-
Notifications
You must be signed in to change notification settings - Fork 37
/
Copy pathpercolator_out.xsd
286 lines (257 loc) · 10.1 KB
/
percolator_out.xsd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns="http://per-colator.com/percolator_out/15"
targetNamespace="http://per-colator.com/percolator_out/15"
elementFormDefault="qualified" attributeFormDefault="unqualified">
<!-- define some general types -->
<xsd:simpleType name="probability_t">
<xsd:annotation>
<xsd:documentation>Probability (Double in [0-1] or NaN)</xsd:documentation>
</xsd:annotation>
<xsd:union memberTypes="xsd:double">
<xsd:simpleType>
<xsd:restriction base="xsd:double">
<xsd:enumeration value="NaN"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType>
<xsd:restriction base="xsd:double">
<xsd:maxInclusive value="1.0"/>
<xsd:minInclusive value="0.0"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType name="aa_seq_t">
<xsd:restriction base="xsd:string">
<xsd:pattern value="([A-Z]*(\[[^\]]+\])*[A-Z]*)*"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:simpleType name="aa_term_t">
<xsd:restriction base="xsd:string">
<xsd:pattern value="[A-Z\-]"/>
</xsd:restriction>
</xsd:simpleType>
<!-- end general types -->
<!-- define process_info-->
<xsd:element name="process_info">
<xsd:complexType>
<xsd:sequence>
<xsd:element name="command_line" type="xsd:string"/>
<xsd:element name="other_command_line" type="xsd:string"/>
<xsd:element name="pi_0_psms" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="pi_0_peptides" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="pi_0_proteins" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="fdr_proteins" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="alpha" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="beta" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="gamma" type="probability_t" minOccurs="0" maxOccurs="1"/>
<xsd:element name="psms_qlevel" type="xsd:double" minOccurs="0" maxOccurs="1"/>
<xsd:element name="peptides_qlevel" type="xsd:double" minOccurs="0" maxOccurs="1"/>
<xsd:element name="proteins_qlevel" type="xsd:double" minOccurs="0" maxOccurs="1"/>
<xsd:element minOccurs="0" name="average_delta_mass" type="xsd:double"/>
<xsd:element minOccurs="0" name="average_pi" type="xsd:double"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" name="comment">
<xsd:complexType>
<xsd:attribute name="name" type="xsd:string" use="required"/>
<xsd:attribute name="value" type="xsd:string" use="required"/>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
</xsd:element><!-- end process_info-->
<!-- define elements for psm and peptide-->
<xsd:element name="svm_score" type="xsd:double">
<xsd:annotation>
<xsd:documentation xml:lang="en">The score stemming from the SVM. Higher score corresponds to a better PSM than a lower score.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="q_value" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The PSMs q-value, i.e. the expected fraction of incorrect identifications up to this PSM score</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="q_value_emp" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The Protein empirical q-value, i.e. the expected fraction of incorrect identifications up to this Protein score</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="pep" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The PSMs posterior error probability, i.e. the probability that this PSM is incorrect.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="exp_mass" type="xsd:double">
<xsd:annotation>
<xsd:documentation xml:lang="en">The experimental (observed) mass of the PSM</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="calc_mass" type="xsd:double">
<xsd:annotation>
<xsd:documentation xml:lang="en">The calculated mass of the PSM</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="retentionTime">
<xsd:annotation>
<xsd:documentation xml:lang="en">This field contains the observed and predicted retention time in minutes</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:attribute name="predicted" type="xsd:double"/>
<xsd:attribute name="observed" type="xsd:double"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="peptide_seq">
<xsd:annotation>
<xsd:documentation xml:lang="en">Peptide sequence of this PSM including the amino acids N- and C-terminal of the peptide in the proteins sequence.</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:attribute name="n" type="aa_term_t"/>
<xsd:attribute name="c" type="aa_term_t"/>
<xsd:attribute name="seq" type="aa_seq_t" use="required"/>
</xsd:complexType>
</xsd:element>
<xsd:element name="protein_id" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Protein identifier.</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="psm_ids">
<xsd:annotation>
<xsd:documentation xml:lang="en">List of Psm for a particular peptide.</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element name="psm_id" maxOccurs="unbounded" type="xsd:string"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<xsd:element name="p_value" type="probability_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">The PSMs p-value</xsd:documentation>
</xsd:annotation>
</xsd:element>
<!-- end elements for psm and peptide-->
<!-- define attributes for psm, peptide and protein-->
<xsd:attribute name="psm_id" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Unique PSM identifier</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="peptide_id" type="aa_seq_t">
<xsd:annotation>
<xsd:documentation xml:lang="en">Unique peptiude identifier</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="decoy" type="xsd:boolean"/>
<xsd:attribute name="protein_id" type="xsd:string">
<xsd:annotation>
<xsd:documentation xml:lang="en">Unique protein identifier</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<!-- define attributes for psm, peptide and protein-->
<!-- define psm-->
<xsd:element name="psm">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="svm_score"/>
<xsd:element ref="q_value"/>
<xsd:element ref="pep"/>
<xsd:element ref="exp_mass" minOccurs="0"/>
<xsd:element ref="calc_mass" minOccurs="0"/>
<xsd:element ref="retentionTime" minOccurs="0"/>
<xsd:element ref="peptide_seq"/>
<xsd:element ref="protein_id" maxOccurs="unbounded"/>
<xsd:element ref="p_value"/>
</xsd:sequence>
<xsd:attribute ref="psm_id" use="required"/>
<xsd:attribute ref="decoy"/>
</xsd:complexType>
</xsd:element> <!-- end psm-->
<!-- define psms-->
<xsd:element name="psms">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="psm" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element><!-- end psms-->
<!-- define peptide-->
<xsd:element name="peptide">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="svm_score"/>
<xsd:element ref="q_value"/>
<xsd:element ref="pep"/>
<xsd:element ref="exp_mass" minOccurs="0"/>
<xsd:element ref="calc_mass" minOccurs="0"/>
<xsd:element ref="retentionTime" minOccurs="0"/>
<xsd:element ref="protein_id" maxOccurs="unbounded"/>
<xsd:element ref="p_value"/>
<xsd:element ref="psm_ids" minOccurs="1" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute ref="peptide_id" use="required"/>
<xsd:attribute ref="decoy"/>
</xsd:complexType>
</xsd:element><!-- end peptide-->
<!-- define peptides-->
<xsd:element name="peptides">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="peptide" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<!-- define protein-->
<xsd:element name="protein">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="pep" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="q_value" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="q_value_emp" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="p_value" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="peptide_seq" maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute ref="protein_id" use="required"/>
<xsd:attribute ref="decoy"/>
</xsd:complexType>
</xsd:element><!-- end protein-->
<!-- define proteins-->
<xsd:element name="proteins">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="protein" maxOccurs="unbounded"/>
</xsd:sequence>
</xsd:complexType>
</xsd:element>
<!-- define attributes of percolator_output-->
<xsd:attribute name="percolator_version" type="xsd:string">
<xsd:annotation>
<xsd:documentation>Version of percolator</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="majorVersion" type="xsd:unsignedShort">
<xsd:annotation>
<xsd:documentation>Major version number</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="minorVersion" type="xsd:unsignedShort">
<xsd:annotation>
<xsd:documentation>Minor version number</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<!-- end attributes of percolator_output-->
<!-- define percolator_output-->
<xsd:element name="percolator_output">
<xsd:complexType>
<xsd:sequence>
<xsd:element ref="process_info" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="psms" minOccurs="1" maxOccurs="1"/>
<xsd:element ref="peptides" minOccurs="0" maxOccurs="1"/>
<xsd:element ref="proteins" minOccurs="0" maxOccurs="1"/>
</xsd:sequence>
<xsd:attribute ref="percolator_version" use="required" />
<xsd:attribute ref="majorVersion" use="required" fixed="2"/>
<xsd:attribute ref="minorVersion" use="required" />
</xsd:complexType>
</xsd:element><!-- end percolator_output-->
</xsd:schema>