source: trunk/misc/mage/rawdatatypes/QT_Spotfinder.xml @ 2925

Last change on this file since 2925 was 2925, checked in by Jari Häkkinen, 17 years ago

Added svndigest:ignore property tom some items.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
  • Property svndigest:ignore set to *
File size: 12.2 KB
Line 
1<?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>
2<?xml-stylesheet type="text/xsl" href="QT.xsl"?>
3<!DOCTYPE MAGE-ML PUBLIC "-//OMG//DTD MAGE-ML 1.0//EN" "http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd">
4<MAGE-ML identifier="EBI:eleh:Spotfinder QT XML">
5  <QuantitationType_package>
6    <QuantitationType_assnlist>
7      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:R" name="R" isBackground="false">
8  <Descriptions_assnlist>
9    <Description text="Spot row number in slide.">
10    </Description>
11  </Descriptions_assnlist>
12  <Scale_assn>
13    <OntologyEntry category="Scale" value="unscaled">
14    </OntologyEntry>
15  </Scale_assn>
16  <DataType_assn>
17    <OntologyEntry category="DataType" value="integer">
18    </OntologyEntry>
19  </DataType_assn>
20      </SpecializedQuantitationType>
21      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:C" name="C" isBackground="false">
22  <Descriptions_assnlist>
23    <Description text="Spot column number in slide.">
24    </Description>
25  </Descriptions_assnlist>
26  <Scale_assn>
27    <OntologyEntry category="Scale" value="unscaled">
28    </OntologyEntry>
29  </Scale_assn>
30  <DataType_assn>
31    <OntologyEntry category="DataType" value="integer">
32    </OntologyEntry>
33  </DataType_assn>
34      </SpecializedQuantitationType>
35      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:MR" name="MR" isBackground="false">
36  <Descriptions_assnlist>
37    <Description text="Spot metarow number or subrow number.">
38    </Description>
39  </Descriptions_assnlist>
40  <Scale_assn>
41    <OntologyEntry category="Scale" value="unscaled">
42    </OntologyEntry>
43  </Scale_assn>
44  <DataType_assn>
45    <OntologyEntry category="DataType" value="integer">
46    </OntologyEntry>
47  </DataType_assn>
48      </SpecializedQuantitationType>
49      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:MC" name="MC" isBackground="false">
50  <Descriptions_assnlist>
51    <Description text="Spot metacolumn number or subcolumn number.">
52    </Description>
53  </Descriptions_assnlist>
54  <Scale_assn>
55    <OntologyEntry category="Scale" value="unscaled">
56    </OntologyEntry>
57  </Scale_assn>
58  <DataType_assn>
59    <OntologyEntry category="DataType" value="integer">
60    </OntologyEntry>
61  </DataType_assn>
62      </SpecializedQuantitationType>
63      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:SR" name="SR" isBackground="false">
64  <Descriptions_assnlist>
65    <Description text="Spot row number in a block/grid.">
66    </Description>
67  </Descriptions_assnlist>
68  <Scale_assn>
69    <OntologyEntry category="Scale" value="unscaled">
70    </OntologyEntry>
71  </Scale_assn>
72  <DataType_assn>
73    <OntologyEntry category="DataType" value="integer">
74    </OntologyEntry>
75  </DataType_assn>
76      </SpecializedQuantitationType>
77      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:SC" name="SC" isBackground="false">
78  <Descriptions_assnlist>
79    <Description text="Spot column number in a block/grid.">
80    </Description>
81  </Descriptions_assnlist>
82  <Scale_assn>
83    <OntologyEntry category="Scale" value="unscaled">
84    </OntologyEntry>
85  </Scale_assn>
86  <DataType_assn>
87    <OntologyEntry category="DataType" value="integer">
88    </OntologyEntry>
89  </DataType_assn>
90      </SpecializedQuantitationType>
91      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:IA" name="IA" isBackground="false">
92  <Descriptions_assnlist>
93    <Description text="Spot intensity in channel A corrected for background.">
94    </Description>
95  </Descriptions_assnlist>
96  <Channel_assnref>
97    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
98  </Channel_assnref>
99  <Scale_assn>
100    <OntologyEntry category="Scale" value="linear_scale">
101    </OntologyEntry>
102  </Scale_assn>
103  <DataType_assn>
104    <OntologyEntry category="DataType" value="integer">
105    </OntologyEntry>
106  </DataType_assn>
107      </MeasuredSignal>
108      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:IB" name="IB" isBackground="false">
109  <Descriptions_assnlist>
110    <Description text="Spot intensity in channel B corrected for background.">
111    </Description>
112  </Descriptions_assnlist>
113  <Channel_assnref>
114    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
115  </Channel_assnref>
116  <Scale_assn>
117    <OntologyEntry category="Scale" value="linear_scale">
118    </OntologyEntry>
119  </Scale_assn>
120  <DataType_assn>
121    <OntologyEntry category="DataType" value="integer">
122    </OntologyEntry>
123  </DataType_assn>
124      </MeasuredSignal>
125      <Ratio identifier="TIGR:Spotfinder_QuantitationType:MeanR" name="MeanR" isBackground="false">
126  <Descriptions_assnlist>
127    <Description text="Spot mean ratio.">
128    </Description>
129  </Descriptions_assnlist>
130  <Scale_assn>
131    <OntologyEntry category="Scale" value="linear_scale">
132    </OntologyEntry>
133  </Scale_assn>
134  <DataType_assn>
135    <OntologyEntry category="DataType" value="float">
136    </OntologyEntry>
137  </DataType_assn>
138      </Ratio>
139      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:SA" name="SA" isBackground="false">
140  <Descriptions_assnlist>
141    <Description text="Spot total area in pixels.">
142    </Description>
143  </Descriptions_assnlist>
144  <Scale_assn>
145    <OntologyEntry category="Scale" value="linear_scale">
146    </OntologyEntry>
147  </Scale_assn>
148  <DataType_assn>
149    <OntologyEntry category="DataType" value="integer">
150    </OntologyEntry>
151  </DataType_assn>
152      </SpecializedQuantitationType>
153      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:Sat" name="Sat" isBackground="false">
154  <Descriptions_assnlist>
155    <Description text="Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration.">
156    </Description>
157  </Descriptions_assnlist>
158  <Scale_assn>
159    <OntologyEntry category="Scale" value="linear_scale">
160    </OntologyEntry>
161  </Scale_assn>
162  <DataType_assn>
163    <OntologyEntry category="DataType" value="float">
164    </OntologyEntry>
165  </DataType_assn>
166      </SpecializedQuantitationType>
167      <Ratio identifier="TIGR:Spotfinder_QuantitationType:MedianR" name="MedianR" isBackground="false">
168  <Descriptions_assnlist>
169    <Description text="Spot median ratio.">
170    </Description>
171  </Descriptions_assnlist>
172  <Scale_assn>
173    <OntologyEntry category="Scale" value="linear_scale">
174    </OntologyEntry>
175  </Scale_assn>
176  <DataType_assn>
177    <OntologyEntry category="DataType" value="float">
178    </OntologyEntry>
179  </DataType_assn>
180      </Ratio>
181      <Ratio identifier="TIGR:Spotfinder_QuantitationType:ModeR" name="ModeR" isBackground="false">
182  <Descriptions_assnlist>
183    <Description text="Spot mode ratio.">
184    </Description>
185  </Descriptions_assnlist>
186  <Scale_assn>
187    <OntologyEntry category="Scale" value="linear_scale">
188    </OntologyEntry>
189  </Scale_assn>
190  <DataType_assn>
191    <OntologyEntry category="DataType" value="float">
192    </OntologyEntry>
193  </DataType_assn>
194      </Ratio>
195      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:BGA" name="BGA" isBackground="true">
196  <Descriptions_assnlist>
197    <Description text="Spot background in channel A.">
198    </Description>
199  </Descriptions_assnlist>
200  <Channel_assnref>
201    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
202  </Channel_assnref>
203  <Scale_assn>
204    <OntologyEntry category="Scale" value="linear_scale">
205    </OntologyEntry>
206  </Scale_assn>
207  <DataType_assn>
208    <OntologyEntry category="DataType" value="integer">
209    </OntologyEntry>
210  </DataType_assn>
211      </MeasuredSignal>
212      <MeasuredSignal identifier="TIGR:Spotfinder_QuantitationType:BGB" name="BGB" isBackground="true">
213  <Descriptions_assnlist>
214    <Description text="Spot background in channel B.">
215    </Description>
216  </Descriptions_assnlist>
217  <Channel_assnref>
218    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
219  </Channel_assnref>
220  <Scale_assn>
221    <OntologyEntry category="Scale" value="linear_scale">
222    </OntologyEntry>
223  </Scale_assn>
224  <DataType_assn>
225    <OntologyEntry category="DataType" value="integer">
226    </OntologyEntry>
227  </DataType_assn>
228      </MeasuredSignal>
229      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:FlagA" name="FlagA" isBackground="false">
230  <Descriptions_assnlist>
231    <Description text="Spot flag in channel A. This flag is set by QC filter.">
232    </Description>
233  </Descriptions_assnlist>
234  <Channel_assnref>
235    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
236  </Channel_assnref>
237  <Scale_assn>
238    <OntologyEntry category="Scale" value="unscaled">
239    </OntologyEntry>
240  </Scale_assn>
241  <DataType_assn>
242    <OntologyEntry category="DataType" value="string_datatype">
243    </OntologyEntry>
244  </DataType_assn>
245      </SpecializedQuantitationType>
246      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:FlagB" name="FlagB" isBackground="false">
247  <Descriptions_assnlist>
248    <Description text="Spot flag in channel B. This flag is set by QC filter.">
249    </Description>
250  </Descriptions_assnlist>
251  <Channel_assnref>
252    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
253  </Channel_assnref>
254  <Scale_assn>
255    <OntologyEntry category="Scale" value="unscaled">
256    </OntologyEntry>
257  </Scale_assn>
258  <DataType_assn>
259    <OntologyEntry category="DataType" value="string_datatype">
260    </OntologyEntry>
261  </DataType_assn>
262      </SpecializedQuantitationType>
263      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:QCA" name="QCA" isBackground="false">
264  <Descriptions_assnlist>
265    <Description text="Spot QC score in channel A. This is a geometric mean of shape and S/N QC scores in channel A. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1.">
266    </Description>
267  </Descriptions_assnlist>
268  <Channel_assnref>
269    <Channel_ref identifier="ebi.ac.uk:Channel:A"/>
270  </Channel_assnref>
271  <Scale_assn>
272    <OntologyEntry category="Scale" value="linear_scale">
273    </OntologyEntry>
274  </Scale_assn>
275  <DataType_assn>
276    <OntologyEntry category="DataType" value="float">
277    </OntologyEntry>
278  </DataType_assn>
279      </SpecializedQuantitationType>
280      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:QCB" name="QCB" isBackground="false">
281  <Descriptions_assnlist>
282    <Description text="Spot QC score in channel B. This is a geometric mean of shape and S/N QC scores in channel B. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to spot perimeter scaled into the range between 0 and 1.">
283    </Description>
284  </Descriptions_assnlist>
285  <Channel_assnref>
286    <Channel_ref identifier="ebi.ac.uk:Channel:B"/>
287  </Channel_assnref>
288  <Scale_assn>
289    <OntologyEntry category="Scale" value="linear_scale">
290    </OntologyEntry>
291  </Scale_assn>
292  <DataType_assn>
293    <OntologyEntry category="DataType" value="float">
294    </OntologyEntry>
295  </DataType_assn>
296      </SpecializedQuantitationType>
297      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:QC" name="QC" isBackground="false">
298  <Descriptions_assnlist>
299    <Description text="Spot total QC score. This is a mean of QC scores in channels A and B.">
300    </Description>
301  </Descriptions_assnlist>
302  <Scale_assn>
303    <OntologyEntry category="Scale" value="linear_scale">
304    </OntologyEntry>
305  </Scale_assn>
306  <DataType_assn>
307    <OntologyEntry category="DataType" value="float">
308    </OntologyEntry>
309  </DataType_assn>
310      </SpecializedQuantitationType>
311      <SpecializedQuantitationType identifier="TIGR:Spotfinder_QuantitationType:Flag" name="Flag" isBackground="false">
312  <Descriptions_assnlist>
313    <Description text="Flag values are generated based on next conditions: A - the number of non-saturated pixels in spot is 0; B- number of non-saturated pixels in spot is between 30 and 50; C- number of non saturated pixels in spot is more then 50; S- fully or partially saturated spot, this is a warning flag. User should evaluate used spot area. X- spot was detected and rejected based on spot shape and spot intensity relative to surrounding background; Z- spot was not detected by the program; Y- spot background is higher than spot intensity.">
314    </Description>
315  </Descriptions_assnlist>
316  <Scale_assn>
317    <OntologyEntry category="Scale" value="unscaled">
318    </OntologyEntry>
319  </Scale_assn>
320  <DataType_assn>
321    <OntologyEntry category="DataType" value="string_datatype">
322    </OntologyEntry>
323  </DataType_assn>
324      </SpecializedQuantitationType>
325    </QuantitationType_assnlist>
326  </QuantitationType_package>
327</MAGE-ML>
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