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PMC:1892049 / 9652-10755 JSONTXT

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craft-ca-core-ex-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T15045 33-36 CHEBI_SO_EXT:DNA denotes DNA
T15046 168-174 SO_EXT:0001023 denotes allele
T15047 212-213 CHEBI_SO_EXT:base denotes b
T15048 231-248 SO_EXT:0000105 denotes arm of Chromosome
T15049 238-248 GO_SO_EXT:chromosome denotes Chromosome
T15050 326-329 SO_EXT:0000694 denotes SNP
T15051 336-339 SO_EXT:0000694 denotes SNP
T15052 389-393 SO_EXT:sequence_copy_entity denotes copy
T15053 418-424 SO_EXT:0001023 denotes allele
T15054 482-489 SO_EXT:0001023 denotes alleles
T15055 523-526 SO_EXT:0000694 denotes SNP
T15056 560-564 SO_EXT:0000694 denotes SNPs
T15057 574-580 SO_EXT:0001023 denotes allele
T15058 628-632 SO_EXT:0000694 denotes SNPs
T15059 642-648 SO_EXT:0001023 denotes allele
T15060 717-723 SO_EXT:0001023 denotes allele
T15061 824-825 CHEBI_SO_EXT:base denotes b
T15062 846-850 SO_EXT:sequence_copy_entity denotes copy
T15063 981-988 SO_EXT:0001026 denotes genomic
T15064 989-997 SO_EXT:sequence_deletion_entity_or_process denotes deletion
T15065 1054-1059 SO_EXT:0000704 denotes genes
T15066 1077-1085 SO_EXT:sequence_deletion_entity_or_process denotes deletion
T15067 1087-1092 PR_EXT:000009158 denotes ITPR1
T15068 1097-1102 PR_EXT:000015827 denotes SUMF1

craft-ca-core-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T15029 168-174 SO:0001023 denotes allele
T15030 231-248 SO:0000105 denotes arm of Chromosome
T15031 326-329 SO:0000694 denotes SNP
T15032 336-339 SO:0000694 denotes SNP
T15033 418-424 SO:0001023 denotes allele
T15034 482-489 SO:0001023 denotes alleles
T15035 523-526 SO:0000694 denotes SNP
T15036 560-564 SO:0000694 denotes SNPs
T15037 574-580 SO:0001023 denotes allele
T15038 628-632 SO:0000694 denotes SNPs
T15039 642-648 SO:0001023 denotes allele
T15040 717-723 SO:0001023 denotes allele
T15041 981-988 SO:0001026 denotes genomic
T15042 1054-1059 SO:0000704 denotes genes
T15043 1087-1092 PR:000009158 denotes ITPR1
T15044 1097-1102 PR:000015827 denotes SUMF1

craft-sa-dev

Id Subject Object Predicate Lexical cue
T15069 0-7 NNS denotes Metrics
T15070 8-15 VBN denotes Derived
T15071 16-20 IN denotes from
T15072 21-29 NN denotes Analysis
T15073 30-32 IN denotes of
T15074 33-36 NN denotes DNA
T15075 37-41 IN denotes from
T15076 42-50 VBN denotes Affected
T15077 58-64 NN denotes Member
T15078 51-57 NN denotes Family
T15079 65-66 CD denotes 7
T15080 67-72 VBG denotes Using
T15081 73-81 NNP denotes Illumina
T15082 91-102 NNP denotes HumanHap550
T15083 82-90 NNP denotes Infinium
T15084 114-119 NNS denotes Chips
T15085 103-113 NN denotes Genotyping
T15086 119-251 sentence denotes The upper and lower plots are log R ratio and B allele frequency, respectively, at an ~800-kb segment on the p arm of Chromosome 3.
T15087 120-123 DT denotes The
T15088 140-145 NNS denotes plots
T15089 124-129 JJ denotes upper
T15090 130-133 CC denotes and
T15091 134-139 JJ denotes lower
T15092 146-149 VBP denotes are
T15093 150-153 NN denotes log
T15094 154-155 NN denotes R
T15095 156-161 NN denotes ratio
T15096 162-165 CC denotes and
T15097 166-167 NN denotes B
T15098 168-174 NN denotes allele
T15099 175-184 NN denotes frequency
T15100 184-186 , denotes ,
T15101 186-198 RB denotes respectively
T15102 198-200 , denotes ,
T15103 200-202 IN denotes at
T15104 203-205 DT denotes an
T15105 214-221 NN denotes segment
T15106 206-207 SYM denotes ~
T15107 207-210 CD denotes 800
T15108 211-213 NN denotes kb
T15109 210-211 HYPH denotes -
T15110 222-224 IN denotes on
T15111 225-228 DT denotes the
T15112 231-234 NN denotes arm
T15113 229-230 NN denotes p
T15114 235-237 IN denotes of
T15115 238-248 NN denotes Chromosome
T15116 249-250 CD denotes 3
T15117 250-251 . denotes .
T15118 251-415 sentence denotes Log R ratio is the ratio of normalized, observed R to expected R for each SNP (each SNP is a blue dot) and thus serves as a surrogate of copy number at each locus.
T15119 252-255 NN denotes Log
T15120 256-257 NN denotes R
T15121 258-263 NN denotes ratio
T15122 264-266 VBZ denotes is
T15123 267-270 DT denotes the
T15124 271-276 NN denotes ratio
T15125 277-279 IN denotes of
T15126 280-290 VBN denotes normalized
T15127 301-302 NN denotes R
T15128 290-292 , denotes ,
T15129 292-300 VBN denotes observed
T15130 303-305 IN denotes to
T15131 306-314 VBN denotes expected
T15132 315-316 NN denotes R
T15133 317-320 IN denotes for
T15134 321-325 DT denotes each
T15135 326-329 NN denotes SNP
T15136 330-331 -LRB- denotes (
T15137 340-342 VBZ denotes is
T15138 331-335 DT denotes each
T15139 336-339 NN denotes SNP
T15140 343-344 DT denotes a
T15141 350-353 NN denotes dot
T15142 345-349 JJ denotes blue
T15143 353-354 -RRB- denotes )
T15144 355-358 CC denotes and
T15145 359-363 RB denotes thus
T15146 364-370 VBZ denotes serves
T15147 371-373 IN denotes as
T15148 374-375 DT denotes a
T15149 376-385 NN denotes surrogate
T15150 386-388 IN denotes of
T15151 389-393 NN denotes copy
T15152 394-400 NN denotes number
T15153 401-403 IN denotes at
T15154 404-408 DT denotes each
T15155 409-414 NN denotes locus
T15156 414-415 . denotes .
T15157 415-553 sentence denotes B allele frequency is a measure of the number of times the A or B alleles are detected at each locus (each SNP is denoted by a blue dot).
T15158 416-417 NN denotes B
T15159 418-424 NN denotes allele
T15160 425-434 NN denotes frequency
T15161 435-437 VBZ denotes is
T15162 438-439 DT denotes a
T15163 440-447 NN denotes measure
T15164 448-450 IN denotes of
T15165 451-454 DT denotes the
T15166 455-461 NN denotes number
T15167 462-464 IN denotes of
T15168 465-470 NNS denotes times
T15169 471-474 DT denotes the
T15170 482-489 NNS denotes alleles
T15171 475-476 NN denotes A
T15172 477-479 CC denotes or
T15173 480-481 NN denotes B
T15174 494-502 VBN denotes detected
T15175 490-493 VBP denotes are
T15176 503-505 IN denotes at
T15177 506-510 DT denotes each
T15178 511-516 NN denotes locus
T15179 517-518 -LRB- denotes (
T15180 530-537 VBN denotes denoted
T15181 518-522 DT denotes each
T15182 523-526 NN denotes SNP
T15183 527-529 VBZ denotes is
T15184 538-540 IN denotes by
T15185 541-542 DT denotes a
T15186 548-551 NN denotes dot
T15187 543-547 JJ denotes blue
T15188 551-552 -RRB- denotes )
T15189 552-553 . denotes .
T15190 553-771 sentence denotes Thus, SNPs with a B allele frequency of one are apparent B/B homozygotes, SNPs with a B allele frequency of 0.5 are apparent A/B heterozygotes, and those with a B allele frequency of zero are apparent A/A homozygotes.
T15191 554-558 RB denotes Thus
T15192 666-669 VBP denotes are
T15193 558-560 , denotes ,
T15194 560-564 NNS denotes SNPs
T15195 598-601 VBP denotes are
T15196 565-569 IN denotes with
T15197 570-571 DT denotes a
T15198 581-590 NN denotes frequency
T15199 572-573 NN denotes B
T15200 574-580 NN denotes allele
T15201 591-593 IN denotes of
T15202 594-597 CD denotes one
T15203 602-610 JJ denotes apparent
T15204 615-626 NNS denotes homozygotes
T15205 611-612 NN denotes B
T15206 613-614 NN denotes B
T15207 612-613 HYPH denotes /
T15208 626-628 , denotes ,
T15209 628-632 NNS denotes SNPs
T15210 633-637 IN denotes with
T15211 638-639 DT denotes a
T15212 649-658 NN denotes frequency
T15213 640-641 NN denotes B
T15214 642-648 NN denotes allele
T15215 659-661 IN denotes of
T15216 662-665 CD denotes 0.5
T15217 670-678 JJ denotes apparent
T15218 683-696 NNS denotes heterozygotes
T15219 679-680 NN denotes A
T15220 681-682 NN denotes B
T15221 680-681 HYPH denotes /
T15222 696-698 , denotes ,
T15223 698-701 CC denotes and
T15224 702-707 DT denotes those
T15225 742-745 VBP denotes are
T15226 708-712 IN denotes with
T15227 713-714 DT denotes a
T15228 724-733 NN denotes frequency
T15229 715-716 NN denotes B
T15230 717-723 NN denotes allele
T15231 734-736 IN denotes of
T15232 737-741 CD denotes zero
T15233 746-754 JJ denotes apparent
T15234 759-770 NNS denotes homozygotes
T15235 755-756 NN denotes A
T15236 757-758 NN denotes A
T15237 756-757 HYPH denotes /
T15238 770-771 . denotes .
T15239 771-907 sentence denotes Clearly, these plots show a contiguous region ~200 kb long with decreased copy number and apparent homozygosity (bounded by a red box).
T15240 772-779 RB denotes Clearly
T15241 793-797 VBP denotes show
T15242 779-781 , denotes ,
T15243 781-786 DT denotes these
T15244 787-792 NNS denotes plots
T15245 798-799 DT denotes a
T15246 811-817 NN denotes region
T15247 800-810 JJ denotes contiguous
T15248 818-819 SYM denotes ~
T15249 819-822 CD denotes 200
T15250 823-825 NN denotes kb
T15251 826-830 JJ denotes long
T15252 831-835 IN denotes with
T15253 836-845 VBN denotes decreased
T15254 851-857 NN denotes number
T15255 846-850 NN denotes copy
T15256 858-861 CC denotes and
T15257 862-870 JJ denotes apparent
T15258 871-883 NN denotes homozygosity
T15259 884-885 -LRB- denotes (
T15260 885-892 VBN denotes bounded
T15261 893-895 IN denotes by
T15262 896-897 DT denotes a
T15263 902-905 NN denotes box
T15264 898-901 JJ denotes red
T15265 905-906 -RRB- denotes )
T15266 906-907 . denotes .
T15267 907-1003 sentence denotes As we have demonstrated previously, this is indicative of a heterozygous genomic deletion [15].
T15268 908-910 IN denotes As
T15269 919-931 VBN denotes demonstrated
T15270 911-913 PRP denotes we
T15271 914-918 VBP denotes have
T15272 949-951 VBZ denotes is
T15273 932-942 RB denotes previously
T15274 942-944 , denotes ,
T15275 944-948 DT denotes this
T15276 952-962 JJ denotes indicative
T15277 963-965 IN denotes of
T15278 966-967 DT denotes a
T15279 989-997 NN denotes deletion
T15280 968-980 JJ denotes heterozygous
T15281 981-988 JJ denotes genomic
T15282 998-999 -LRB- denotes [
T15283 999-1001 CD denotes 15
T15284 1001-1002 -RRB- denotes ]
T15285 1002-1003 . denotes .
T15286 1003-1103 sentence denotes Below these plots is a schematic of the two known genes affected by this deletion, ITPR1 and SUMF1.
T15287 1004-1009 IN denotes Below
T15288 1022-1024 VBZ denotes is
T15289 1010-1015 DT denotes these
T15290 1016-1021 NNS denotes plots
T15291 1025-1026 DT denotes a
T15292 1027-1036 NN denotes schematic
T15293 1037-1039 IN denotes of
T15294 1040-1043 DT denotes the
T15295 1054-1059 NNS denotes genes
T15296 1044-1047 CD denotes two
T15297 1048-1053 VBN denotes known
T15298 1060-1068 VBN denotes affected
T15299 1069-1071 IN denotes by
T15300 1072-1076 DT denotes this
T15301 1077-1085 NN denotes deletion
T15302 1085-1087 , denotes ,
T15303 1087-1092 NN denotes ITPR1
T15304 1093-1096 CC denotes and
T15305 1097-1102 NN denotes SUMF1
T15306 1102-1103 . denotes .
R4391 T15070 T15069 acl Derived,Metrics
R4392 T15071 T15070 prep from,Derived
R4393 T15072 T15071 pobj Analysis,from
R4394 T15073 T15072 prep of,Analysis
R4395 T15074 T15073 pobj DNA,of
R4396 T15075 T15074 prep from,DNA
R4397 T15076 T15077 amod Affected,Member
R4398 T15077 T15075 pobj Member,from
R4399 T15078 T15077 compound Family,Member
R4400 T15079 T15077 nummod 7,Member
R4401 T15080 T15070 advcl Using,Derived
R4402 T15081 T15082 compound Illumina,HumanHap550
R4403 T15082 T15084 compound HumanHap550,Chips
R4404 T15083 T15082 compound Infinium,HumanHap550
R4405 T15084 T15080 dobj Chips,Using
R4406 T15085 T15084 compound Genotyping,Chips
R4407 T15087 T15088 det The,plots
R4408 T15088 T15092 nsubj plots,are
R4409 T15089 T15088 amod upper,plots
R4410 T15090 T15089 cc and,upper
R4411 T15091 T15089 conj lower,upper
R4412 T15093 T15094 compound log,R
R4413 T15094 T15095 compound R,ratio
R4414 T15095 T15092 attr ratio,are
R4415 T15096 T15095 cc and,ratio
R4416 T15097 T15098 compound B,allele
R4417 T15098 T15099 compound allele,frequency
R4418 T15099 T15095 conj frequency,ratio
R4419 T15100 T15092 punct ", ",are
R4420 T15101 T15092 advmod respectively,are
R4421 T15102 T15092 punct ", ",are
R4422 T15103 T15092 prep at,are
R4423 T15104 T15105 det an,segment
R4424 T15105 T15103 pobj segment,at
R4425 T15106 T15107 punct ~,800
R4426 T15107 T15108 nummod 800,kb
R4427 T15108 T15105 compound kb,segment
R4428 T15109 T15108 punct -,kb
R4429 T15110 T15105 prep on,segment
R4430 T15111 T15112 det the,arm
R4431 T15112 T15110 pobj arm,on
R4432 T15113 T15112 compound p,arm
R4433 T15114 T15112 prep of,arm
R4434 T15115 T15114 pobj Chromosome,of
R4435 T15116 T15115 nummod 3,Chromosome
R4436 T15117 T15092 punct .,are
R4437 T15119 T15120 compound Log,R
R4438 T15120 T15121 compound R,ratio
R4439 T15121 T15122 nsubj ratio,is
R4440 T15123 T15124 det the,ratio
R4441 T15124 T15122 attr ratio,is
R4442 T15125 T15124 prep of,ratio
R4443 T15126 T15127 amod normalized,R
R4444 T15127 T15125 pobj R,of
R4445 T15128 T15127 punct ", ",R
R4446 T15129 T15127 amod observed,R
R4447 T15130 T15124 prep to,ratio
R4448 T15131 T15132 amod expected,R
R4449 T15132 T15130 pobj R,to
R4450 T15133 T15124 prep for,ratio
R4451 T15134 T15135 det each,SNP
R4452 T15135 T15133 pobj SNP,for
R4453 T15136 T15137 punct (,is
R4454 T15137 T15124 parataxis is,ratio
R4455 T15138 T15139 det each,SNP
R4456 T15139 T15137 nsubj SNP,is
R4457 T15140 T15141 det a,dot
R4458 T15141 T15137 attr dot,is
R4459 T15142 T15141 amod blue,dot
R4460 T15143 T15137 punct ),is
R4461 T15144 T15122 cc and,is
R4462 T15145 T15146 advmod thus,serves
R4463 T15146 T15122 conj serves,is
R4464 T15147 T15146 prep as,serves
R4465 T15148 T15149 det a,surrogate
R4466 T15149 T15147 pobj surrogate,as
R4467 T15150 T15149 prep of,surrogate
R4468 T15151 T15152 compound copy,number
R4469 T15152 T15150 pobj number,of
R4470 T15153 T15146 prep at,serves
R4471 T15154 T15155 det each,locus
R4472 T15155 T15153 pobj locus,at
R4473 T15156 T15122 punct .,is
R4474 T15158 T15159 compound B,allele
R4475 T15159 T15160 compound allele,frequency
R4476 T15160 T15161 nsubj frequency,is
R4477 T15162 T15163 det a,measure
R4478 T15163 T15161 attr measure,is
R4479 T15164 T15163 prep of,measure
R4480 T15165 T15166 det the,number
R4481 T15166 T15164 pobj number,of
R4482 T15167 T15166 prep of,number
R4483 T15168 T15167 pobj times,of
R4484 T15169 T15170 det the,alleles
R4485 T15170 T15174 nsubjpass alleles,detected
R4486 T15171 T15170 nmod A,alleles
R4487 T15172 T15171 cc or,A
R4488 T15173 T15171 conj B,A
R4489 T15174 T15168 advcl detected,times
R4490 T15175 T15174 auxpass are,detected
R4491 T15176 T15174 prep at,detected
R4492 T15177 T15178 det each,locus
R4493 T15178 T15176 pobj locus,at
R4494 T15179 T15180 punct (,denoted
R4495 T15180 T15161 parataxis denoted,is
R4496 T15181 T15182 det each,SNP
R4497 T15182 T15180 nsubjpass SNP,denoted
R4498 T15183 T15180 auxpass is,denoted
R4499 T15184 T15180 agent by,denoted
R4500 T15185 T15186 det a,dot
R4501 T15186 T15184 pobj dot,by
R4502 T15187 T15186 amod blue,dot
R4503 T15188 T15180 punct ),denoted
R4504 T15189 T15161 punct .,is
R4505 T15191 T15192 advmod Thus,are
R4506 T15193 T15192 punct ", ",are
R4507 T15194 T15195 nsubj SNPs,are
R4508 T15195 T15192 ccomp are,are
R4509 T15196 T15194 prep with,SNPs
R4510 T15197 T15198 det a,frequency
R4511 T15198 T15196 pobj frequency,with
R4512 T15199 T15200 compound B,allele
R4513 T15200 T15198 compound allele,frequency
R4514 T15201 T15198 prep of,frequency
R4515 T15202 T15201 pobj one,of
R4516 T15203 T15204 amod apparent,homozygotes
R4517 T15204 T15195 attr homozygotes,are
R4518 T15205 T15206 compound B,B
R4519 T15206 T15204 compound B,homozygotes
R4520 T15207 T15206 punct /,B
R4521 T15208 T15192 punct ", ",are
R4522 T15209 T15192 nsubj SNPs,are
R4523 T15210 T15209 prep with,SNPs
R4524 T15211 T15212 det a,frequency
R4525 T15212 T15210 pobj frequency,with
R4526 T15213 T15214 compound B,allele
R4527 T15214 T15212 compound allele,frequency
R4528 T15215 T15212 prep of,frequency
R4529 T15216 T15215 pobj 0.5,of
R4530 T15217 T15218 amod apparent,heterozygotes
R4531 T15218 T15192 attr heterozygotes,are
R4532 T15219 T15220 compound A,B
R4533 T15220 T15218 compound B,heterozygotes
R4534 T15221 T15220 punct /,B
R4535 T15222 T15192 punct ", ",are
R4536 T15223 T15192 cc and,are
R4537 T15224 T15225 nsubj those,are
R4538 T15225 T15192 conj are,are
R4539 T15226 T15224 prep with,those
R4540 T15227 T15228 det a,frequency
R4541 T15228 T15226 pobj frequency,with
R4542 T15229 T15230 compound B,allele
R4543 T15230 T15228 compound allele,frequency
R4544 T15231 T15228 prep of,frequency
R4545 T15232 T15231 pobj zero,of
R4546 T15233 T15234 amod apparent,homozygotes
R4547 T15234 T15225 attr homozygotes,are
R4548 T15235 T15236 compound A,A
R4549 T15236 T15234 compound A,homozygotes
R4550 T15237 T15236 punct /,A
R4551 T15238 T15225 punct .,are
R4552 T15240 T15241 advmod Clearly,show
R4553 T15242 T15241 punct ", ",show
R4554 T15243 T15244 det these,plots
R4555 T15244 T15241 nsubj plots,show
R4556 T15245 T15246 det a,region
R4557 T15246 T15241 dobj region,show
R4558 T15247 T15246 amod contiguous,region
R4559 T15248 T15249 punct ~,200
R4560 T15249 T15250 nummod 200,kb
R4561 T15250 T15251 npadvmod kb,long
R4562 T15251 T15246 amod long,region
R4563 T15252 T15246 prep with,region
R4564 T15253 T15254 amod decreased,number
R4565 T15254 T15252 pobj number,with
R4566 T15255 T15254 compound copy,number
R4567 T15256 T15254 cc and,number
R4568 T15257 T15258 amod apparent,homozygosity
R4569 T15258 T15254 conj homozygosity,number
R4570 T15259 T15246 punct (,region
R4571 T15260 T15246 acl bounded,region
R4572 T15261 T15260 agent by,bounded
R4573 T15262 T15263 det a,box
R4574 T15263 T15261 pobj box,by
R4575 T15264 T15263 amod red,box
R4576 T15265 T15241 punct ),show
R4577 T15266 T15241 punct .,show
R4578 T15268 T15269 mark As,demonstrated
R4579 T15269 T15272 advcl demonstrated,is
R4580 T15270 T15269 nsubj we,demonstrated
R4581 T15271 T15269 aux have,demonstrated
R4582 T15273 T15269 advmod previously,demonstrated
R4583 T15274 T15272 punct ", ",is
R4584 T15275 T15272 nsubj this,is
R4585 T15276 T15272 acomp indicative,is
R4586 T15277 T15276 prep of,indicative
R4587 T15278 T15279 det a,deletion
R4588 T15279 T15277 pobj deletion,of
R4589 T15280 T15279 amod heterozygous,deletion
R4590 T15281 T15279 amod genomic,deletion
R4591 T15282 T15283 punct [,15
R4592 T15283 T15272 parataxis 15,is
R4593 T15284 T15283 punct ],15
R4594 T15285 T15272 punct .,is
R4595 T15287 T15288 prep Below,is
R4596 T15289 T15290 det these,plots
R4597 T15290 T15287 pobj plots,Below
R4598 T15291 T15292 det a,schematic
R4599 T15292 T15288 nsubj schematic,is
R4600 T15293 T15292 prep of,schematic
R4601 T15294 T15295 det the,genes
R4602 T15295 T15293 pobj genes,of
R4603 T15296 T15295 nummod two,genes
R4604 T15297 T15295 amod known,genes
R4605 T15298 T15295 acl affected,genes
R4606 T15299 T15298 agent by,affected
R4607 T15300 T15301 det this,deletion
R4608 T15301 T15299 pobj deletion,by
R4609 T15302 T15295 punct ", ",genes
R4610 T15303 T15295 appos ITPR1,genes
R4611 T15304 T15303 cc and,ITPR1
R4612 T15305 T15303 conj SUMF1,ITPR1
R4613 T15306 T15288 punct .,is

2_test

Id Subject Object Predicate Lexical cue
17590087-17116639-85657851 999-1001 17116639 denotes 15
T87082 999-1001 17116639 denotes 15