎validator/resources/mzIdentML-mapping_1.2.0.xml‎

Lines changed: 1 addition & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<!-- mzIdentML 1.1.1 mapping file derived by SMDB from mzIdentML 1.1.0 mapping file -->
66
<!-- mzIdentML 1.2.0 mapping file derived by SMDB from mzIdentML 1.1.1 mapping file -->
77
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
8-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.2.0.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd" modelVersion="1.2.0">
8+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.2.0.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd" modelVersion="1.2.0">
99

1010
<CvReferenceList>
1111
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>
@@ -27,7 +27,6 @@
2727
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2828
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2929
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
30-
<Description>Terms describing the contact information for a Person.</Description>
3130
</CvMappingRule>
3231

3332
<CvMappingRule id="AuditCollectionOrganization_should_rule" cvElementPath="/MzIdentML/AuditCollection/organization/cvParam/@accession" requirementLevel="SHOULD" scopePath="/MzIdentML/AuditCollection/organization" cvTermsCombinationLogic="OR">
@@ -38,7 +37,6 @@
3837
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
3938
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
4039
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
41-
<Description>Terms describing the contact information for an Organization.</Description>
4240
</CvMappingRule>
4341

4442
<CvMappingRule id="AnalysisSoftwareContactRole_must_rule" cvElementPath="/MzIdentML/AnalysisSoftwareList/AnalysisSoftware/contactRole/role/cvParam/@accession" requirementLevel="MUST" scopePath="/MzIdentML/AnalysisSoftwareList/AnalysisSoftware/contactRole/role" cvTermsCombinationLogic="OR">
@@ -324,7 +322,6 @@
324322
<CvTerm termAccession="MS:1002538" useTermName="false" useTerm="false" termName="PTM localization confidence metric" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
325323
<CvTerm termAccession="MS:1002549" useTermName="false" useTerm="false" termName="PTM localization distinct peptide-level statistic" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
326324
<CvTerm termAccession="MS:1002555" useTermName="false" useTerm="false" termName="PTM localization score threshold" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
327-
<Description>PTM location scores and thresholds.</Description>
328325
</CvMappingRule>
329326

330327
<!-- addition for mzIdentML 1.2 validation: -->
@@ -368,7 +365,6 @@
368365
<CvTerm termAccession="MS:1002538" useTermName="false" useTerm="false" termName="PTM localization confidence metric" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
369366
<CvTerm termAccession="MS:1002549" useTermName="false" useTerm="false" termName="PTM localization distinct peptide-level statistic" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
370367
<CvTerm termAccession="MS:1002555" useTermName="false" useTerm="false" termName="PTM localization score threshold" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
371-
<Description>Term that must be present under SpectrumIdentificationItem in case of modification location scoring.</Description>
372368
</CvMappingRule>
373369

374370
<!-- addition for mzIdentML 1.2 validation: -->

‎validator/trunk/src/main/resources/miape-msi-rules.1.1.0.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
<!-- mzIdentML 1.1.0 mapping file derived by ME from mzIdentML 1.0.0 mapping file -->
55
<!-- mzIdentML 1.1.0 MIAPE MSI mapping file derived by SMB from mzIdentML 1.1.0 mapping file -->
66
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
7-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
7+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
88

99
<CvReferenceList>
1010
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>

‎validator/trunk/src/main/resources/miape-msi-rules.1.2.0.xml‎

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<!-- mzIdentML 1.1.1 mapping file derived by SMDB from mzIdentML 1.1.0 mapping file -->
66
<!-- mzIdentML 1.2.0 MIAPE MSI mapping file derived by SMB from mzIdentML 1.1.0 mapping file -->
77
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
8-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.2.0.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd" modelVersion="1.2.0">
8+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.2.0.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd" modelVersion="1.2.0">
99

1010
<CvReferenceList>
1111
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>
@@ -27,7 +27,6 @@
2727
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2828
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2929
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
30-
<Description>Terms describing the contact information for a Person.</Description>
3130
</CvMappingRule>
3231

3332
<CvMappingRule id="AuditCollectionOrganization_should_rule" cvElementPath="/MzIdentML/AuditCollection/organization/cvParam/@accession" requirementLevel="SHOULD" scopePath="/MzIdentML/AuditCollection/organization" cvTermsCombinationLogic="OR">
@@ -38,7 +37,6 @@
3837
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
3938
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
4039
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
41-
<Description>Terms describing the contact information for an Organization.</Description>
4240
</CvMappingRule>
4341

4442
<CvMappingRule id="AnalysisSoftwareContactRole_must_rule" cvElementPath="/MzIdentML/AnalysisSoftwareList/AnalysisSoftware/contactRole/role/cvParam/@accession" requirementLevel="MUST" scopePath="/MzIdentML/AnalysisSoftwareList/AnalysisSoftware/contactRole/role" cvTermsCombinationLogic="OR">
@@ -350,7 +348,6 @@
350348
<CvTerm termAccession="MS:1002538" useTermName="false" useTerm="false" termName="PTM localization confidence metric" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
351349
<CvTerm termAccession="MS:1002549" useTermName="false" useTerm="false" termName="PTM localization distinct peptide-level statistic" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
352350
<CvTerm termAccession="MS:1002555" useTermName="false" useTerm="false" termName="PTM localization score threshold" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
353-
<Description>PTM location scores and thresholds.</Description>
354351
</CvMappingRule>
355352

356353
<!-- addition for mzIdentML 1.2 validation: -->
@@ -388,9 +385,8 @@
388385
<CvTerm termAccession="MS:1002549" useTermName="false" useTerm="false" termName="PTM localization distinct peptide-level statistic" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
389386
<CvTerm termAccession="MS:1002555" useTermName="false" useTerm="false" termName="PTM localization score threshold" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
390387
<!--
391-
<CvTerm termAccession="MS:1002505" useTermName="false" useTerm="false" termName="regular expression for modification localization scoring" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
388+
<CvTerm termAccession="MS:1002505" useTermName="false" useTerm="false" termName="regular expression for modification localization scoring" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"/>
392389
-->
393-
<Description>Term that must be present under SpectrumIdentificationItem in case of modification location scoring.</Description>
394390
</CvMappingRule>
395391

396392
<!-- addition for mzIdentML 1.2 validation: -->

‎validator/trunk/src/main/resources/mzIdentML-mapping_1.1.0.xml‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
<!-- mzIdentML 1.0.0 mapping file created by ARJ and AB and the whole PSI-PI group -->
44
<!-- mzIdentML 1.1.0 mapping file derived by ME from mzIdentML 1.0.0 mapping file -->
55
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
6-
xsi:noNamespaceSchemaLocation="http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/cv-rule-reader/trunk/src/main/resources/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
6+
xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/CvMappingRules.xsd" modelName="mzIdentML1.1.1.xsd" modelURI="https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.1.1.xsd" modelVersion="1.1.1">
77

88
<CvReferenceList>
99
<CvReference cvName="PSI-MS" cvIdentifier="MS"/>
@@ -24,7 +24,6 @@
2424
<CvTerm termAccession="MS:1001755" useTermName="false" useTerm="true" termName="contact phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2525
<CvTerm termAccession="MS:1001756" useTermName="false" useTerm="true" termName="contact fax number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
2626
<CvTerm termAccession="MS:1001757" useTermName="false" useTerm="true" termName="contact toll-free phone number" isRepeatable="true" allowChildren="false" cvIdentifierRef="MS" />
27-
<Description>some text to describe this rule</Description>
2827
</CvMappingRule>
2928

3029
<CvMappingRule id="AuditCollectionOrganization_should_rule" cvElementPath="/MzIdentML/AuditCollection/organization/cvParam/@accession" requirementLevel="SHOULD" scopePath="/MzIdentML/AuditCollection/organization" cvTermsCombinationLogic="OR">

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