Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison test-data/MAPPING/TraML-mapping.xml @ 18:6daaa75ccb99 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
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17:6f6c1cb968a0 18:6daaa75ccb99
1 <?xml version="1.0" encoding="UTF-8"?>
2 <CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.psidev.info/files/validator/CvMapping.xsd"
3 modelName="TraML.xsd" modelURI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/TraML/schema/TraML0.9.3.xsd" modelVersion="0.9.3">
4
5 <CvReferenceList>
6 <CvReference cvName="PSI-MS" cvIdentifier="MS"/>
7 <CvReference cvName="UO" cvIdentifier="UO"/>
8 <CvReference cvName="UNIMOD" cvIdentifier="UNIMOD"/>
9 </CvReferenceList>
10
11 <CvMappingRuleList>
12
13 <!-- sourceFile -->
14 <CvMappingRule id="sourceFile_must" cvElementPath="/TraML/SourceFileList/SourceFile/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/SourceFileList/SourceFile" cvTermsCombinationLogic="AND" >
15 <CvTerm termAccession="MS:1001459" useTermName="false" useTerm="true" termName="file format" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS" />
16 </CvMappingRule>
17 <CvMappingRule id="sourceFile_may" cvElementPath="/TraML/SourceFileList/SourceFile/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/SourceFileList/SourceFile/cvParam" cvTermsCombinationLogic="OR" >
18 <CvTerm termAccession="MS:1000561" useTermName="false" useTerm="false" termName="data file checksum type" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS" />
19 </CvMappingRule>
20
21 <!-- contact -->
22 <CvMappingRule id="contact_must" cvElementPath="/TraML/ContactList/Contact/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/ContactList/Contact" cvTermsCombinationLogic="AND" >
23 <CvTerm termAccession="MS:1000586" useTermName="false" useTerm="true" termName="contact name" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS" />
24 <CvTerm termAccession="MS:1000590" useTermName="false" useTerm="true" termName="contact organization" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS" />
25 </CvMappingRule>
26 <CvMappingRule id="contact_may" cvElementPath="/TraML/ContactList/Contact/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/ContactList/Contact/cvParam" cvTermsCombinationLogic="OR" >
27 <CvTerm termAccession="MS:1000585" useTermName="false" useTerm="false" termName="contact person attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
28 </CvMappingRule>
29
30 <!-- publication -->
31 <CvMappingRule id="publication_must" cvElementPath="/TraML/PublicationList/Publication/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/PublicationList/Publication" cvTermsCombinationLogic="AND">
32 <CvTerm termAccession="MS:1000879" useTerm="true" termName="PubMed identifier" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
33 </CvMappingRule>
34
35 <!-- instrument -->
36 <CvMappingRule id="instrument_must" cvElementPath="/TraML/InstrumentList/Instrument/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/InstrumentList/Instrument" cvTermsCombinationLogic="AND">
37 <CvTerm termAccession="MS:1000031" useTerm="false" termName="instrument model" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
38 </CvMappingRule>
39
40 <!-- software-->
41 <CvMappingRule id="software_must" cvElementPath="/TraML/SoftwareList/Software/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/SoftwareList/Software" cvTermsCombinationLogic="AND">
42 <CvTerm termAccession="MS:1000531" useTerm="false" termName="software" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
43 </CvMappingRule>
44
45 <!-- protein -->
46 <CvMappingRule id="protein_may" cvElementPath="/TraML/ProteinList/Protein/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/ProteinList/Protein" cvTermsCombinationLogic="OR">
47 <CvTerm termAccession="MS:1000884" useTerm="false" termName="protein attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
48 </CvMappingRule>
49
50 <!-- peptide -->
51 <CvMappingRule id="peptide_may" cvElementPath="/TraML/CompoundList/Peptide/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/CompoundList/Peptide" cvTermsCombinationLogic="OR">
52 <CvTerm termAccession="MS:1000863" useTerm="true" termName="predicted pI" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
53 <CvTerm termAccession="MS:1001117" useTerm="true" termName="theoretical mass" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
54 <CvTerm termAccession="MS:1000890" useTerm="false" termName="peptide labeling state" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
55 <CvTerm termAccession="MS:1000893" useTerm="true" termName="peptide group label" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
56 </CvMappingRule>
57
58 <!-- modification -->
59 <CvMappingRule id="modification_may" cvElementPath="/TraML/CompoundList/Peptide/Modification/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/CompoundList/Peptide/Modification" cvTermsCombinationLogic="OR">
60 <CvTerm termAccession="UNIMOD:0" useTerm="false" termName="unimod root node" isRepeatable="true" allowChildren="true" cvIdentifierRef="UNIMOD"></CvTerm>
61 </CvMappingRule>
62
63 <!-- peptide retentionTime -->
64 <CvMappingRule id="peptide_retentionTime_may" cvElementPath="/TraML/CompoundList/Peptide/RetentionTimeList/RetentionTime/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/CompoundList/Peptide/RetentionTimeList/RetentionTime" cvTermsCombinationLogic="OR">
65 <CvTerm termAccession="MS:1000894" useTerm="false" termName="retention time" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
66 <CvTerm termAccession="MS:1000915" useTerm="false" termName="retention time window attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
67 <CvTerm termAccession="MS:1000901" useTerm="false" termName="retention time normalization standard" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
68 </CvMappingRule>
69
70 <!-- compound -->
71 <CvMappingRule id="compound_may" cvElementPath="/TraML/CompoundList/Compound/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/CompoundList/Compound" cvTermsCombinationLogic="OR">
72 <CvTerm termAccession="MS:1000863" useTerm="true" termName="predicted pI" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
73 <CvTerm termAccession="MS:1001117" useTerm="true" termName="theoretical mass" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
74 <CvTerm termAccession="MS:1000864" useTerm="false" termName="chemical compound formula" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
75 </CvMappingRule>
76
77 <!-- compound retentionTime -->
78 <CvMappingRule id="compound_retentionTime_may" cvElementPath="/TraML/CompoundList/Compound/RetentionTimeList/RetentionTime/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/CompoundList/Compound/RetentionTimeList/RetentionTime" cvTermsCombinationLogic="OR">
79 <CvTerm termAccession="MS:1000894" useTerm="false" termName="retention time" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
80 <CvTerm termAccession="MS:1000915" useTerm="false" termName="retention time window attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
81 <CvTerm termAccession="MS:1000901" useTerm="false" termName="retention time normalization standard" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
82 </CvMappingRule>
83
84 <!-- transition precursor -->
85 <CvMappingRule id="transition_precursor_must" cvElementPath="/TraML/TransitionList/Transition/Precursor/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/TransitionList/Transition/Precursor" cvTermsCombinationLogic="AND">
86 <CvTerm termAccession="MS:1000827" useTerm="true" termName="isolation window target m/z" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
87 </CvMappingRule>
88 <CvMappingRule id="transition_precursor_may" cvElementPath="/TraML/TransitionList/Transition/Precursor/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TransitionList/Transition/Precursor" cvTermsCombinationLogic="AND">
89 <CvTerm termAccession="MS:1000041" useTerm="true" termName="charge state" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
90 </CvMappingRule>
91
92 <!-- target include precursor -->
93 <CvMappingRule id="target_include_precursor_must" cvElementPath="/TraML/TargetList/TargetIncludeList/Target/Precursor/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/TargetList/TargetIncludeList/Target/Precursor" cvTermsCombinationLogic="AND">
94 <CvTerm termAccession="MS:1000827" useTerm="true" termName="isolation window target m/z" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
95 </CvMappingRule>
96 <CvMappingRule id="target_include_precursor_may" cvElementPath="/TraML/TargetList/TargetIncludeList/Target/Precursor/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TargetList/TargetIncludeList/Target/Precursor" cvTermsCombinationLogic="AND">
97 <CvTerm termAccession="MS:1000041" useTerm="true" termName="charge state" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
98 </CvMappingRule>
99
100 <!-- target exclude precursor -->
101 <CvMappingRule id="target_exclude_precursor_must" cvElementPath="/TraML/TargetList/TargetExcludeList/Target/Precursor/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/TargetList/TargetExcludeList/Target/Precursor" cvTermsCombinationLogic="AND">
102 <CvTerm termAccession="MS:1000827" useTerm="true" termName="isolation window target m/z" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
103 </CvMappingRule>
104 <CvMappingRule id="target_exclude_precursor_may" cvElementPath="/TraML/TargetList/TargetExcludeList/Target/Precursor/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TargetList/TargetExcludeList/Target/Precursor" cvTermsCombinationLogic="AND">
105 <CvTerm termAccession="MS:1000041" useTerm="true" termName="charge state" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
106 </CvMappingRule>
107
108 <!-- product -->
109 <CvMappingRule id="product_must" cvElementPath="/TraML/TransitionList/Transition/Product/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/TransitionList/Transition/Product" cvTermsCombinationLogic="AND">
110 <CvTerm termAccession="MS:1000827" useTerm="true" termName="isolation window target m/z" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
111 </CvMappingRule>
112 <CvMappingRule id="product_may" cvElementPath="/TraML/TransitionList/Transition/Product/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TransitionList/Transition/Product" cvTermsCombinationLogic="AND">
113 <CvTerm termAccession="MS:1000041" useTerm="true" termName="charge state" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
114 </CvMappingRule>
115
116 <!-- interpretation -->
117 <CvMappingRule id="interpretation_must" cvElementPath="/TraML/TransitionList/Transition/InterpretationList/Interpretation/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/TransitionList/Transition/InterpretationList/Interpretation" cvTermsCombinationLogic="AND">
118 <CvTerm termAccession="MS:1000926" useTerm="true" termName="product interpretation rank" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
119 <CvTerm termAccession="MS:1001221" useTerm="false" termName="fragmentation information" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
120 <CvTerm termAccession="MS:1000903" useTerm="true" termName="product ion series ordinal" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
121 </CvMappingRule>
122 <CvMappingRule id="interpretation_may" cvElementPath="/TraML/TransitionList/Transition/InterpretationList/Interpretation/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TransitionList/Transition/InterpretationList/Interpretation" cvTermsCombinationLogic="AND">
123 <CvTerm termAccession="MS:1000904" useTerm="true" termName="product ion m/z delta" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
124 </CvMappingRule>
125
126 <!-- prediction -->
127 <CvMappingRule id="prediction_may" cvElementPath="/TraML/TransitionList/Transition/Prediction/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TransitionList/Transition/Prediction" cvTermsCombinationLogic="OR">
128 <CvTerm termAccession="MS:1000909" useTerm="false" termName="transition validation method" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
129 <CvTerm termAccession="MS:1000907" useTerm="true" termName="peak targeting suitability rank" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
130 <CvTerm termAccession="MS:1000042" useTerm="true" termName="peak intensity" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
131 <CvTerm termAccession="MS:1000906" useTerm="true" termName="peak intensity rank" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
132 <CvTerm termAccession="MS:1000443" useTerm="true" termName="mass analyzer type" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
133 <CvTerm termAccession="MS:1000031" useTerm="true" termName="instrument model" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
134 </CvMappingRule>
135
136 <!-- validation -->
137 <CvMappingRule id="validation_may" cvElementPath="/TraML/TransitionList/Transition/ConfigurationList/Configuration/Validation/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TransitionList/Transition/ConfigurationList/Configuration/Validation" cvTermsCombinationLogic="OR">
138 <CvTerm termAccession="MS:1000909" useTerm="false" termName="transition validation method" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
139 <CvTerm termAccession="MS:1000907" useTerm="true" termName="peak targeting suitability rank" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
140 <CvTerm termAccession="MS:1000042" useTerm="true" termName="peak intensity" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
141 <CvTerm termAccession="MS:1000906" useTerm="true" termName="peak intensity rank" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
142 <CvTerm termAccession="MS:1000031" useTerm="true" termName="instrument model" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
143 </CvMappingRule>
144
145 <!-- evidence -->
146 <CvMappingRule id="evidence_may" cvElementPath="/TraML/CompoundList/Peptide/Evidence/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/CompoundList/Peptide/Evidence" cvTermsCombinationLogic="OR">
147 <CvTerm termAccession="MS:1001100" useTerm="true" termName="confident peptide" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
148 </CvMappingRule>
149
150 <!-- transition configuration -->
151 <CvMappingRule id="transition_configuration_may" cvElementPath="/TraML/TransitionList/Transition/ConfigurationList/Configuration/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TransitionList/Transition/ConfigurationList/Configuration" cvTermsCombinationLogic="OR">
152 <CvTerm termAccession="MS:1000502" useTerm="true" termName="dwell time" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
153 <CvTerm termAccession="MS:1000482" useTerm="false" termName="source attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
154 <CvTerm termAccession="MS:1000510" useTerm="false" termName="precursor activation attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
155 </CvMappingRule>
156
157 <!-- target configuration -->
158 <CvMappingRule id="target_configuration_may" cvElementPath="/TraML/TargetList/TargetIncludeList/Target/ConfigurationList/Configuration/cvParam/@accession" requirementLevel="MAY" scopePath="/TraML/TargetList/TargetIncludeList/Target/ConfigurationList/Configuration" cvTermsCombinationLogic="OR">
159 <CvTerm termAccession="MS:1000502" useTerm="true" termName="dwell time" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm>
160 <CvTerm termAccession="MS:1000482" useTerm="false" termName="source attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
161 <CvTerm termAccession="MS:1000510" useTerm="false" termName="precursor activation attribute" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
162 </CvMappingRule>
163
164 <!-- targetList -->
165 <CvMappingRule id="targetList_must" cvElementPath="/TraML/TargetList/cvParam/@accession" requirementLevel="MUST" scopePath="/TraML/TargetList" cvTermsCombinationLogic="OR">
166 <CvTerm termAccession="MS:1000919" useTerm="false" termName="target inclusion exclusion priority" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>
167 </CvMappingRule>
168
169
170 </CvMappingRuleList>
171 </CvMapping>