HUMAN CANCER BIOPSY experiment annotation
1-4-2005
Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl, and others;
Organism specific part by Judith Boer, Andrea Bauer and others.
common_annotations
array
1 -
array_source
10 - self_made
11 - genome_systems
12 - clontech
13 - research_genetics
2 -
array_series
3 -
array_individual
4 -
array_support
14 - nylon
15 - polypropylene
16 - glass
67 -
array_support_width
mm
68 -
array_support_length
mm
41 -
array_surface_chemistry
117 - unknown_positive_charge
118 - poly_L_lysine
119 - aldehyde
120 - aminosilane
395 - epoxy
42 -
support_manufacturer
121 - Hybond
122 - Pall
123 - TeleChem
124 - Corning
250 - Quantifoil
511 - Nexterion
125 - diehl
126 - stephan
396 - Eppendorf
397 - teifel
398 - loukachova
92 -
Eppendorf_support_brand
399 - non_Eppendorf
400 - Creative_Oligo
401 - Creative_PCR
43 -
Hybond_support_brand
127 - non_Hybond
128 - N+
44 -
Pall_support_brand
129 - non_Pall
130 - Biodyne_B
223 - polypropylene
45 -
Corning_support_brand
131 - non_Corning
132 - CMT_GAPS
46 -
TeleChem_support_brand
133 - non_TeleChem
134 - Aldehyde
135 - SuperAldehyde
79 -
Quantifoil_support_brand
251 - non_Quantifoil
252 - QMT_Amino
253 - QMT_Aldehyd
254 - QMT_Epoxy
109 -
Nexterion_support_brand
512 - non_Nexterion
513 - Nexterion_A
514 - Nexterion_Aplus
515 - Nexterion_E
516 - Nexterion_AL
517 - Nexterion_H
518 - Nexterion_MPX
5 -
spotted_material
17 - PCR
236 - cDNA
18 - spotted_bacteria
263 - isolated_plasmids
19 - DNA-oligo
402 - DNA-oligo50_MWG
403 - DNA-oligo70_Operon
20 - PNA-oligo
69 -
spotted_material_property
200 - single_stranded
201 - double_stranded
70 -
number_of_elements_on_array_(without_duplicates)
80 -
external_controls_spotted
269 - no
270 - yes
71 -
elements_spotted_as
202 - single
203 - duplicate
204 - triplicate
404 - quadruplicate
47 -
spotted_material_purification
136 - non
137 - isopropanol_precipitation
138 - QIAquick
139 - Multiscreen_NU_Millipore
405 - NucleoFast96_MN_centrifuge
48 -
spotting_buffer
140 - 1.5M_NaCl_0.5M_NaOH
141 - 28mM_EDC_4.4volpromill_NMI
142 - spottingsolution_by_diehl
143 - MicroSpotting_solution_TeleChem
144 - 3xSSC
145 - 3xSSC_50%DMSO
406 - 3xSSC_1.5M_Betaine
407 - 2xSSC_1M_Betaine_200mM_sodiumphosphate_pH7.2
255 - 3xSSC_1.5M_Betaine_150mM_sodiumphosphate_pH8.5
528 - 3xSSC_3M_Betaine_150mM_sodiumphosphate_pH8.5
227 - 150mM_sodiumphosphate_pH8.5
228 - 150mM_sodiumphosphate_pH8.5_0.01%SDS
533 - 3M_Betaine_in_PCR_Buffer
49 -
spotting_robot
146 - SDDC-2_ESI
147 - Biogrid_Biorobotics
148 - Microgrid_II_Biorobotics
149 - Omnigrid_Genemachines
150 - QArray_Genetix
50 -
spotting_pins
151 - solid
152 - SMP-3_Telechem
153 - Biogrid_Biorobotics
51 -
relative_humidity
154 - defined
155 - estimated
156 - unknown(enter_0%)
52 -
relative_humidity
%
53 -
temperature
157 - defined
158 - estimated
159 - unknown(enter_0deg.C)
54 -
temperature
deg.C
55 -
postprocessing
160 - neutralizing_by_1.5MNaCL_0.5MTrispH7.5_1mMEDTA
264 - neutralizing_by_0.3MNaCL_20mMNaH2PO4_2mMEDTA
161 - 2h_at_65deg.C
408 - 2h_at_80deg.C
257 - 4h_at_80deg.C
409 - 30min_at_120deg.C
410 - 60min_at_120deg.C
411 - 15min_humidChamber_RT
412 - 30min_humidChamber_RT
162 - succinic_anhydride_Stanford_protocol
163 - succinic_anhydride_protocol_by_diehl
164 - BSA_Tigr_protocol
165 - NaBH4_Telechem_protocol
256 - Quantifoil_protocol
77 -
uv_crosslink_applicable
224 - no(enter_0)
225 - yes
78 -
uv_crosslink_energy
x100microJpercm2
6 -
readfile
7 -
array_hybridisation
hybridisation
RNA_preparation
8 -
material_source
21 - fresh
22 - frozen
23 - RNA_later
94 - cDNA_subtraction
502 - DNA_from_ChIP_(chromatine_immuno_precipitation)
110 -
ribosomal_RNA
522 - no_enrichment
523 - spinning_down_ribosomes
9 -
preparation_of_total_RNA
24 - trizol
25 - columns
26 - phenol
237 - trizol+columns
238 - phenol+columns
95 - not_applicable
98 -
DNAse_digest
455 - no
456 - yes
457 - unknown
81 -
A260_A280_ratio
10 -
preparation_of_PolyA+
27 - none
28 - dynabeads
29 - oligotex
30 - cellulose
96 - not_applicable
labeling
11 -
amount_of_RNA
microgram
40 -
amount_of_cDNA
microgram
108 -
amount_of_DNA
microgram
12 -
enzyme
31 - superscript
32 - AMV
413 - FluoroScript_Invitrogen
414 - LabelStar_qiagen
33 - M-MLV
166 - OmniScript
97 - klenow
13 -
priming
34 - oligo_dT
35 - anchored_oligo_dT
36 - random_hexamer
503 - random_octamer
37 - combined_oligo_dT-random_hexamer
98 - pcr_select
239 - ClonTech_specific1
240 - ClonTech_specific2
519 - gene_specific_primer_mix
14 -
nucleotide
38 - dCTP
39 - dATP
167 - aa-dUTP
168 - dUTP
56 -
nucleotide_removal
169 - G50_Pharmacia
170 - ammium_acetate_isopropanol_precipitation
226 - Na_acetate_isopropanol_precipitation
171 - QIAquick_Qiagen
172 - GFX_columns_Pharmacia
415 - columns_FluoroScriptKit_Invitrogen
416 - columns_LabelStarKit_qiagen
173 - YM30_Amicon
15 -
label
40 - 33P
41 - 32P
42 - Cy3
43 - Cy5
417 - Dy555
418 - Dy630
174 - Alexa488
175 - Alexa594
66 -
days_from_calibration_date_applicable
193 - yes
194 - no(enter_0d)
38 -
days_from_calibration_date
d
16 -
label_incorporation_rate
%
17 -
total_activity
cpm
hybridisation_conditions
18 -
buffer
44 - 0.5M_Na_phosphate_pH7.2_7%_SDS
229 - 5x_SSC_0.1%_SDS
230 - Genisphere3DNA
231 - Genisphere3DNAformamide
419 - 4x_SSC_0.1%_SDS
232 - 3x_SSC_2.5x_denhardts_0.08%_SDS
45 - 5x_SSC_5x_denhardts_0.5%_SDS
46 - 4x_SSC_7.2%_Na_sarcosyl
47 - Clontech_Express_hyb
48 - ambion_Northern_max
258 - ambion_slidehyb1
420 - QMT_hybridisation_buffer
221 - 3x_SSC_5x_denhardts_1%_SDS_5%_dextransulfate_50%_formamide
57 -
prehybridization_without_target
176 - no
177 - yes
82 -
pre_hyb_temperature
deg.C
83 -
pre_hyb_length
min
19 -
competitors
49 - none
50 - tRNA
51 - Cot1
217 - dA20
52 - dA40
53 - salmon_sperm
241 - Cot1_salmonsperm
421 - polydA_humanCot1
99 - dA40_Cot1_salmonsperm
100 - dA40_Cot1_tRNA_salmonsperm
101 - dA40_Cot1_specificoligos_salmonsperm
102 - dA40_Cot1_specificoligos_tRNA_salmonsperm
75 -
hybridisation_device
211 - water_bath
212 - rotating_oven
76 -
hybridisation_instrument
213 - hybridisation_bottle
271 - hybridization_chamber_ArrayIt
422 - hybridization_chamber_ArrayIt_equivalent_red
214 - hybridisation_chamber_corning
215 - hybridisation_chamber_TeleChem
216 - hybridisation_chamber_ClonTech
20 -
hybridisation_temp
deg.C
21 -
buffer_volume
ml
58 -
coverslip_used
178 - no_(enter_size_0)
179 - yes
59 -
coverslip_size
mmxmm
84 -
coverslip_material
272 - glass
273 - plastic
85 -
coverslip_provider
274 - Metzler
275 - Sigma
276 - Roth
277 - Erie_Scientific
86 -
coverslip_spacer_thickness_(0_for_none)
mm
87 -
spikes_included
278 - no
279 - yes
22 -
hybridisation_length
h
stringency_wash
23 -
wash_buffer
54 - 0.1xSSC_0.1%SDS
55 - 0.6xSSC_1%SDS
56 - 0.2xSSC_0.1%SDS
222 - 0.2xSSC
233 - 0.1xSSC
234 - 0.06xSSC
259 - 2xSSC_0.2%SDS
57 - 40mMNaPipH7_0.1%SDS
242 - ClonTech_protocol
423 - Corning_protocol
24 -
times
25 -
wash_length
min
26 -
temperature
deg.C
88 -
drying
280 - centrifuge_10_min_500_rpm
281 - nitrogen
454 - air_pressure
detection
96 -
days_from_washing_applicable
450 - yes
451 - no_(enter_-1)
97 -
days_from_washing
d
60 -
exposure_time_applicable
180 - yes
181 - no_(enter_0h)
27 -
exposure_time
h
28 -
measuring_device
58 - MD_storm860_phos
59 - MD_storm860_red
60 - MD_storm860_blue
113 - MD_425
114 - MD_475A_phos
265 - MD_typhoon_phos
61 - Fuji_BAS1500
109 - Fuji_FLA3000
62 - BioRad
63 - ScanArray3000_GSI_Lumonics
182 - ScanArray5000_GSI_Lumonics
424 - ArrayWorX_AppliedPrecision
183 - Axon_4000a_Axon
72 -
scanning_software
205 - Fuji_Image_Reader_FLA3000_3000G_V1.0
243 - BAS_reader_V2.11
206 - BAS_reader_V2.26beta
207 - Storm_scanner_control
208 - Typhoon_scanner_control_V1.0
209 - Scan_Array3000_V3.11_Controller_V2.03
210 - Scan_Array_V2.1
425 - ArrayWorX
73 -
spacial_resolution
microm
61 -
pixelsize
micromxmicrom
62 -
PMT_setting_applicable
184 - no(enter_0%)
185 - yes
63 -
PMT_setting
%
64 -
laser_power_setting_applicable
186 - no(enter_0%)
187 - yes
65 -
laser_power_setting
%
93 -
CCD_camera_setting_applicable
426 - no(enter_0s)
427 - yes
94 -
CCD_camera_exposure_time
s
95 -
pixel_binning
428 - no_binning
429 - high_dynamic_range
430 - high_precision
431 - high_SNR
29 -
imaging_software
64 - AIS
244 - AIDA_Image_Analyzer_V3.0
432 - AIDA_Image_Analyzer_V3.25
520 - AIDA_Image_Analyzer_V3.35
521 - AIDA_Image_Analyzer_V4
65 - HDG
66 - XDotsReader
67 - imagene
68 - Xdigitise
188 - GenePixPro_V3.0.6.89
268 - GenePixPro_V4.0.0.54
452 - GenePixPro_V4.1
189 - QuantArray
30 -
background_correction
69 - none
70 - local_background
71 - block_background
72 - empty_spots_average
73 - empty_spots_per_block
433 - global_background
31 -
spot_detection
74 - all_spots
75 - only_positive_spots
74 -
spot_dimension_(diameter)
microm
32 -
spot_size
76 - fixed
77 - variable
33 -
intensity_measurement
78 - highest_value_in_spot_centre
79 - sum_of_pixels_within_boundary
80 - mean_of_pixels_times_no_of_pixels_within_boundary
282 - median_of_pixels_times_no_of_pixels_within_boundary
99 -
overall_image_quality
458 - 1-perfect
459 - 2
460 - 3
461 - 4
462 - 5-bad
100 -
color_comparison_applicable
463 - yes
464 - no
101 -
color_comparison
465 - Cy3_much_lower_than_Cy5
466 - Cy3_lower_than_Cy5
467 - Cy3_similar_to_Cy5
468 - Cy3_higher_than_Cy5
469 - Cy3_much_higher_than_Cy5
102 -
background_stars_abundance
470 - 1-no_stars
471 - 2
472 - 3
473 - 4
474 - 5-many_stars
103 -
background_stars_occupied_area
475 - 1-limited_to_small_area
476 - 2
477 - 3
478 - 4
479 - 5-all_over_chip
104 -
background_smere_intensity
480 - 1-none
481 - 2
482 - 3
483 - 4
484 - 5-strong
105 -
background_smere_occupied_area
485 - 1-limited_to_small_area
486 - 2
487 - 3
488 - 4
489 - 5-all_over_chip
106 -
background_high_intensity_artifacts_(funny_pictures)
490 - 1-limited_to_small_area
491 - 2
492 - 3
493 - 4
494 - 5-all_over_chip
107 -
background_dust_abundance
495 - 1-no_dust
496 - 2
497 - 3
498 - 4
499 - 5-many_dust_particles
sample
34 -
organism
81 - Saccharomyces_cerevisiae
82 - Arabidopsis_thaliana
83 - murine_biopsy
103 - murine_cell_line
245 - rat_biopsy
246 - rat_cell_line
84 - human_biopsy
85 - human_cell_line
86 - Bacillus_subtilis
192 - Trypanosoma_brucei
534 - Trypanosoma_equiperdum
535 - Trypanosoma_evansi
199 - Candida_albicans
220 - Neurospora_crassa
260 - Drosophila_melanogaster
266 - Antirrhinum_majus
283 - Pseudomonas_putida
284 - Pseudomonas_aeruginosa
285 - Pseudomonas_fluorescens
submission
35 -
date_of_entry_day
36 -
date_of_entry_month
37 -
date_of_entry_year
39 -
experimentator_hybridization_and_washing
218 - aign
104 - bastuk
235 - bauer
115 - becerra
261 - beckmann
267 - bey
105 - bier
387 - boehm
88 - boer
248 - bosse
524 - brems
446 - busch
190 - diehl
196 - fischer
191 - grahlmann
219 - grees
247 - hasenpuschtheil
87 - hauser
391 - klopp
436 - konrad
91 - kornacker
249 - kuery
112 - lagorce
107 - lombardia
434 - loukachova
90 - lutz
108 - meijer
92 - mendel
504 - radke
198 - reile
195 - scheideler
197 - schrenk
111 - steiner
286 - stjepandic
110 - sueltmann
435 - teifel
106 - tournu
262 - werdermann
89 - wilmer
93 - wittig
532 - xu
116 - yin
505 - zelt
89 -
experimentator_spotting
287 - aign
288 - bastuk
289 - bauer
290 - becerra
291 - beckmann
292 - bey
293 - bier
388 - boehm
294 - boer
295 - bosse
525 - brems
447 - busch
296 - diehl
297 - fischer
298 - grahlmann
299 - grees
300 - hasenpuschtheil
301 - hauser
392 - klopp
438 - konrad
302 - kornacker
303 - kuery
304 - lagorce
305 - lombardia
437 - loukachova
306 - lutz
307 - meijer
308 - mendel
506 - radke
309 - reile
310 - scheideler
311 - schrenk
312 - steiner
313 - stjepandic
314 - sueltmann
439 - teifel
315 - tournu
316 - werdermann
317 - wilmer
501 - witt
318 - wittig
531 - xu
319 - yin
320 - zelt
90 -
experimentator_RNA_isolation
321 - aign
322 - bastuk
323 - bauer
324 - becerra
325 - beckmann
326 - bey
327 - bier
389 - boehm
328 - boer
329 - bosse
526 - brenndoerfer
448 - busch
330 - diehl
331 - fischer
332 - grahlmann
333 - grees
334 - hasenpuschtheil
335 - hauser
393 - heinfried
530 - klopp
442 - konrad
336 - kornacker
337 - kuery
338 - lagorce
339 - lombardia
440 - loukachova
340 - lutz
341 - meijer
342 - mendel
507 - radke
343 - reile
344 - scheideler
345 - schrenk
346 - steiner
347 - stjepandic
348 - sueltmann
441 - teifel
349 - tournu
350 - werdermann
351 - wilmer
453 - wirtz
500 - witt
352 - wittig
353 - yin
508 - zelt
91 -
experimentator_labeling
354 - aign
355 - bastuk
356 - bauer
357 - becerra
358 - beckmann
359 - bey
360 - bier
390 - boehm
361 - boer
362 - bosse
527 - brems
449 - busch
363 - diehl
364 - fischer
365 - grahlmann
366 - grees
367 - hasenpuschtheil
368 - hauser
394 - klopp
444 - konrad
369 - kornacker
370 - kuery
371 - lagorce
372 - lombardia
443 - loukachova
373 - lutz
374 - meijer
375 - mendel
509 - radke
376 - reile
377 - scheideler
378 - schrenk
379 - steiner
380 - stjepandic
381 - sueltmann
445 - teifel
382 - tournu
383 - werdermann
384 - wilmer
385 - wittig
529 - xu
386 - yin
510 - zelt
organism_specific_annotations
sample_id
2110 -
hybridisation_length_2nd_filter
h
2107 -
total_activity_2nd_filter
cpm
2108 -
exposure_time_2nd_filter
h
2109 -
array_individual_2nd_filter
2105 -
array_hybridisation_2nd_filter
2106 -
label_incorporation_rate_2nd_filter
%
2057 -
cancer_express_id
2058 -
sample_date_day
2059 -
sample_date_month
2060 -
sample_date_year
2061 -
institute
2140 - georg_august_university
2141 - duke_university_medical_center
2436 - klinikum_heidelberg
2142 - klinikum_mannheim
2337 - klinikum_ulm
2408 - robert_bosch_krankenhause_stuttgart
2143 - unknown
2062 -
institute_sample_id_firstpart
2063 -
institute_sample_id_secondpart
2064 -
physician
2144 - jakse
2145 - sturm
2331 - ringert
2146 - unknown
2065 -
pathologist
2445 - esposito
2147 - fuezesi
2148 - lindenberger
2149 - riggins
2444 - zimmerman
2343 - unknown
cell_culture_(see_e.g._
ATCC
)
2111 -
experimentator
2344 - not_applicable
2345 - bauer
2346 - bier
2452 - witt
2112 -
cell_line
2347 - not_applicable
2354 - panc1
2348 - mia_paca_2
2349 - capan1
2350 - suit_007
2351 - suit_028
2352 - paTu2
2353 - imimPC2
2409 - MCF-7
2410 - MDA-MB231
2447 - pool_of_Gimen_Kelly_IMR_Midi
2448 - Gimen
2449 - Kelly
2450 - IMR
2451 - Midi
2138 -
current_differentiation_grade_(may_or_may_not_differ_from_differentiation_grade_of_original_tumor(2092))
2453 - X_(unknown)
2454 - 1
2455 - 2
2456 - 3
2457 - 4
2113 -
treatment_cis_platin
mM
2114 -
treatment_taxol
mM
2129 -
treatment_TNFalpha
mM
2130 -
treatment_ICI.182.780
mM
2136 -
treatment_Valproate
mM
2137 -
treatment_Cycloheximide
mM
2115 -
timepoint_after_treatment
h
patient_info
patient_characteristics_(some_also_relevant_for_cell_line_origin)
2131 -
birth_date
2413 - specified
2414 - unknown
2415 - pooled
2458 - not_applicable_(e.g._cell_line)
2066 -
birth_date_day
2067 -
birth_date_month
2068 -
birth_date_year
2069 -
sex
2150 - male
2151 - female
2422 - pooled
2152 - unknown_(also_for_cell_line_of_undescribed_origin)
2070 -
race
2153 - caucasian
2154 - african
2155 - asian
2156 - other
2421 - pooled
2157 - unknown_(also_for_cell_line_of_undescribed_origin)
2116 -
smoking
2355 - past
2356 - present
2357 - never
2423 - pooled
2424 - unknown
2425 - not_applicable
2117 -
alcohol_consumption
2358 - past
2359 - present
2360 - never
2412 - pooled
2434 - unknown
2435 - not_applicable
2118 -
Diabetes_mellitus
2361 - none(no_finding/results_negative)
2459 - not_applicable_(e.g._cell_line)
2362 - latent_less_than_1_year
2363 - latent_more_than_1_year
2364 - manifest_less_than_1_year
2365 - manifest_less_than_1_year
2119 -
jaundice
2366 - none(no_finding/results_negative)
2460 - not_applicable_(e.g._cell_line)
2367 - yes
2368 - unknown
2120 -
pain
2369 - no
2370 - moderate
2371 - severe
2372 - unknown
2417 - not_applicable
2121 -
weight_loss
2373 - no
2374 - yes
2375 - unknown
2430 - not_applicable
2122 -
weight_loss_in_last_4_weeks
kg
2123 -
pancreatitis_in_history
2376 - none(no_finding/results_negative)
2377 - yes
2378 - unknown
2418 - not_applicable
2124 -
CA_19_9
units
2125 -
OP_procedure
2379 - Whipple
2411 - none(no_finding/results_negative)
2461 - not_applicable_(e.g._cell_line)
2380 - pp_Whipple
2381 - DPPHR
2382 - pancreatic_left_resection
2383 - total_pancreatectomy
2384 - other
2133 -
OP_date_day
2134 -
OP_date_day_month
2135 -
OP_date_day_year
patient_status
2071 -
previous_malignancy
2158 - yes
2159 - none(no_finding/results_negative)
2462 - not_applicable_(e.g._cell_line)
2160 - unknown
2072 -
live_status
2161 - alive_with_disease
2162 - alive_without_disease
2163 - died_of_disease
2164 - died_of_other
2165 - unknown
2463 - not_applicable_(e.g._cell_line)
2132 -
survival_time(put_0_both_if_unknown_or_died_in_op)
months
2073 -
pre_op_treatment
2166 - chemotherapy
2167 - no_therapy
2168 - radiotherapy
2397 - other
2169 - unknown
2420 - no_tumor_resection(e.g._cell_line_or_biopsy_of_normal_tissue)
2074 -
post_op_treatment
2170 - chemotherapy
2171 - no_therapy
2172 - radiotherapy
2398 - other
2173 - unknown
2419 - no_tumor_resection(e.g._cell_line_or_biopsy_of_normal_tissue)
tumor_info
tumor_general_(also_relevant_for_cell_line_origin)
2075 -
tumor_or_normal
2174 - tumor
2464 - cell_line
2175 - normal
2338 - inflammation_(non_tumor)
2176 - tumor_minus_normal
2177 - normal_minus_tumor
2076 -
tumor
2181 - brain_tumor
2180 - colon_carcinoma
2179 - mamma_carcinoma
2339 - pancreas_carcinoma
2178 - renal_cell_carcinoma
2465 - neuroblastoma_GNB
2466 - neuroblastoma_poorly_diff
2467 - neuroblastoma_diff
2468 - cell_line
2340 - none_(normal/no_finding/results_negative)
2139 -
normal
2472 - not_applicable_(tumor_or_cell_line)
2473 - pancreas
2474 - sympathetic_ganglia
2475 - adrenal_medulla
2077 -
tumor_type
2182 - renal_clear_cell
2183 - renal_chromophil
2184 - renal_chromophobe
2185 - renal_oncocytoma
2335 - renal_papillary
2186 - mamma_invasive_ductal
2187 - mamma_invasive_lobular
2188 - mamma_invasive_ductal_lobular
2189 - colon_unknown
2190 - rectum_unknown
2191 - brain_glial_astrocytic
2192 - brain_glial_oligodendroglial
2342 - pancreas_unknown
2403 - pancreas_ductal_adenocarcinoma
2404 - pancreas_cystadenoma
2405 - pancreas_cystadenocarcinoma
2437 - pancreas_endocrine
2438 - pancreas_serous_cystadenoma
2439 - pancreas_mucinous_cystadenoma
2440 - pancreas_mucinous_cystadenocarcinoma
2480 - pancreas_IPMC
2481 - pancreas_IPMN
2406 - pancreas_IPMT
2407 - pancreas_other
2479 - neuroblastoma
2193 - unknown_(also_for_cell_line_of_undescribed_origin)
2341 - no_tumor_(normal/no_finding/results_negative)
tumor_tnm_(also_for_cell_lines_of_well-known_origin)
2078 -
pT_stage
2194 - X_(also_for_cell_line_of_undescribed_origin)
2195 - 0
2196 - is
2197 - 1
2198 - 1a
2199 - 1b
2200 - 1c
2201 - 2
2202 - 3
2203 - 3a
2204 - 3b
2205 - 3c
2206 - 4
2207 - 4a
2208 - 4b
2209 - 4c
2248 - 4d
2079 -
pN_stage
2210 - X_(also_for_cell_line_of_undescribed_origin)
2211 - 0
2212 - 1
2213 - 1a
2214 - 1b
2215 - 2
2080 -
pM_stage
2216 - X_(also_for_cell_line_of_undescribed_origin)
2217 - 0
2218 - 1
2081 -
metastasis_location
2313 - not_applicable
2416 - none(no_finding/results_negative)
2314 - unknown
2315 - lung
2316 - bone
2317 - liver
2318 - brain
2319 - lymphnodes
2320 - bonemarrow
2321 - pleura
2322 - peritoneum
2323 - adrenal_glands
2324 - skin
2325 - pancreas
2326 - other
tumor_site_(also_for_cell_lines_of_well-known_origin)
2082 -
tumor_site
2219 - kidney
2220 - breast
2221 - colon
2222 - rectum
2223 - brain
2224 - liver
2225 - lung
2336 - pancreas
2226 - other
2428 - no_tumor(no_finding/results_negative)
2469 - unknown_(also_for_cell_line_of_undescribed_origin)
2083 -
tumor_subregion
2227 - unknown_(also_for_cell_line_of_undescribed_origin)
2429 - no_tumor(no_finding/results_negative)
2228 - kidney_unknown
2229 - breast_mamille_C50.0
2230 - breast_central_C50.1
2231 - breast_inside_top_quadrant_C50.2
2232 - breast_inside_bottom_quadrant_C50.3
2233 - breast_outside_top_quadrant_C50.4
2234 - breast_outside_bottom_quadrant_C50.5
2235 - breast_axillary_C50.6
2236 - breast_unknown
2237 - colon_unknown
2238 - rectum_unknown
2239 - brain_Q06_B09
2240 - brain_Q11_B06
2241 - brain_Q12_B01
2242 - brain_Q12_B09
2243 - brain_Q12_B08
2244 - brain_unknown
2399 - pancreas_head
2400 - pancreas_body
2401 - pancreas_tail
2402 - pancreas_papilla
2084 -
tumor_size
cm
tumor_invasion_(also_for_cell_lines_of_very_well-known_origin)
2085 -
lymphnodes_removed
2086 -
lymphnodes_invaded
2087 -
lymphvenes_invaded
2245 - X_(also_for_cell_line_of_undescribed_origin)
2246 - 0
2247 - 1
2088 -
vascular_invasion
2249 - X_(also_for_cell_line_of_undescribed_origin)
2250 - 0
2251 - 1
2252 - 2
2089 -
resection_status
2253 - X_(also_for_cell_line_of_undescribed_origin)
2254 - 0
2255 - 1
2256 - 2
2257 - 3
2258 - 4
2432 - no_tumor_resection(e.g._cell_line_or_biopsy_of_normal_tissue)
tumor_stage_and_histology_(also_for_cell_lines_of_well-known_origin)
2090 -
WHO_stage
2259 - 0
2260 - I
2261 - II
2327 - IIA
2328 - IIB
2262 - III
2329 - IIIA
2330 - IIIB
2263 - IV
2332 - not_applicable
2091 -
Duke_stage
2264 - A
2265 - B
2266 - C
2333 - D
2334 - no_colon_carcinoma_(also_for_cell_line_of_other_origin)
2470 - unknown_(also_for_cell_line_of_undescribed_origin)
2126 -
stroma
2385 - 0
2386 - 1
2387 - 2
2388 - 3
2426 - no_tumor(no_finding/results_negative)
2427 - pooled
2441 - unknown
2127 -
necrosis
2389 - 0
2390 - 1
2391 - 2
2392 - 3
2442 - unknown
2471 - not_applicable_(e.g._cell_line)
2128 -
granulocytes
2393 - 0
2394 - 1
2395 - 2
2396 - 3
2443 - unknown
2476 - not_applicable_(e.g._cell_line)
2092 -
differentiation_grade_(of_tumor_biopsy_or_original_tumor_in_case_of_cell_line)
2267 - X_(also_for_cell_line_of_undescribed_origin)
2268 - 1
2269 - 2
2270 - 3
2271 - 4
2431 - no_tumor(no_finding/results_negative)
percentage_normal
2093 -
percentage_normal
2272 - <5%
2273 - 5-25%
2274 - 25-50%
2275 - 50-75%
2276 - 75-95%
2277 - >95%
2278 - unknown
2433 - no_tumor(no_finding/results_negative)
2478 - not_applicable_(e.g._cell_line)
cytogenetics
cytogenetics_(also_for_current_status_of_cell_line)
2094 -
modal_number
2095 -
aberration_type
2279 - deletion
2280 - duplication
2281 - inversion
2282 - translocation
2283 - none
2446 - not_tested_(put_following_annotations_to_zero/not_applicable)
2096 -
aberration_breakpoint_chromosome
2097 -
aberration_breakpoint_arm
2284 - p
2285 - q
2286 - not_applicable
2098 -
aberration_breakpoint_subregion
2099 -
aberration_gain_chromosome
2100 -
aberration_gain_arm
2287 - p
2288 - q
2289 - not_applicable
2101 -
aberration_gain_subregion
2102 -
aberration_loss_chromosome
2103 -
aberration_loss_arm
2290 - p
2291 - q
2292 - not_applicable
2104 -
aberration_loss_subregion