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source: trunk/misc/mage/rawdatatypes/QT_ImaGene.xml @ 1938

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Last change on this file since 1938 was 1938, checked in by Nicklas Nordborg, 17 years ago
Added QuantArray? raw data types Added some intensity formulas to other raw data types Added MAGE files describing raw data types
Property svn:eol-style set to `native` Property svn:keywords set to `Date Id`
File size: 84.4 KB

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1	<?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>
2	<!DOCTYPE MAGE-ML PUBLIC "-//OMG//DTD MAGE-ML 1.0//EN" "http://schema.omg.org/lsr/gene_expression/1.0/MAGE-ML.dtd">
3	<?xml-stylesheet type="text/xsl" href="QT.xsl"?>
4	<MAGE-ML identifier="EBI:eleh:ImaGene QT XML">
5	<QuantitationType_package>
6	<QuantitationType_assnlist>
7	<SpecializedQuantitationType isBackground="0"
8	identifier="BioDiscovery:ImaGene_QuantitationType:Field"
9	name="Field">
10	<Descriptions_assnlist>
11	<Description text="Name of a field where the spot is located.">
12	</Description>
13	</Descriptions_assnlist>
14	<Scale_assn>
15	<OntologyEntry category="Scale"
16	value="unscaled">
17	</OntologyEntry>
18	</Scale_assn>
19	<DataType_assn>
20	<OntologyEntry category="DataType"
21	value="string_datatype">
22	</OntologyEntry>
23	</DataType_assn>
24	</SpecializedQuantitationType>
25	<SpecializedQuantitationType isBackground="0"
26	identifier="BioDiscovery:ImaGene_QuantitationType:Gene ID"
27	name="Gene ID">
28	<Descriptions_assnlist>
29	<Description text="Gene ID information for the spot.">
30	</Description>
31	</Descriptions_assnlist>
32	<Scale_assn>
33	<OntologyEntry category="Scale"
34	value="unscaled">
35	</OntologyEntry>
36	</Scale_assn>
37	<DataType_assn>
38	<OntologyEntry category="DataType"
39	value="string_datatype">
40	</OntologyEntry>
41	</DataType_assn>
42	</SpecializedQuantitationType>
43	<SpecializedQuantitationType isBackground="0"
44	identifier="BioDiscovery:ImaGene_QuantitationType:Flag_Cy3"
45	name="Flag_Cy3">
46	<Descriptions_assnlist>
47	<Description text="Numeric code for the spot (0 - no flag, flag codes 1,...,7).">
48	</Description>
49	</Descriptions_assnlist>
50	<Channel_assnref>
51	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
52	</Channel_assnref>
53	<Scale_assn>
54	<OntologyEntry category="Scale"
55	value="linear_scale">
56	</OntologyEntry>
57	</Scale_assn>
58	<DataType_assn>
59	<OntologyEntry category="DataType"
60	value="integer">
61	</OntologyEntry>
62	</DataType_assn>
63	</SpecializedQuantitationType>
64	<MeasuredSignal isBackground="0"
65	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Mean_Cy3"
66	name="Signal Mean_Cy3">
67	<Descriptions_assnlist>
68	<Description text="Pixel intensity averaged over the local signal region.">
69	</Description>
70	</Descriptions_assnlist>
71	<Channel_assnref>
72	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
73	</Channel_assnref>
74	<Scale_assn>
75	<OntologyEntry category="Scale"
76	value="linear_scale">
77	</OntologyEntry>
78	</Scale_assn>
79	<DataType_assn>
80	<OntologyEntry category="DataType"
81	value="float">
82	</OntologyEntry>
83	</DataType_assn>
84	<ConfidenceIndicators_assnreflist>
85	<Error_ref identifier="BioDiscovery:ImaGene_QuantitationType:Signal Stdev_Cy3"/>
86	</ConfidenceIndicators_assnreflist>
87	</MeasuredSignal>
88	<Error isBackground="0"
89	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Stdev_Cy3"
90	name="Signal Stdev_Cy3">
91	<Descriptions_assnlist>
92	<Description text="Standard deviation of pixel intensities over the local signal region.">
93	</Description>
94	</Descriptions_assnlist>
95	<Channel_assnref>
96	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
97	</Channel_assnref>
98	<Scale_assn>
99	<OntologyEntry category="Scale"
100	value="linear_scale">
101	</OntologyEntry>
102	</Scale_assn>
103	<DataType_assn>
104	<OntologyEntry category="DataType"
105	value="float">
106	</OntologyEntry>
107	</DataType_assn>
108	<TargetQuantitationType_assnref>
109	<MeasuredSignal_ref identifier="BioDiscovery:ImaGene_QuantitationType:Signal Mean_Cy3"/>
110	</TargetQuantitationType_assnref>
111	</Error>
112	<MeasuredSignal isBackground="1"
113	identifier="BioDiscovery:ImaGene_QuantitationType:Background Mean_Cy3"
114	name="Background Mean_Cy3">
115	<Descriptions_assnlist>
116	<Description text="Pixel intensity averaged over the local background region.">
117	</Description>
118	</Descriptions_assnlist>
119	<Channel_assnref>
120	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
121	</Channel_assnref>
122	<Scale_assn>
123	<OntologyEntry category="Scale"
124	value="linear_scale">
125	</OntologyEntry>
126	</Scale_assn>
127	<DataType_assn>
128	<OntologyEntry category="DataType"
129	value="float">
130	</OntologyEntry>
131	</DataType_assn>
132	<ConfidenceIndicators_assnreflist>
133	<Error_ref identifier="BioDiscovery:ImaGene_QuantitationType:Background Stdev_Cy3"/>
134	</ConfidenceIndicators_assnreflist>
135	</MeasuredSignal>
136	<Error isBackground="1"
137	identifier="BioDiscovery:ImaGene_QuantitationType:Background Stdev_Cy3"
138	name="Background Stdev_Cy3">
139	<Descriptions_assnlist>
140	<Description text="Standard deviation of pixel intensities over the local background region.">
141	</Description>
142	</Descriptions_assnlist>
143	<Channel_assnref>
144	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
145	</Channel_assnref>
146	<Scale_assn>
147	<OntologyEntry category="Scale"
148	value="linear_scale">
149	</OntologyEntry>
150	</Scale_assn>
151	<DataType_assn>
152	<OntologyEntry category="DataType"
153	value="float">
154	</OntologyEntry>
155	</DataType_assn>
156	<TargetQuantitationType_assnref>
157	<MeasuredSignal_ref identifier="BioDiscovery:ImaGene_QuantitationType:Background Mean_Cy3"/>
158	</TargetQuantitationType_assnref>
159	</Error>
160	<SpecializedQuantitationType isBackground="0"
161	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Median_Cy3"
162	name="Signal Median_Cy3">
163	<Descriptions_assnlist>
164	<Description text="Median pixel intensity computed over the local signal region.">
165	</Description>
166	</Descriptions_assnlist>
167	<Channel_assnref>
168	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
169	</Channel_assnref>
170	<Scale_assn>
171	<OntologyEntry category="Scale"
172	value="linear_scale">
173	</OntologyEntry>
174	</Scale_assn>
175	<DataType_assn>
176	<OntologyEntry category="DataType"
177	value="float">
178	</OntologyEntry>
179	</DataType_assn>
180	</SpecializedQuantitationType>
181	<SpecializedQuantitationType isBackground="1"
182	identifier="BioDiscovery:ImaGene_QuantitationType:Background Median_Cy3"
183	name="Background Median_Cy3">
184	<Descriptions_assnlist>
185	<Description text="Median pixel intensity computed over the local background region.">
186	</Description>
187	</Descriptions_assnlist>
188	<Channel_assnref>
189	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
190	</Channel_assnref>
191	<Scale_assn>
192	<OntologyEntry category="Scale"
193	value="linear_scale">
194	</OntologyEntry>
195	</Scale_assn>
196	<DataType_assn>
197	<OntologyEntry category="DataType"
198	value="float">
199	</OntologyEntry>
200	</DataType_assn>
201	</SpecializedQuantitationType>
202	<SpecializedQuantitationType isBackground="0"
203	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Mode_Cy3"
204	name="Signal Mode_Cy3">
205	<Descriptions_assnlist>
206	<Description text="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution).">
207	</Description>
208	</Descriptions_assnlist>
209	<Channel_assnref>
210	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
211	</Channel_assnref>
212	<Scale_assn>
213	<OntologyEntry category="Scale"
214	value="linear_scale">
215	</OntologyEntry>
216	</Scale_assn>
217	<DataType_assn>
218	<OntologyEntry category="DataType"
219	value="float">
220	</OntologyEntry>
221	</DataType_assn>
222	</SpecializedQuantitationType>
223	<SpecializedQuantitationType isBackground="1"
224	identifier="BioDiscovery:ImaGene_QuantitationType:Background Mode_Cy3"
225	name="Background Mode_Cy3">
226	<Descriptions_assnlist>
227	<Description text="Mode pixel intensity computed over the local background region.">
228	</Description>
229	</Descriptions_assnlist>
230	<Channel_assnref>
231	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
232	</Channel_assnref>
233	<Scale_assn>
234	<OntologyEntry category="Scale"
235	value="linear_scale">
236	</OntologyEntry>
237	</Scale_assn>
238	<DataType_assn>
239	<OntologyEntry category="DataType"
240	value="float">
241	</OntologyEntry>
242	</DataType_assn>
243	</SpecializedQuantitationType>
244	<SpecializedQuantitationType isBackground="0"
245	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Area_Cy3"
246	name="Signal Area_Cy3">
247	<Descriptions_assnlist>
248	<Description text="Number of pixels in the local signal region.">
249	</Description>
250	</Descriptions_assnlist>
251	<Channel_assnref>
252	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
253	</Channel_assnref>
254	<Scale_assn>
255	<OntologyEntry category="Scale"
256	value="linear_scale">
257	</OntologyEntry>
258	</Scale_assn>
259	<DataType_assn>
260	<OntologyEntry category="DataType"
261	value="integer">
262	</OntologyEntry>
263	</DataType_assn>
264	</SpecializedQuantitationType>
265	<SpecializedQuantitationType isBackground="1"
266	identifier="BioDiscovery:ImaGene_QuantitationType:Background Area_Cy3"
267	name="Background Area_Cy3">
268	<Descriptions_assnlist>
269	<Description text="Number of pixels in the local background region.">
270	</Description>
271	</Descriptions_assnlist>
272	<Channel_assnref>
273	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
274	</Channel_assnref>
275	<Scale_assn>
276	<OntologyEntry category="Scale"
277	value="linear_scale">
278	</OntologyEntry>
279	</Scale_assn>
280	<DataType_assn>
281	<OntologyEntry category="DataType"
282	value="integer">
283	</OntologyEntry>
284	</DataType_assn>
285	</SpecializedQuantitationType>
286	<SpecializedQuantitationType isBackground="0"
287	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Total_Cy3"
288	name="Signal Total_Cy3">
289	<Descriptions_assnlist>
290	<Description text="Total pixel intensity summed over the local signal region.">
291	</Description>
292	</Descriptions_assnlist>
293	<Channel_assnref>
294	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
295	</Channel_assnref>
296	<Scale_assn>
297	<OntologyEntry category="Scale"
298	value="linear_scale">
299	</OntologyEntry>
300	</Scale_assn>
301	<DataType_assn>
302	<OntologyEntry category="DataType"
303	value="integer">
304	</OntologyEntry>
305	</DataType_assn>
306	</SpecializedQuantitationType>
307	<SpecializedQuantitationType isBackground="1"
308	identifier="BioDiscovery:ImaGene_QuantitationType:Background Total_Cy3"
309	name="Background Total_Cy3">
310	<Descriptions_assnlist>
311	<Description text="Total pixel intensity summed over the local background region.">
312	</Description>
313	</Descriptions_assnlist>
314	<Channel_assnref>
315	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
316	</Channel_assnref>
317	<Scale_assn>
318	<OntologyEntry category="Scale"
319	value="linear_scale">
320	</OntologyEntry>
321	</Scale_assn>
322	<DataType_assn>
323	<OntologyEntry category="DataType"
324	value="integer">
325	</OntologyEntry>
326	</DataType_assn>
327	</SpecializedQuantitationType>
328	<SpecializedQuantitationType isBackground="0"
329	identifier="BioDiscovery:ImaGene_QuantitationType:Shape Regularity_Cy3"
330	name="Shape Regularity_Cy3">
331	<Descriptions_assnlist>
332	<Description text="The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity.">
333	</Description>
334	</Descriptions_assnlist>
335	<Channel_assnref>
336	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
337	</Channel_assnref>
338	<Scale_assn>
339	<OntologyEntry category="Scale"
340	value="linear_scale">
341	</OntologyEntry>
342	</Scale_assn>
343	<DataType_assn>
344	<OntologyEntry category="DataType"
345	value="float">
346	</OntologyEntry>
347	</DataType_assn>
348	</SpecializedQuantitationType>
349	<SpecializedQuantitationType isBackground="0"
350	identifier="BioDiscovery:ImaGene_QuantitationType:Ignored Area_Cy3"
351	name="Ignored Area_Cy3">
352	<Descriptions_assnlist>
353	<Description text="Area of ignored regions directly neighboring ("touching") the signal area is computed.">
354	</Description>
355	</Descriptions_assnlist>
356	<Channel_assnref>
357	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
358	</Channel_assnref>
359	<Scale_assn>
360	<OntologyEntry category="Scale"
361	value="linear_scale">
362	</OntologyEntry>
363	</Scale_assn>
364	<DataType_assn>
365	<OntologyEntry category="DataType"
366	value="integer">
367	</OntologyEntry>
368	</DataType_assn>
369	</SpecializedQuantitationType>
370	<SpecializedQuantitationType isBackground="0"
371	identifier="BioDiscovery:ImaGene_QuantitationType:Spot Area_Cy3"
372	name="Spot Area_Cy3">
373	<Descriptions_assnlist>
374	<Description text="Signal Area plus Ignored Area.">
375	</Description>
376	</Descriptions_assnlist>
377	<Channel_assnref>
378	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
379	</Channel_assnref>
380	<Scale_assn>
381	<OntologyEntry category="Scale"
382	value="linear_scale">
383	</OntologyEntry>
384	</Scale_assn>
385	<DataType_assn>
386	<OntologyEntry category="DataType"
387	value="integer">
388	</OntologyEntry>
389	</DataType_assn>
390	</SpecializedQuantitationType>
391	<SpecializedQuantitationType isBackground="0"
392	identifier="BioDiscovery:ImaGene_QuantitationType:Ignored Median_Cy3"
393	name="Ignored Median_Cy3">
394	<Descriptions_assnlist>
395	<Description text="Median pixel intensity computed over the local ignored region.">
396	</Description>
397	</Descriptions_assnlist>
398	<Channel_assnref>
399	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
400	</Channel_assnref>
401	<Scale_assn>
402	<OntologyEntry category="Scale"
403	value="linear_scale">
404	</OntologyEntry>
405	</Scale_assn>
406	<DataType_assn>
407	<OntologyEntry category="DataType"
408	value="float">
409	</OntologyEntry>
410	</DataType_assn>
411	</SpecializedQuantitationType>
412	<SpecializedQuantitationType isBackground="0"
413	identifier="BioDiscovery:ImaGene_QuantitationType:Area To Perimeter_Cy3"
414	name="Area To Perimeter_Cy3">
415	<Descriptions_assnlist>
416	<Description text="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle).">
417	</Description>
418	</Descriptions_assnlist>
419	<Channel_assnref>
420	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
421	</Channel_assnref>
422	<Scale_assn>
423	<OntologyEntry category="Scale"
424	value="linear_scale">
425	</OntologyEntry>
426	</Scale_assn>
427	<DataType_assn>
428	<OntologyEntry category="DataType"
429	value="float">
430	</OntologyEntry>
431	</DataType_assn>
432	</SpecializedQuantitationType>
433	<SpecializedQuantitationType isBackground="0"
434	identifier="BioDiscovery:ImaGene_QuantitationType:Open Perimeter_Cy3"
435	name="Open Perimeter_Cy3">
436	<Descriptions_assnlist>
437	<Description text="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot.">
438	</Description>
439	</Descriptions_assnlist>
440	<Channel_assnref>
441	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
442	</Channel_assnref>
443	<Scale_assn>
444	<OntologyEntry category="Scale"
445	value="linear_scale">
446	</OntologyEntry>
447	</Scale_assn>
448	<DataType_assn>
449	<OntologyEntry category="DataType"
450	value="float">
451	</OntologyEntry>
452	</DataType_assn>
453	</SpecializedQuantitationType>
454	<SpecializedQuantitationType isBackground="0"
455	identifier="BioDiscovery:ImaGene_QuantitationType:XCoord_Cy3"
456	name="XCoord_Cy3">
457	<Descriptions_assnlist>
458	<Description text="X coordinate (in pixels) of grid circle corresponding to the spot.">
459	</Description>
460	</Descriptions_assnlist>
461	<Channel_assnref>
462	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
463	</Channel_assnref>
464	<Scale_assn>
465	<OntologyEntry category="Scale"
466	value="linear_scale">
467	</OntologyEntry>
468	</Scale_assn>
469	<DataType_assn>
470	<OntologyEntry category="DataType"
471	value="float">
472	</OntologyEntry>
473	</DataType_assn>
474	</SpecializedQuantitationType>
475	<SpecializedQuantitationType isBackground="0"
476	identifier="BioDiscovery:ImaGene_QuantitationType:YCoord_Cy3"
477	name="YCoord_Cy3">
478	<Descriptions_assnlist>
479	<Description text="Y coordinate (in pixels) of grid circle corresponding to the spot.">
480	</Description>
481	</Descriptions_assnlist>
482	<Channel_assnref>
483	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
484	</Channel_assnref>
485	<Scale_assn>
486	<OntologyEntry category="Scale"
487	value="linear_scale">
488	</OntologyEntry>
489	</Scale_assn>
490	<DataType_assn>
491	<OntologyEntry category="DataType"
492	value="float">
493	</OntologyEntry>
494	</DataType_assn>
495	</SpecializedQuantitationType>
496	<SpecializedQuantitationType isBackground="0"
497	identifier="BioDiscovery:ImaGene_QuantitationType:Diameter_Cy3"
498	name="Diameter_Cy3">
499	<Descriptions_assnlist>
500	<Description text="Diameter (in pixels) of grid circle corresponding to the spot.">
501	</Description>
502	</Descriptions_assnlist>
503	<Channel_assnref>
504	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
505	</Channel_assnref>
506	<Scale_assn>
507	<OntologyEntry category="Scale"
508	value="linear_scale">
509	</OntologyEntry>
510	</Scale_assn>
511	<DataType_assn>
512	<OntologyEntry category="DataType"
513	value="integer">
514	</OntologyEntry>
515	</DataType_assn>
516	</SpecializedQuantitationType>
517	<SpecializedQuantitationType isBackground="0"
518	identifier="BioDiscovery:ImaGene_QuantitationType:Position offset_Cy3"
519	name="Position offset_Cy3">
520	<Descriptions_assnlist>
521	<Description text="Offset (in pixels) of the center of the grid circle from the expected position in the grid.">
522	</Description>
523	</Descriptions_assnlist>
524	<Channel_assnref>
525	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
526	</Channel_assnref>
527	<Scale_assn>
528	<OntologyEntry category="Scale"
529	value="linear_scale">
530	</OntologyEntry>
531	</Scale_assn>
532	<DataType_assn>
533	<OntologyEntry category="DataType"
534	value="float">
535	</OntologyEntry>
536	</DataType_assn>
537	</SpecializedQuantitationType>
538	<SpecializedQuantitationType isBackground="0"
539	identifier="BioDiscovery:ImaGene_QuantitationType:Offset X_Cy3"
540	name="Offset X_Cy3">
541	<Descriptions_assnlist>
542	<Description text="X Offset (in pixels) of the center of the grid circle from the expected position in the grid.">
543	</Description>
544	</Descriptions_assnlist>
545	<Channel_assnref>
546	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
547	</Channel_assnref>
548	<Scale_assn>
549	<OntologyEntry category="Scale"
550	value="linear_scale">
551	</OntologyEntry>
552	</Scale_assn>
553	<DataType_assn>
554	<OntologyEntry category="DataType"
555	value="float">
556	</OntologyEntry>
557	</DataType_assn>
558	</SpecializedQuantitationType>
559	<SpecializedQuantitationType isBackground="0"
560	identifier="BioDiscovery:ImaGene_QuantitationType:Offset Y_Cy3"
561	name="Offset Y_Cy3">
562	<Descriptions_assnlist>
563	<Description text="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid.">
564	</Description>
565	</Descriptions_assnlist>
566	<Channel_assnref>
567	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
568	</Channel_assnref>
569	<Scale_assn>
570	<OntologyEntry category="Scale"
571	value="linear_scale">
572	</OntologyEntry>
573	</Scale_assn>
574	<DataType_assn>
575	<OntologyEntry category="DataType"
576	value="float">
577	</OntologyEntry>
578	</DataType_assn>
579	</SpecializedQuantitationType>
580	<SpecializedQuantitationType isBackground="0"
581	identifier="BioDiscovery:ImaGene_QuantitationType:Expected X_Cy3"
582	name="Expected X_Cy3">
583	<Descriptions_assnlist>
584	<Description text="X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.">
585	</Description>
586	</Descriptions_assnlist>
587	<Channel_assnref>
588	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
589	</Channel_assnref>
590	<Scale_assn>
591	<OntologyEntry category="Scale"
592	value="linear_scale">
593	</OntologyEntry>
594	</Scale_assn>
595	<DataType_assn>
596	<OntologyEntry category="DataType"
597	value="float">
598	</OntologyEntry>
599	</DataType_assn>
600	</SpecializedQuantitationType>
601	<SpecializedQuantitationType isBackground="0"
602	identifier="BioDiscovery:ImaGene_QuantitationType:Expected Y_Cy3"
603	name="Expected Y_Cy3">
604	<Descriptions_assnlist>
605	<Description text="Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.">
606	</Description>
607	</Descriptions_assnlist>
608	<Channel_assnref>
609	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
610	</Channel_assnref>
611	<Scale_assn>
612	<OntologyEntry category="Scale"
613	value="linear_scale">
614	</OntologyEntry>
615	</Scale_assn>
616	<DataType_assn>
617	<OntologyEntry category="DataType"
618	value="float">
619	</OntologyEntry>
620	</DataType_assn>
621	</SpecializedQuantitationType>
622	<SpecializedQuantitationType isBackground="0"
623	identifier="BioDiscovery:ImaGene_QuantitationType:CM-X_Cy3"
624	name="CM-X_Cy3">
625	<Descriptions_assnlist>
626	<Description text="X coordinate of the center of the mass of spot's signal region.">
627	</Description>
628	</Descriptions_assnlist>
629	<Channel_assnref>
630	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
631	</Channel_assnref>
632	<Scale_assn>
633	<OntologyEntry category="Scale"
634	value="linear_scale">
635	</OntologyEntry>
636	</Scale_assn>
637	<DataType_assn>
638	<OntologyEntry category="DataType"
639	value="float">
640	</OntologyEntry>
641	</DataType_assn>
642	</SpecializedQuantitationType>
643	<SpecializedQuantitationType isBackground="0"
644	identifier="BioDiscovery:ImaGene_QuantitationType:CM-Y_Cy3"
645	name="CM-Y_Cy3">
646	<Descriptions_assnlist>
647	<Description text="Y coordinate of the center of the mass of spot's signal region.">
648	</Description>
649	</Descriptions_assnlist>
650	<Channel_assnref>
651	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
652	</Channel_assnref>
653	<Scale_assn>
654	<OntologyEntry category="Scale"
655	value="linear_scale">
656	</OntologyEntry>
657	</Scale_assn>
658	<DataType_assn>
659	<OntologyEntry category="DataType"
660	value="float">
661	</OntologyEntry>
662	</DataType_assn>
663	</SpecializedQuantitationType>
664	<SpecializedQuantitationType isBackground="0"
665	identifier="BioDiscovery:ImaGene_QuantitationType:CM Offset_Cy3"
666	name="CM Offset_Cy3">
667	<Descriptions_assnlist>
668	<Description text="Offset (in pixels) of the spot's center of the mass from the expected position in the grid.">
669	</Description>
670	</Descriptions_assnlist>
671	<Channel_assnref>
672	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
673	</Channel_assnref>
674	<Scale_assn>
675	<OntologyEntry category="Scale"
676	value="linear_scale">
677	</OntologyEntry>
678	</Scale_assn>
679	<DataType_assn>
680	<OntologyEntry category="DataType"
681	value="float">
682	</OntologyEntry>
683	</DataType_assn>
684	</SpecializedQuantitationType>
685	<SpecializedQuantitationType isBackground="0"
686	identifier="BioDiscovery:ImaGene_QuantitationType:CM Offset-X_Cy3"
687	name="CM Offset-X_Cy3">
688	<Descriptions_assnlist>
689	<Description text="X offset (in pixels) of the spot's center of the mass from the expected position in the grid.">
690	</Description>
691	</Descriptions_assnlist>
692	<Channel_assnref>
693	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
694	</Channel_assnref>
695	<Scale_assn>
696	<OntologyEntry category="Scale"
697	value="linear_scale">
698	</OntologyEntry>
699	</Scale_assn>
700	<DataType_assn>
701	<OntologyEntry category="DataType"
702	value="float">
703	</OntologyEntry>
704	</DataType_assn>
705	</SpecializedQuantitationType>
706	<SpecializedQuantitationType isBackground="0"
707	identifier="BioDiscovery:ImaGene_QuantitationType:CM Offset-Y_Cy3"
708	name="CM Offset-Y_Cy3">
709	<Descriptions_assnlist>
710	<Description text="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid.">
711	</Description>
712	</Descriptions_assnlist>
713	<Channel_assnref>
714	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
715	</Channel_assnref>
716	<Scale_assn>
717	<OntologyEntry category="Scale"
718	value="linear_scale">
719	</OntologyEntry>
720	</Scale_assn>
721	<DataType_assn>
722	<OntologyEntry category="DataType"
723	value="float">
724	</OntologyEntry>
725	</DataType_assn>
726	</SpecializedQuantitationType>
727	<SpecializedQuantitationType isBackground="0"
728	identifier="BioDiscovery:ImaGene_QuantitationType:Min Diam_Cy3"
729	name="Min Diam_Cy3">
730	<Descriptions_assnlist>
731	<Description text="Diameter of the circle inscribed into the spot's signal region.">
732	</Description>
733	</Descriptions_assnlist>
734	<Channel_assnref>
735	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
736	</Channel_assnref>
737	<Scale_assn>
738	<OntologyEntry category="Scale"
739	value="linear_scale">
740	</OntologyEntry>
741	</Scale_assn>
742	<DataType_assn>
743	<OntologyEntry category="DataType"
744	value="float">
745	</OntologyEntry>
746	</DataType_assn>
747	</SpecializedQuantitationType>
748	<SpecializedQuantitationType isBackground="0"
749	identifier="BioDiscovery:ImaGene_QuantitationType:Max Diam_Cy3"
750	name="Max Diam_Cy3">
751	<Descriptions_assnlist>
752	<Description text="Diameter of the circle, the spot's signal region can be inscribed in.">
753	</Description>
754	</Descriptions_assnlist>
755	<Channel_assnref>
756	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
757	</Channel_assnref>
758	<Scale_assn>
759	<OntologyEntry category="Scale"
760	value="linear_scale">
761	</OntologyEntry>
762	</Scale_assn>
763	<DataType_assn>
764	<OntologyEntry category="DataType"
765	value="float">
766	</OntologyEntry>
767	</DataType_assn>
768	</SpecializedQuantitationType>
769	<SpecializedQuantitationType isBackground="0"
770	identifier="BioDiscovery:ImaGene_QuantitationType:Control_Cy3"
771	name="Control_Cy3">
772	<Descriptions_assnlist>
773	<Description text="Name of a control type for current spot (no name means the spot is not a control spot).">
774	</Description>
775	</Descriptions_assnlist>
776	<Channel_assnref>
777	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
778	</Channel_assnref>
779	<Scale_assn>
780	<OntologyEntry category="Scale"
781	value="unscaled">
782	</OntologyEntry>
783	</Scale_assn>
784	<DataType_assn>
785	<OntologyEntry category="DataType"
786	value="string_datatype">
787	</OntologyEntry>
788	</DataType_assn>
789	</SpecializedQuantitationType>
790	<SpecializedQuantitationType isBackground="0"
791	identifier="BioDiscovery:ImaGene_QuantitationType:Failed Control_Cy3"
792	name="Failed Control_Cy3">
793	<Descriptions_assnlist>
794	<Description text="0 if the control passed all tests, 1 if at least one of the tests failed.">
795	</Description>
796	</Descriptions_assnlist>
797	<Channel_assnref>
798	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
799	</Channel_assnref>
800	<Scale_assn>
801	<OntologyEntry category="Scale"
802	value="linear_scale">
803	</OntologyEntry>
804	</Scale_assn>
805	<DataType_assn>
806	<OntologyEntry category="DataType"
807	value="boolean">
808	</OntologyEntry>
809	</DataType_assn>
810	</SpecializedQuantitationType>
811	<SpecializedQuantitationType isBackground="0"
812	identifier="BioDiscovery:ImaGene_QuantitationType:Background contamination present_Cy3"
813	name="Background contamination present_Cy3">
814	<Descriptions_assnlist>
815	<Description text="0 if the spot passed background contamination test, 1 if it did not.">
816	</Description>
817	</Descriptions_assnlist>
818	<Channel_assnref>
819	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
820	</Channel_assnref>
821	<Scale_assn>
822	<OntologyEntry category="Scale"
823	value="linear_scale">
824	</OntologyEntry>
825	</Scale_assn>
826	<DataType_assn>
827	<OntologyEntry category="DataType"
828	value="boolean">
829	</OntologyEntry>
830	</DataType_assn>
831	</SpecializedQuantitationType>
832	<SpecializedQuantitationType isBackground="0"
833	identifier="BioDiscovery:ImaGene_QuantitationType:Signal contamination present_Cy3"
834	name="Signal contamination present_Cy3">
835	<Descriptions_assnlist>
836	<Description text="0 if the spot passed signal contamination test, 1 if it did not.">
837	</Description>
838	</Descriptions_assnlist>
839	<Channel_assnref>
840	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
841	</Channel_assnref>
842	<Scale_assn>
843	<OntologyEntry category="Scale"
844	value="linear_scale">
845	</OntologyEntry>
846	</Scale_assn>
847	<DataType_assn>
848	<OntologyEntry category="DataType"
849	value="boolean">
850	</OntologyEntry>
851	</DataType_assn>
852	</SpecializedQuantitationType>
853	<SpecializedQuantitationType isBackground="0"
854	identifier="BioDiscovery:ImaGene_QuantitationType:Ignored % failed_Cy3"
855	name="Ignored % failed_Cy3">
856	<Descriptions_assnlist>
857	<Description text="0 if the spot passed ignored percentage test, 1 if it did not.">
858	</Description>
859	</Descriptions_assnlist>
860	<Channel_assnref>
861	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
862	</Channel_assnref>
863	<Scale_assn>
864	<OntologyEntry category="Scale"
865	value="linear_scale">
866	</OntologyEntry>
867	</Scale_assn>
868	<DataType_assn>
869	<OntologyEntry category="DataType"
870	value="boolean">
871	</OntologyEntry>
872	</DataType_assn>
873	</SpecializedQuantitationType>
874	<SpecializedQuantitationType isBackground="0"
875	identifier="BioDiscovery:ImaGene_QuantitationType:Open perimeter failed_Cy3"
876	name="Open perimeter failed_Cy3">
877	<Descriptions_assnlist>
878	<Description text="0 if the spot passed open perimeter test, 1 if it did not.">
879	</Description>
880	</Descriptions_assnlist>
881	<Channel_assnref>
882	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
883	</Channel_assnref>
884	<Scale_assn>
885	<OntologyEntry category="Scale"
886	value="linear_scale">
887	</OntologyEntry>
888	</Scale_assn>
889	<DataType_assn>
890	<OntologyEntry category="DataType"
891	value="boolean">
892	</OntologyEntry>
893	</DataType_assn>
894	</SpecializedQuantitationType>
895	<SpecializedQuantitationType isBackground="0"
896	identifier="BioDiscovery:ImaGene_QuantitationType:Shape regularity failed_Cy3"
897	name="Shape regularity failed_Cy3">
898	<Descriptions_assnlist>
899	<Description text="0 if the spot passed shape regularity test, 1 if it did not.">
900	</Description>
901	</Descriptions_assnlist>
902	<Channel_assnref>
903	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
904	</Channel_assnref>
905	<Scale_assn>
906	<OntologyEntry category="Scale"
907	value="linear_scale">
908	</OntologyEntry>
909	</Scale_assn>
910	<DataType_assn>
911	<OntologyEntry category="DataType"
912	value="boolean">
913	</OntologyEntry>
914	</DataType_assn>
915	</SpecializedQuantitationType>
916	<SpecializedQuantitationType isBackground="0"
917	identifier="BioDiscovery:ImaGene_QuantitationType:Perim-to-area failed_Cy3"
918	name="Perim-to-area failed_Cy3">
919	<Descriptions_assnlist>
920	<Description text="0 if the spot passed perimeter-to-area test, 1 if it did not.">
921	</Description>
922	</Descriptions_assnlist>
923	<Channel_assnref>
924	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
925	</Channel_assnref>
926	<Scale_assn>
927	<OntologyEntry category="Scale"
928	value="linear_scale">
929	</OntologyEntry>
930	</Scale_assn>
931	<DataType_assn>
932	<OntologyEntry category="DataType"
933	value="boolean">
934	</OntologyEntry>
935	</DataType_assn>
936	</SpecializedQuantitationType>
937	<SpecializedQuantitationType isBackground="0"
938	identifier="BioDiscovery:ImaGene_QuantitationType:Offset failed_Cy3"
939	name="Offset failed_Cy3">
940	<Descriptions_assnlist>
941	<Description text="0 if the spot passed offset test, 1 if it did not.">
942	</Description>
943	</Descriptions_assnlist>
944	<Channel_assnref>
945	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
946	</Channel_assnref>
947	<Scale_assn>
948	<OntologyEntry category="Scale"
949	value="linear_scale">
950	</OntologyEntry>
951	</Scale_assn>
952	<DataType_assn>
953	<OntologyEntry category="DataType"
954	value="boolean">
955	</OntologyEntry>
956	</DataType_assn>
957	</SpecializedQuantitationType>
958	<SpecializedQuantitationType isBackground="0"
959	identifier="BioDiscovery:ImaGene_QuantitationType:Empty spot_Cy3"
960	name="Empty spot_Cy3">
961	<Descriptions_assnlist>
962	<Description text="0 if the spot passed offset test, 1 if it did not.">
963	</Description>
964	</Descriptions_assnlist>
965	<Channel_assnref>
966	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
967	</Channel_assnref>
968	<Scale_assn>
969	<OntologyEntry category="Scale"
970	value="linear_scale">
971	</OntologyEntry>
972	</Scale_assn>
973	<DataType_assn>
974	<OntologyEntry category="DataType"
975	value="boolean">
976	</OntologyEntry>
977	</DataType_assn>
978	</SpecializedQuantitationType>
979	<SpecializedQuantitationType isBackground="0"
980	identifier="BioDiscovery:ImaGene_QuantitationType:Negative spot_Cy3"
981	name="Negative spot_Cy3">
982	<Descriptions_assnlist>
983	<Description text="1 if the spot was qualified as negative, 0 if it was not.">
984	</Description>
985	</Descriptions_assnlist>
986	<Channel_assnref>
987	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
988	</Channel_assnref>
989	<Scale_assn>
990	<OntologyEntry category="Scale"
991	value="linear_scale">
992	</OntologyEntry>
993	</Scale_assn>
994	<DataType_assn>
995	<OntologyEntry category="DataType"
996	value="boolean">
997	</OntologyEntry>
998	</DataType_assn>
999	</SpecializedQuantitationType>
1000	<SpecializedQuantitationType isBackground="0"
1001	identifier="BioDiscovery:ImaGene_QuantitationType:Selected spot_Cy3"
1002	name="Selected spot_Cy3">
1003	<Descriptions_assnlist>
1004	<Description text="1 if the spot was selected in the software view at time of save, 0 if not.">
1005	</Description>
1006	</Descriptions_assnlist>
1007	<Channel_assnref>
1008	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
1009	</Channel_assnref>
1010	<Scale_assn>
1011	<OntologyEntry category="Scale"
1012	value="linear_scale">
1013	</OntologyEntry>
1014	</Scale_assn>
1015	<DataType_assn>
1016	<OntologyEntry category="DataType"
1017	value="boolean">
1018	</OntologyEntry>
1019	</DataType_assn>
1020	</SpecializedQuantitationType>
1021	<SpecializedQuantitationType isBackground="0"
1022	identifier="BioDiscovery:ImaGene_QuantitationType:Saturated spot_Cy3"
1023	name="Saturated spot_Cy3">
1024	<Descriptions_assnlist>
1025	<Description text="1 if the spot was qualified as saturated, 0 if it was not.">
1026	</Description>
1027	</Descriptions_assnlist>
1028	<Channel_assnref>
1029	<Channel_ref identifier="ebi.ac.uk:Channel:Cy3"/>
1030	</Channel_assnref>
1031	<Scale_assn>
1032	<OntologyEntry category="Scale"
1033	value="linear_scale">
1034	</OntologyEntry>
1035	</Scale_assn>
1036	<DataType_assn>
1037	<OntologyEntry category="DataType"
1038	value="boolean">
1039	</OntologyEntry>
1040	</DataType_assn>
1041	</SpecializedQuantitationType>
1042	<SpecializedQuantitationType isBackground="0"
1043	identifier="BioDiscovery:ImaGene_QuantitationType:Flag_Cy5"
1044	name="Flag_Cy5">
1045	<Descriptions_assnlist>
1046	<Description text="Numeric code for the spot (0 - no flag, flag codes 1,...,7).">
1047	</Description>
1048	</Descriptions_assnlist>
1049	<Channel_assnref>
1050	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1051	</Channel_assnref>
1052	<Scale_assn>
1053	<OntologyEntry category="Scale"
1054	value="linear_scale">
1055	</OntologyEntry>
1056	</Scale_assn>
1057	<DataType_assn>
1058	<OntologyEntry category="DataType"
1059	value="integer">
1060	</OntologyEntry>
1061	</DataType_assn>
1062	</SpecializedQuantitationType>
1063	<MeasuredSignal isBackground="0"
1064	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Mean_Cy5"
1065	name="Signal Mean_Cy5">
1066	<Descriptions_assnlist>
1067	<Description text="Pixel intensity averaged over the local signal region.">
1068	</Description>
1069	</Descriptions_assnlist>
1070	<Channel_assnref>
1071	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1072	</Channel_assnref>
1073	<Scale_assn>
1074	<OntologyEntry category="Scale"
1075	value="linear_scale">
1076	</OntologyEntry>
1077	</Scale_assn>
1078	<DataType_assn>
1079	<OntologyEntry category="DataType"
1080	value="float">
1081	</OntologyEntry>
1082	</DataType_assn>
1083	<ConfidenceIndicators_assnreflist>
1084	<Error_ref identifier="BioDiscovery:ImaGene_QuantitationType:Signal Stdev_Cy5"/>
1085	</ConfidenceIndicators_assnreflist>
1086	</MeasuredSignal>
1087	<Error isBackground="0"
1088	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Stdev_Cy5"
1089	name="Signal Stdev_Cy5">
1090	<Descriptions_assnlist>
1091	<Description text="Standard deviation of pixel intensities over the local signal region.">
1092	</Description>
1093	</Descriptions_assnlist>
1094	<Channel_assnref>
1095	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1096	</Channel_assnref>
1097	<Scale_assn>
1098	<OntologyEntry category="Scale"
1099	value="linear_scale">
1100	</OntologyEntry>
1101	</Scale_assn>
1102	<DataType_assn>
1103	<OntologyEntry category="DataType"
1104	value="float">
1105	</OntologyEntry>
1106	</DataType_assn>
1107	<TargetQuantitationType_assnref>
1108	<MeasuredSignal_ref identifier="BioDiscovery:ImaGene_QuantitationType:Signal Mean_Cy5"/>
1109	</TargetQuantitationType_assnref>
1110	</Error>
1111	<MeasuredSignal isBackground="1"
1112	identifier="BioDiscovery:ImaGene_QuantitationType:Background Mean_Cy5"
1113	name="Background Mean_Cy5">
1114	<Descriptions_assnlist>
1115	<Description text="Pixel intensity averaged over the local background region.">
1116	</Description>
1117	</Descriptions_assnlist>
1118	<Channel_assnref>
1119	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1120	</Channel_assnref>
1121	<Scale_assn>
1122	<OntologyEntry category="Scale"
1123	value="linear_scale">
1124	</OntologyEntry>
1125	</Scale_assn>
1126	<DataType_assn>
1127	<OntologyEntry category="DataType"
1128	value="float">
1129	</OntologyEntry>
1130	</DataType_assn>
1131	<ConfidenceIndicators_assnreflist>
1132	<Error_ref identifier="BioDiscovery:ImaGene_QuantitationType:Background Stdev_Cy5"/>
1133	</ConfidenceIndicators_assnreflist>
1134	</MeasuredSignal>
1135	<Error isBackground="1"
1136	identifier="BioDiscovery:ImaGene_QuantitationType:Background Stdev_Cy5"
1137	name="Background Stdev_Cy5">
1138	<Descriptions_assnlist>
1139	<Description text="Standard deviation of pixel intensities over the local background region.">
1140	</Description>
1141	</Descriptions_assnlist>
1142	<Channel_assnref>
1143	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1144	</Channel_assnref>
1145	<Scale_assn>
1146	<OntologyEntry category="Scale"
1147	value="linear_scale">
1148	</OntologyEntry>
1149	</Scale_assn>
1150	<DataType_assn>
1151	<OntologyEntry category="DataType"
1152	value="float">
1153	</OntologyEntry>
1154	</DataType_assn>
1155	<TargetQuantitationType_assnref>
1156	<MeasuredSignal_ref identifier="BioDiscovery:ImaGene_QuantitationType:Background Mean_Cy5"/>
1157	</TargetQuantitationType_assnref>
1158	</Error>
1159	<SpecializedQuantitationType isBackground="0"
1160	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Median_Cy5"
1161	name="Signal Median_Cy5">
1162	<Descriptions_assnlist>
1163	<Description text="Median pixel intensity computed over the local signal region.">
1164	</Description>
1165	</Descriptions_assnlist>
1166	<Channel_assnref>
1167	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1168	</Channel_assnref>
1169	<Scale_assn>
1170	<OntologyEntry category="Scale"
1171	value="linear_scale">
1172	</OntologyEntry>
1173	</Scale_assn>
1174	<DataType_assn>
1175	<OntologyEntry category="DataType"
1176	value="float">
1177	</OntologyEntry>
1178	</DataType_assn>
1179	</SpecializedQuantitationType>
1180	<SpecializedQuantitationType isBackground="1"
1181	identifier="BioDiscovery:ImaGene_QuantitationType:Background Median_Cy5"
1182	name="Background Median_Cy5">
1183	<Descriptions_assnlist>
1184	<Description text="Median pixel intensity computed over the local background region.">
1185	</Description>
1186	</Descriptions_assnlist>
1187	<Channel_assnref>
1188	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1189	</Channel_assnref>
1190	<Scale_assn>
1191	<OntologyEntry category="Scale"
1192	value="linear_scale">
1193	</OntologyEntry>
1194	</Scale_assn>
1195	<DataType_assn>
1196	<OntologyEntry category="DataType"
1197	value="float">
1198	</OntologyEntry>
1199	</DataType_assn>
1200	</SpecializedQuantitationType>
1201	<SpecializedQuantitationType isBackground="0"
1202	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Mode_Cy5"
1203	name="Signal Mode_Cy5">
1204	<Descriptions_assnlist>
1205	<Description text="Mode pixel intensity computed over the local signal region (mode corresponds to the peak location in intensity distribution).">
1206	</Description>
1207	</Descriptions_assnlist>
1208	<Channel_assnref>
1209	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1210	</Channel_assnref>
1211	<Scale_assn>
1212	<OntologyEntry category="Scale"
1213	value="linear_scale">
1214	</OntologyEntry>
1215	</Scale_assn>
1216	<DataType_assn>
1217	<OntologyEntry category="DataType"
1218	value="float">
1219	</OntologyEntry>
1220	</DataType_assn>
1221	</SpecializedQuantitationType>
1222	<SpecializedQuantitationType isBackground="1"
1223	identifier="BioDiscovery:ImaGene_QuantitationType:Background Mode_Cy5"
1224	name="Background Mode_Cy5">
1225	<Descriptions_assnlist>
1226	<Description text="Mode pixel intensity computed over the local background region.">
1227	</Description>
1228	</Descriptions_assnlist>
1229	<Channel_assnref>
1230	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1231	</Channel_assnref>
1232	<Scale_assn>
1233	<OntologyEntry category="Scale"
1234	value="linear_scale">
1235	</OntologyEntry>
1236	</Scale_assn>
1237	<DataType_assn>
1238	<OntologyEntry category="DataType"
1239	value="float">
1240	</OntologyEntry>
1241	</DataType_assn>
1242	</SpecializedQuantitationType>
1243	<SpecializedQuantitationType isBackground="0"
1244	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Area_Cy5"
1245	name="Signal Area_Cy5">
1246	<Descriptions_assnlist>
1247	<Description text="Number of pixels in the local signal region.">
1248	</Description>
1249	</Descriptions_assnlist>
1250	<Channel_assnref>
1251	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1252	</Channel_assnref>
1253	<Scale_assn>
1254	<OntologyEntry category="Scale"
1255	value="linear_scale">
1256	</OntologyEntry>
1257	</Scale_assn>
1258	<DataType_assn>
1259	<OntologyEntry category="DataType"
1260	value="integer">
1261	</OntologyEntry>
1262	</DataType_assn>
1263	</SpecializedQuantitationType>
1264	<SpecializedQuantitationType isBackground="1"
1265	identifier="BioDiscovery:ImaGene_QuantitationType:Background Area_Cy5"
1266	name="Background Area_Cy5">
1267	<Descriptions_assnlist>
1268	<Description text="Number of pixels in the local background region.">
1269	</Description>
1270	</Descriptions_assnlist>
1271	<Channel_assnref>
1272	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1273	</Channel_assnref>
1274	<Scale_assn>
1275	<OntologyEntry category="Scale"
1276	value="linear_scale">
1277	</OntologyEntry>
1278	</Scale_assn>
1279	<DataType_assn>
1280	<OntologyEntry category="DataType"
1281	value="integer">
1282	</OntologyEntry>
1283	</DataType_assn>
1284	</SpecializedQuantitationType>
1285	<SpecializedQuantitationType isBackground="0"
1286	identifier="BioDiscovery:ImaGene_QuantitationType:Signal Total_Cy5"
1287	name="Signal Total_Cy5">
1288	<Descriptions_assnlist>
1289	<Description text="Total pixel intensity summed over the local signal region.">
1290	</Description>
1291	</Descriptions_assnlist>
1292	<Channel_assnref>
1293	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1294	</Channel_assnref>
1295	<Scale_assn>
1296	<OntologyEntry category="Scale"
1297	value="linear_scale">
1298	</OntologyEntry>
1299	</Scale_assn>
1300	<DataType_assn>
1301	<OntologyEntry category="DataType"
1302	value="integer">
1303	</OntologyEntry>
1304	</DataType_assn>
1305	</SpecializedQuantitationType>
1306	<SpecializedQuantitationType isBackground="1"
1307	identifier="BioDiscovery:ImaGene_QuantitationType:Background Total_Cy5"
1308	name="Background Total_Cy5">
1309	<Descriptions_assnlist>
1310	<Description text="Total pixel intensity summed over the local background region.">
1311	</Description>
1312	</Descriptions_assnlist>
1313	<Channel_assnref>
1314	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1315	</Channel_assnref>
1316	<Scale_assn>
1317	<OntologyEntry category="Scale"
1318	value="linear_scale">
1319	</OntologyEntry>
1320	</Scale_assn>
1321	<DataType_assn>
1322	<OntologyEntry category="DataType"
1323	value="integer">
1324	</OntologyEntry>
1325	</DataType_assn>
1326	</SpecializedQuantitationType>
1327	<SpecializedQuantitationType isBackground="0"
1328	identifier="BioDiscovery:ImaGene_QuantitationType:Shape Regularity_Cy5"
1329	name="Shape Regularity_Cy5">
1330	<Descriptions_assnlist>
1331	<Description text="The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity.">
1332	</Description>
1333	</Descriptions_assnlist>
1334	<Channel_assnref>
1335	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1336	</Channel_assnref>
1337	<Scale_assn>
1338	<OntologyEntry category="Scale"
1339	value="linear_scale">
1340	</OntologyEntry>
1341	</Scale_assn>
1342	<DataType_assn>
1343	<OntologyEntry category="DataType"
1344	value="float">
1345	</OntologyEntry>
1346	</DataType_assn>
1347	</SpecializedQuantitationType>
1348	<SpecializedQuantitationType isBackground="0"
1349	identifier="BioDiscovery:ImaGene_QuantitationType:Ignored Area_Cy5"
1350	name="Ignored Area_Cy5">
1351	<Descriptions_assnlist>
1352	<Description text="Area of ignored regions directly neighboring ("touching") the signal area is computed.">
1353	</Description>
1354	</Descriptions_assnlist>
1355	<Channel_assnref>
1356	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1357	</Channel_assnref>
1358	<Scale_assn>
1359	<OntologyEntry category="Scale"
1360	value="linear_scale">
1361	</OntologyEntry>
1362	</Scale_assn>
1363	<DataType_assn>
1364	<OntologyEntry category="DataType"
1365	value="integer">
1366	</OntologyEntry>
1367	</DataType_assn>
1368	</SpecializedQuantitationType>
1369	<SpecializedQuantitationType isBackground="0"
1370	identifier="BioDiscovery:ImaGene_QuantitationType:Spot Area_Cy5"
1371	name="Spot Area_Cy5">
1372	<Descriptions_assnlist>
1373	<Description text="Signal Area plus Ignored Area.">
1374	</Description>
1375	</Descriptions_assnlist>
1376	<Channel_assnref>
1377	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1378	</Channel_assnref>
1379	<Scale_assn>
1380	<OntologyEntry category="Scale"
1381	value="linear_scale">
1382	</OntologyEntry>
1383	</Scale_assn>
1384	<DataType_assn>
1385	<OntologyEntry category="DataType"
1386	value="integer">
1387	</OntologyEntry>
1388	</DataType_assn>
1389	</SpecializedQuantitationType>
1390	<SpecializedQuantitationType isBackground="0"
1391	identifier="BioDiscovery:ImaGene_QuantitationType:Ignored Median_Cy5"
1392	name="Ignored Median_Cy5">
1393	<Descriptions_assnlist>
1394	<Description text="Median pixel intensity computed over the local ignored region.">
1395	</Description>
1396	</Descriptions_assnlist>
1397	<Channel_assnref>
1398	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1399	</Channel_assnref>
1400	<Scale_assn>
1401	<OntologyEntry category="Scale"
1402	value="linear_scale">
1403	</OntologyEntry>
1404	</Scale_assn>
1405	<DataType_assn>
1406	<OntologyEntry category="DataType"
1407	value="float">
1408	</OntologyEntry>
1409	</DataType_assn>
1410	</SpecializedQuantitationType>
1411	<SpecializedQuantitationType isBackground="0"
1412	identifier="BioDiscovery:ImaGene_QuantitationType:Area To Perimeter_Cy5"
1413	name="Area To Perimeter_Cy5">
1414	<Descriptions_assnlist>
1415	<Description text="This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle).">
1416	</Description>
1417	</Descriptions_assnlist>
1418	<Channel_assnref>
1419	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1420	</Channel_assnref>
1421	<Scale_assn>
1422	<OntologyEntry category="Scale"
1423	value="linear_scale">
1424	</OntologyEntry>
1425	</Scale_assn>
1426	<DataType_assn>
1427	<OntologyEntry category="DataType"
1428	value="float">
1429	</OntologyEntry>
1430	</DataType_assn>
1431	</SpecializedQuantitationType>
1432	<SpecializedQuantitationType isBackground="0"
1433	identifier="BioDiscovery:ImaGene_QuantitationType:Open Perimeter_Cy5"
1434	name="Open Perimeter_Cy5">
1435	<Descriptions_assnlist>
1436	<Description text="Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot.">
1437	</Description>
1438	</Descriptions_assnlist>
1439	<Channel_assnref>
1440	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1441	</Channel_assnref>
1442	<Scale_assn>
1443	<OntologyEntry category="Scale"
1444	value="linear_scale">
1445	</OntologyEntry>
1446	</Scale_assn>
1447	<DataType_assn>
1448	<OntologyEntry category="DataType"
1449	value="float">
1450	</OntologyEntry>
1451	</DataType_assn>
1452	</SpecializedQuantitationType>
1453	<SpecializedQuantitationType isBackground="0"
1454	identifier="BioDiscovery:ImaGene_QuantitationType:XCoord_Cy5"
1455	name="XCoord_Cy5">
1456	<Descriptions_assnlist>
1457	<Description text="X coordinate (in pixels) of grid circle corresponding to the spot.">
1458	</Description>
1459	</Descriptions_assnlist>
1460	<Channel_assnref>
1461	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1462	</Channel_assnref>
1463	<Scale_assn>
1464	<OntologyEntry category="Scale"
1465	value="linear_scale">
1466	</OntologyEntry>
1467	</Scale_assn>
1468	<DataType_assn>
1469	<OntologyEntry category="DataType"
1470	value="float">
1471	</OntologyEntry>
1472	</DataType_assn>
1473	</SpecializedQuantitationType>
1474	<SpecializedQuantitationType isBackground="0"
1475	identifier="BioDiscovery:ImaGene_QuantitationType:YCoord_Cy5"
1476	name="YCoord_Cy5">
1477	<Descriptions_assnlist>
1478	<Description text="Y coordinate (in pixels) of grid circle corresponding to the spot.">
1479	</Description>
1480	</Descriptions_assnlist>
1481	<Channel_assnref>
1482	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1483	</Channel_assnref>
1484	<Scale_assn>
1485	<OntologyEntry category="Scale"
1486	value="linear_scale">
1487	</OntologyEntry>
1488	</Scale_assn>
1489	<DataType_assn>
1490	<OntologyEntry category="DataType"
1491	value="float">
1492	</OntologyEntry>
1493	</DataType_assn>
1494	</SpecializedQuantitationType>
1495	<SpecializedQuantitationType isBackground="0"
1496	identifier="BioDiscovery:ImaGene_QuantitationType:Diameter_Cy5"
1497	name="Diameter_Cy5">
1498	<Descriptions_assnlist>
1499	<Description text="Diameter (in pixels) of grid circle corresponding to the spot.">
1500	</Description>
1501	</Descriptions_assnlist>
1502	<Channel_assnref>
1503	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1504	</Channel_assnref>
1505	<Scale_assn>
1506	<OntologyEntry category="Scale"
1507	value="linear_scale">
1508	</OntologyEntry>
1509	</Scale_assn>
1510	<DataType_assn>
1511	<OntologyEntry category="DataType"
1512	value="integer">
1513	</OntologyEntry>
1514	</DataType_assn>
1515	</SpecializedQuantitationType>
1516	<SpecializedQuantitationType isBackground="0"
1517	identifier="BioDiscovery:ImaGene_QuantitationType:Position offset_Cy5"
1518	name="Position offset_Cy5">
1519	<Descriptions_assnlist>
1520	<Description text="Offset (in pixels) of the center of the grid circle from the expected position in the grid.">
1521	</Description>
1522	</Descriptions_assnlist>
1523	<Channel_assnref>
1524	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1525	</Channel_assnref>
1526	<Scale_assn>
1527	<OntologyEntry category="Scale"
1528	value="linear_scale">
1529	</OntologyEntry>
1530	</Scale_assn>
1531	<DataType_assn>
1532	<OntologyEntry category="DataType"
1533	value="float">
1534	</OntologyEntry>
1535	</DataType_assn>
1536	</SpecializedQuantitationType>
1537	<SpecializedQuantitationType isBackground="0"
1538	identifier="BioDiscovery:ImaGene_QuantitationType:Offset X_Cy5"
1539	name="Offset X_Cy5">
1540	<Descriptions_assnlist>
1541	<Description text="X Offset (in pixels) of the center of the grid circle from the expected position in the grid.">
1542	</Description>
1543	</Descriptions_assnlist>
1544	<Channel_assnref>
1545	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1546	</Channel_assnref>
1547	<Scale_assn>
1548	<OntologyEntry category="Scale"
1549	value="linear_scale">
1550	</OntologyEntry>
1551	</Scale_assn>
1552	<DataType_assn>
1553	<OntologyEntry category="DataType"
1554	value="float">
1555	</OntologyEntry>
1556	</DataType_assn>
1557	</SpecializedQuantitationType>
1558	<SpecializedQuantitationType isBackground="0"
1559	identifier="BioDiscovery:ImaGene_QuantitationType:Offset Y_Cy5"
1560	name="Offset Y_Cy5">
1561	<Descriptions_assnlist>
1562	<Description text="Y Offset (in pixels) of the center of the grid circle from the expected position in the grid.">
1563	</Description>
1564	</Descriptions_assnlist>
1565	<Channel_assnref>
1566	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1567	</Channel_assnref>
1568	<Scale_assn>
1569	<OntologyEntry category="Scale"
1570	value="linear_scale">
1571	</OntologyEntry>
1572	</Scale_assn>
1573	<DataType_assn>
1574	<OntologyEntry category="DataType"
1575	value="float">
1576	</OntologyEntry>
1577	</DataType_assn>
1578	</SpecializedQuantitationType>
1579	<SpecializedQuantitationType isBackground="0"
1580	identifier="BioDiscovery:ImaGene_QuantitationType:Expected X_Cy5"
1581	name="Expected X_Cy5">
1582	<Descriptions_assnlist>
1583	<Description text="X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.">
1584	</Description>
1585	</Descriptions_assnlist>
1586	<Channel_assnref>
1587	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1588	</Channel_assnref>
1589	<Scale_assn>
1590	<OntologyEntry category="Scale"
1591	value="linear_scale">
1592	</OntologyEntry>
1593	</Scale_assn>
1594	<DataType_assn>
1595	<OntologyEntry category="DataType"
1596	value="float">
1597	</OntologyEntry>
1598	</DataType_assn>
1599	</SpecializedQuantitationType>
1600	<SpecializedQuantitationType isBackground="0"
1601	identifier="BioDiscovery:ImaGene_QuantitationType:Expected Y_Cy5"
1602	name="Expected Y_Cy5">
1603	<Descriptions_assnlist>
1604	<Description text="Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.">
1605	</Description>
1606	</Descriptions_assnlist>
1607	<Channel_assnref>
1608	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1609	</Channel_assnref>
1610	<Scale_assn>
1611	<OntologyEntry category="Scale"
1612	value="linear_scale">
1613	</OntologyEntry>
1614	</Scale_assn>
1615	<DataType_assn>
1616	<OntologyEntry category="DataType"
1617	value="float">
1618	</OntologyEntry>
1619	</DataType_assn>
1620	</SpecializedQuantitationType>
1621	<SpecializedQuantitationType isBackground="0"
1622	identifier="BioDiscovery:ImaGene_QuantitationType:CM-X_Cy5"
1623	name="CM-X_Cy5">
1624	<Descriptions_assnlist>
1625	<Description text="X coordinate of the center of the mass of spot's signal region.">
1626	</Description>
1627	</Descriptions_assnlist>
1628	<Channel_assnref>
1629	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1630	</Channel_assnref>
1631	<Scale_assn>
1632	<OntologyEntry category="Scale"
1633	value="linear_scale">
1634	</OntologyEntry>
1635	</Scale_assn>
1636	<DataType_assn>
1637	<OntologyEntry category="DataType"
1638	value="float">
1639	</OntologyEntry>
1640	</DataType_assn>
1641	</SpecializedQuantitationType>
1642	<SpecializedQuantitationType isBackground="0"
1643	identifier="BioDiscovery:ImaGene_QuantitationType:CM-Y_Cy5"
1644	name="CM-Y_Cy5">
1645	<Descriptions_assnlist>
1646	<Description text="Y coordinate of the center of the mass of spot's signal region.">
1647	</Description>
1648	</Descriptions_assnlist>
1649	<Channel_assnref>
1650	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1651	</Channel_assnref>
1652	<Scale_assn>
1653	<OntologyEntry category="Scale"
1654	value="linear_scale">
1655	</OntologyEntry>
1656	</Scale_assn>
1657	<DataType_assn>
1658	<OntologyEntry category="DataType"
1659	value="float">
1660	</OntologyEntry>
1661	</DataType_assn>
1662	</SpecializedQuantitationType>
1663	<SpecializedQuantitationType isBackground="0"
1664	identifier="BioDiscovery:ImaGene_QuantitationType:CM Offset_Cy5"
1665	name="CM Offset_Cy5">
1666	<Descriptions_assnlist>
1667	<Description text="Offset (in pixels) of the spot's center of the mass from the expected position in the grid.">
1668	</Description>
1669	</Descriptions_assnlist>
1670	<Channel_assnref>
1671	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1672	</Channel_assnref>
1673	<Scale_assn>
1674	<OntologyEntry category="Scale"
1675	value="linear_scale">
1676	</OntologyEntry>
1677	</Scale_assn>
1678	<DataType_assn>
1679	<OntologyEntry category="DataType"
1680	value="float">
1681	</OntologyEntry>
1682	</DataType_assn>
1683	</SpecializedQuantitationType>
1684	<SpecializedQuantitationType isBackground="0"
1685	identifier="BioDiscovery:ImaGene_QuantitationType:CM Offset-X_Cy5"
1686	name="CM Offset-X_Cy5">
1687	<Descriptions_assnlist>
1688	<Description text="X offset (in pixels) of the spot's center of the mass from the expected position in the grid.">
1689	</Description>
1690	</Descriptions_assnlist>
1691	<Channel_assnref>
1692	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1693	</Channel_assnref>
1694	<Scale_assn>
1695	<OntologyEntry category="Scale"
1696	value="linear_scale">
1697	</OntologyEntry>
1698	</Scale_assn>
1699	<DataType_assn>
1700	<OntologyEntry category="DataType"
1701	value="float">
1702	</OntologyEntry>
1703	</DataType_assn>
1704	</SpecializedQuantitationType>
1705	<SpecializedQuantitationType isBackground="0"
1706	identifier="BioDiscovery:ImaGene_QuantitationType:CM Offset-Y_Cy5"
1707	name="CM Offset-Y_Cy5">
1708	<Descriptions_assnlist>
1709	<Description text="Y offset (in pixels) of the spot's center of the mass from the expected position in the grid.">
1710	</Description>
1711	</Descriptions_assnlist>
1712	<Channel_assnref>
1713	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1714	</Channel_assnref>
1715	<Scale_assn>
1716	<OntologyEntry category="Scale"
1717	value="linear_scale">
1718	</OntologyEntry>
1719	</Scale_assn>
1720	<DataType_assn>
1721	<OntologyEntry category="DataType"
1722	value="float">
1723	</OntologyEntry>
1724	</DataType_assn>
1725	</SpecializedQuantitationType>
1726	<SpecializedQuantitationType isBackground="0"
1727	identifier="BioDiscovery:ImaGene_QuantitationType:Min Diam_Cy5"
1728	name="Min Diam_Cy5">
1729	<Descriptions_assnlist>
1730	<Description text="Diameter of the circle inscribed into the spot's signal region.">
1731	</Description>
1732	</Descriptions_assnlist>
1733	<Channel_assnref>
1734	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1735	</Channel_assnref>
1736	<Scale_assn>
1737	<OntologyEntry category="Scale"
1738	value="linear_scale">
1739	</OntologyEntry>
1740	</Scale_assn>
1741	<DataType_assn>
1742	<OntologyEntry category="DataType"
1743	value="float">
1744	</OntologyEntry>
1745	</DataType_assn>
1746	</SpecializedQuantitationType>
1747	<SpecializedQuantitationType isBackground="0"
1748	identifier="BioDiscovery:ImaGene_QuantitationType:Max Diam_Cy5"
1749	name="Max Diam_Cy5">
1750	<Descriptions_assnlist>
1751	<Description text="Diameter of the circle, the spot's signal region can be inscribed in.">
1752	</Description>
1753	</Descriptions_assnlist>
1754	<Channel_assnref>
1755	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1756	</Channel_assnref>
1757	<Scale_assn>
1758	<OntologyEntry category="Scale"
1759	value="linear_scale">
1760	</OntologyEntry>
1761	</Scale_assn>
1762	<DataType_assn>
1763	<OntologyEntry category="DataType"
1764	value="float">
1765	</OntologyEntry>
1766	</DataType_assn>
1767	</SpecializedQuantitationType>
1768	<SpecializedQuantitationType isBackground="0"
1769	identifier="BioDiscovery:ImaGene_QuantitationType:Control_Cy5"
1770	name="Control_Cy5">
1771	<Descriptions_assnlist>
1772	<Description text="Name of a control type for current spot (no name means the spot is not a control spot).">
1773	</Description>
1774	</Descriptions_assnlist>
1775	<Channel_assnref>
1776	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1777	</Channel_assnref>
1778	<Scale_assn>
1779	<OntologyEntry category="Scale"
1780	value="unscaled">
1781	</OntologyEntry>
1782	</Scale_assn>
1783	<DataType_assn>
1784	<OntologyEntry category="DataType"
1785	value="string_datatype">
1786	</OntologyEntry>
1787	</DataType_assn>
1788	</SpecializedQuantitationType>
1789	<SpecializedQuantitationType isBackground="0"
1790	identifier="BioDiscovery:ImaGene_QuantitationType:Failed Control_Cy5"
1791	name="Failed Control_Cy5">
1792	<Descriptions_assnlist>
1793	<Description text="0 if the control passed all tests, 1 if at least one of the tests failed.">
1794	</Description>
1795	</Descriptions_assnlist>
1796	<Channel_assnref>
1797	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1798	</Channel_assnref>
1799	<Scale_assn>
1800	<OntologyEntry category="Scale"
1801	value="linear_scale">
1802	</OntologyEntry>
1803	</Scale_assn>
1804	<DataType_assn>
1805	<OntologyEntry category="DataType"
1806	value="boolean">
1807	</OntologyEntry>
1808	</DataType_assn>
1809	</SpecializedQuantitationType>
1810	<SpecializedQuantitationType isBackground="0"
1811	identifier="BioDiscovery:ImaGene_QuantitationType:Background contamination present_Cy5"
1812	name="Background contamination present_Cy5">
1813	<Descriptions_assnlist>
1814	<Description text="0 if the spot passed background contamination test, 1 if it did not.">
1815	</Description>
1816	</Descriptions_assnlist>
1817	<Channel_assnref>
1818	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1819	</Channel_assnref>
1820	<Scale_assn>
1821	<OntologyEntry category="Scale"
1822	value="linear_scale">
1823	</OntologyEntry>
1824	</Scale_assn>
1825	<DataType_assn>
1826	<OntologyEntry category="DataType"
1827	value="boolean">
1828	</OntologyEntry>
1829	</DataType_assn>
1830	</SpecializedQuantitationType>
1831	<SpecializedQuantitationType isBackground="0"
1832	identifier="BioDiscovery:ImaGene_QuantitationType:Signal contamination present_Cy5"
1833	name="Signal contamination present_Cy5">
1834	<Descriptions_assnlist>
1835	<Description text="0 if the spot passed signal contamination test, 1 if it did not.">
1836	</Description>
1837	</Descriptions_assnlist>
1838	<Channel_assnref>
1839	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1840	</Channel_assnref>
1841	<Scale_assn>
1842	<OntologyEntry category="Scale"
1843	value="linear_scale">
1844	</OntologyEntry>
1845	</Scale_assn>
1846	<DataType_assn>
1847	<OntologyEntry category="DataType"
1848	value="boolean">
1849	</OntologyEntry>
1850	</DataType_assn>
1851	</SpecializedQuantitationType>
1852	<SpecializedQuantitationType isBackground="0"
1853	identifier="BioDiscovery:ImaGene_QuantitationType:Ignored % failed_Cy5"
1854	name="Ignored % failed_Cy5">
1855	<Descriptions_assnlist>
1856	<Description text="0 if the spot passed ignored percentage test, 1 if it did not.">
1857	</Description>
1858	</Descriptions_assnlist>
1859	<Channel_assnref>
1860	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1861	</Channel_assnref>
1862	<Scale_assn>
1863	<OntologyEntry category="Scale"
1864	value="linear_scale">
1865	</OntologyEntry>
1866	</Scale_assn>
1867	<DataType_assn>
1868	<OntologyEntry category="DataType"
1869	value="boolean">
1870	</OntologyEntry>
1871	</DataType_assn>
1872	</SpecializedQuantitationType>
1873	<SpecializedQuantitationType isBackground="0"
1874	identifier="BioDiscovery:ImaGene_QuantitationType:Open perimeter failed_Cy5"
1875	name="Open perimeter failed_Cy5">
1876	<Descriptions_assnlist>
1877	<Description text="0 if the spot open perimeter test, 1 if it did not.">
1878	</Description>
1879	</Descriptions_assnlist>
1880	<Channel_assnref>
1881	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1882	</Channel_assnref>
1883	<Scale_assn>
1884	<OntologyEntry category="Scale"
1885	value="linear_scale">
1886	</OntologyEntry>
1887	</Scale_assn>
1888	<DataType_assn>
1889	<OntologyEntry category="DataType"
1890	value="boolean">
1891	</OntologyEntry>
1892	</DataType_assn>
1893	</SpecializedQuantitationType>
1894	<SpecializedQuantitationType isBackground="0"
1895	identifier="BioDiscovery:ImaGene_QuantitationType:Shape regularity failed_Cy5"
1896	name="Shape regularity failed_Cy5">
1897	<Descriptions_assnlist>
1898	<Description text="0 if the spot passed shape regularity test, 1 if it did not.">
1899	</Description>
1900	</Descriptions_assnlist>
1901	<Channel_assnref>
1902	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1903	</Channel_assnref>
1904	<Scale_assn>
1905	<OntologyEntry category="Scale"
1906	value="linear_scale">
1907	</OntologyEntry>
1908	</Scale_assn>
1909	<DataType_assn>
1910	<OntologyEntry category="DataType"
1911	value="boolean">
1912	</OntologyEntry>
1913	</DataType_assn>
1914	</SpecializedQuantitationType>
1915	<SpecializedQuantitationType isBackground="0"
1916	identifier="BioDiscovery:ImaGene_QuantitationType:Perim-to-area failed_Cy5"
1917	name="Perim-to-area failed_Cy5">
1918	<Descriptions_assnlist>
1919	<Description text="0 if the spot passed perimeter-to-area test, 1 if it did not.">
1920	</Description>
1921	</Descriptions_assnlist>
1922	<Channel_assnref>
1923	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1924	</Channel_assnref>
1925	<Scale_assn>
1926	<OntologyEntry category="Scale"
1927	value="linear_scale">
1928	</OntologyEntry>
1929	</Scale_assn>
1930	<DataType_assn>
1931	<OntologyEntry category="DataType"
1932	value="boolean">
1933	</OntologyEntry>
1934	</DataType_assn>
1935	</SpecializedQuantitationType>
1936	<SpecializedQuantitationType isBackground="0"
1937	identifier="BioDiscovery:ImaGene_QuantitationType:Offset failed_Cy5"
1938	name="Offset failed_Cy5">
1939	<Descriptions_assnlist>
1940	<Description text="0 if the spot passed offset test, 1 if it did not.">
1941	</Description>
1942	</Descriptions_assnlist>
1943	<Channel_assnref>
1944	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1945	</Channel_assnref>
1946	<Scale_assn>
1947	<OntologyEntry category="Scale"
1948	value="linear_scale">
1949	</OntologyEntry>
1950	</Scale_assn>
1951	<DataType_assn>
1952	<OntologyEntry category="DataType"
1953	value="boolean">
1954	</OntologyEntry>
1955	</DataType_assn>
1956	</SpecializedQuantitationType>
1957	<SpecializedQuantitationType isBackground="0"
1958	identifier="BioDiscovery:ImaGene_QuantitationType:Empty spot_Cy5"
1959	name="Empty spot_Cy5">
1960	<Descriptions_assnlist>
1961	<Description text="0 if the spot passed offset test, 1 if it did not.">
1962	</Description>
1963	</Descriptions_assnlist>
1964	<Channel_assnref>
1965	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1966	</Channel_assnref>
1967	<Scale_assn>
1968	<OntologyEntry category="Scale"
1969	value="linear_scale">
1970	</OntologyEntry>
1971	</Scale_assn>
1972	<DataType_assn>
1973	<OntologyEntry category="DataType"
1974	value="boolean">
1975	</OntologyEntry>
1976	</DataType_assn>
1977	</SpecializedQuantitationType>
1978	<SpecializedQuantitationType isBackground="0"
1979	identifier="BioDiscovery:ImaGene_QuantitationType:Negative spot_Cy5"
1980	name="Negative spot_Cy5">
1981	<Descriptions_assnlist>
1982	<Description text="1 if the spot was qualified as negative, 0 if it was not.">
1983	</Description>
1984	</Descriptions_assnlist>
1985	<Channel_assnref>
1986	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
1987	</Channel_assnref>
1988	<Scale_assn>
1989	<OntologyEntry category="Scale"
1990	value="linear_scale">
1991	</OntologyEntry>
1992	</Scale_assn>
1993	<DataType_assn>
1994	<OntologyEntry category="DataType"
1995	value="boolean">
1996	</OntologyEntry>
1997	</DataType_assn>
1998	</SpecializedQuantitationType>
1999	<SpecializedQuantitationType isBackground="0"
2000	identifier="BioDiscovery:ImaGene_QuantitationType:Selected spot_Cy5"
2001	name="Selected spot_Cy5">
2002	<Descriptions_assnlist>
2003	<Description text="1 if the spot was selected in the software view at time of save, 0 if not.">
2004	</Description>
2005	</Descriptions_assnlist>
2006	<Channel_assnref>
2007	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
2008	</Channel_assnref>
2009	<Scale_assn>
2010	<OntologyEntry category="Scale"
2011	value="linear_scale">
2012	</OntologyEntry>
2013	</Scale_assn>
2014	<DataType_assn>
2015	<OntologyEntry category="DataType"
2016	value="boolean">
2017	</OntologyEntry>
2018	</DataType_assn>
2019	</SpecializedQuantitationType>
2020	<SpecializedQuantitationType isBackground="0"
2021	identifier="BioDiscovery:ImaGene_QuantitationType:Saturated spot_Cy5"
2022	name="Saturated spot_Cy5">
2023	<Descriptions_assnlist>
2024	<Description text="1 if the spot was qualified as saturated, 0 if it was not.">
2025	</Description>
2026	</Descriptions_assnlist>
2027	<Channel_assnref>
2028	<Channel_ref identifier="ebi.ac.uk:Channel:Cy5"/>
2029	</Channel_assnref>
2030	<Scale_assn>
2031	<OntologyEntry category="Scale"
2032	value="linear_scale">
2033	</OntologyEntry>
2034	</Scale_assn>
2035	<DataType_assn>
2036	<OntologyEntry category="DataType"
2037	value="boolean">
2038	</OntologyEntry>
2039	</DataType_assn>
2040	</SpecializedQuantitationType>
2041	</QuantitationType_assnlist>
2042	</QuantitationType_package>
2043	</MAGE-ML>

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