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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-100 Sentence denotes Common BRCA2 variants and modification of breast and ovarian cancer risk in BRCA1 mutation carriers.
T2 101-306 Sentence denotes The HH genotype of the nonconservative amino acid substitution polymorphism N372H in the BRCA2 gene was reported to be associated with a 1.3- to 1.5-fold increase in risk of both breast and ovarian cancer.
T3 307-545 Sentence denotes As these studies concerned sporadic cancer cases, we investigated whether N372H and another common variant located in the 5'-untranslated region (203G > A) of the BRCA2 gene modify breast or ovarian cancer risk in BRCA1 mutation carriers.
T4 546-637 Sentence denotes The study includes 778 women carrying a BRCA1 germ-line mutation belonging to 403 families.
T5 638-722 Sentence denotes The two BRCA2 variants were analyzed by the TaqMan allelic discrimination technique.
T6 723-820 Sentence denotes Genotypes were analyzed by disease-free survival analysis using a Cox proportional hazards model.
T7 821-950 Sentence denotes We found no evidence of a significant modification of breast cancer penetrance in BRCA1 mutation carriers by either polymorphism.
T8 951-1155 Sentence denotes In respect of ovarian cancer risk, we also saw no effect with the N372H variant but we did observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00).
T9 1156-1366 Sentence denotes In contrast to the result of Healey et al. on newborn females and adult female controls, we found no departure from Hardy-Weinberg equilibrium in the distribution of N372H alleles for our female BRCA1 carriers.
T10 1367-1590 Sentence denotes We conclude that if these single-nucleotide polymorphisms do modify the risk of cancer in BRCA1 mutation carriers, their effects are not significantly larger than that of N372H previously observed in the general population.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
1408 7-12 GeneOrGeneProduct denotes BRCA2 NCBIGene:675
1409 42-67 DiseaseOrPhenotypicFeature denotes breast and ovarian cancer MESH:D010051|MESH:D001943
1410 76-81 GeneOrGeneProduct denotes BRCA1 NCBIGene:672
1411 177-182 SequenceVariant denotes N372H DBSNP:rs144848
1412 190-195 GeneOrGeneProduct denotes BRCA2 NCBIGene:675
1413 280-305 DiseaseOrPhenotypicFeature denotes breast and ovarian cancer MESH:D001943|MESH:D010051
1414 343-349 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
1415 381-386 SequenceVariant denotes N372H DBSNP:rs144848
1416 453-461 SequenceVariant denotes 203G > A g|SUB|G|203|A
1417 470-475 GeneOrGeneProduct denotes BRCA2 NCBIGene:675
1418 488-512 DiseaseOrPhenotypicFeature denotes breast or ovarian cancer MESH:D001943|MESH:D010051
1419 521-526 GeneOrGeneProduct denotes BRCA1 NCBIGene:672
1420 569-574 OrganismTaxon denotes women NCBITaxon:9606
1421 586-591 GeneOrGeneProduct denotes BRCA1 NCBIGene:672
1422 646-651 GeneOrGeneProduct denotes BRCA2 NCBIGene:675
1423 875-888 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
1424 903-908 GeneOrGeneProduct denotes BRCA1 NCBIGene:672
1425 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer MESH:D010051
1426 1017-1022 SequenceVariant denotes N372H DBSNP:rs144848
1427 1107-1111 SequenceVariant denotes 203A g|Allele|A|203
1428 1322-1327 SequenceVariant denotes N372H DBSNP:rs144848
1429 1351-1356 GeneOrGeneProduct denotes BRCA1 NCBIGene:672
1430 1447-1453 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
1431 1457-1462 GeneOrGeneProduct denotes BRCA1 NCBIGene:672
1432 1538-1543 SequenceVariant denotes N372H DBSNP:rs144848

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 53-67 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170
T2 61-67 DiseaseOrPhenotypicFeature denotes cancer 0004992
T3 291-305 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170
T4 299-305 DiseaseOrPhenotypicFeature denotes cancer 0004992
T5 343-349 DiseaseOrPhenotypicFeature denotes cancer 0004992
T6 498-512 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170
T7 506-512 DiseaseOrPhenotypicFeature denotes cancer 0004992
T8 875-888 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T9 882-888 DiseaseOrPhenotypicFeature denotes cancer 0004992
T10 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170
T11 973-979 DiseaseOrPhenotypicFeature denotes cancer 0004992
T12 1447-1453 DiseaseOrPhenotypicFeature denotes cancer 0004992

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 177-182 SequenceVariant denotes N372H
T2 381-386 SequenceVariant denotes N372H
T3 453-457 SequenceVariant denotes 203G
T4 1017-1022 SequenceVariant denotes N372H
T5 1107-1111 SequenceVariant denotes 203A
T6 1322-1327 SequenceVariant denotes N372H
T7 1538-1543 SequenceVariant denotes N372H

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 7-12 GeneOrGeneProduct denotes BRCA2
T2 76-81 GeneOrGeneProduct denotes BRCA1
T3 82-90 GeneOrGeneProduct denotes mutation
T4 91-99 GeneOrGeneProduct denotes carriers
T5 140-150 GeneOrGeneProduct denotes amino acid
T6 190-195 GeneOrGeneProduct denotes BRCA2
T7 250-254 GeneOrGeneProduct denotes fold
T8 350-355 GeneOrGeneProduct denotes cases
T9 470-475 GeneOrGeneProduct denotes BRCA2
T10 521-526 GeneOrGeneProduct denotes BRCA1
T11 527-535 GeneOrGeneProduct denotes mutation
T12 536-544 GeneOrGeneProduct denotes carriers
T13 586-591 GeneOrGeneProduct denotes BRCA1
T14 592-596 GeneOrGeneProduct denotes germ
T15 597-601 GeneOrGeneProduct denotes line
T16 602-610 GeneOrGeneProduct denotes mutation
T17 646-651 GeneOrGeneProduct denotes BRCA2
T18 787-792 GeneOrGeneProduct denotes a Cox
T19 903-908 GeneOrGeneProduct denotes BRCA1
T20 909-917 GeneOrGeneProduct denotes mutation
T21 918-926 GeneOrGeneProduct denotes carriers
T22 1159-1167 GeneOrGeneProduct denotes contrast
T23 1272-1277 GeneOrGeneProduct denotes Hardy
T24 1351-1356 GeneOrGeneProduct denotes BRCA1
T25 1357-1365 GeneOrGeneProduct denotes carriers
T26 1457-1462 GeneOrGeneProduct denotes BRCA1
T27 1463-1471 GeneOrGeneProduct denotes mutation
T28 1472-1480 GeneOrGeneProduct denotes carriers

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 7-12 GeneOrGeneProduct denotes BRCA2
T2 76-81 GeneOrGeneProduct denotes BRCA1
T3 140-150 GeneOrGeneProduct denotes amino acid
T4 190-195 GeneOrGeneProduct denotes BRCA2
T5 250-254 GeneOrGeneProduct denotes fold
T6 470-475 GeneOrGeneProduct denotes BRCA2
T7 521-526 GeneOrGeneProduct denotes BRCA1
T8 586-591 GeneOrGeneProduct denotes BRCA1
T9 646-651 GeneOrGeneProduct denotes BRCA2
T10 903-908 GeneOrGeneProduct denotes BRCA1
T11 1351-1356 GeneOrGeneProduct denotes BRCA1
T12 1457-1462 GeneOrGeneProduct denotes BRCA1

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 53-67 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T2 291-305 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T3 343-349 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 498-512 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T5 750-757 DiseaseOrPhenotypicFeature denotes disease D004194
T6 875-888 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T7 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T8 1447-1453 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 7-12 GeneOrGeneProduct denotes BRCA2
T2 190-195 GeneOrGeneProduct denotes BRCA2
T3 470-475 GeneOrGeneProduct denotes BRCA2
T4 646-651 GeneOrGeneProduct denotes BRCA2

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 53-67 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170|0005140
T3 291-305 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170|0005140
T5 498-512 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170|0005140
T7 875-888 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T9 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer 0008170|0005140

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 53-67 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T2 291-305 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T3 343-349 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 498-512 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T5 750-757 DiseaseOrPhenotypicFeature denotes disease D004194
T6 875-888 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T7 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T8 1447-1453 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 53-67 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T2 291-305 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T3 343-349 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 498-512 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T5 875-888 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T6 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T7 1447-1453 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 569-574 OrganismTaxon denotes women

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label
T4 646-651 GeneOrGeneProduct denotes BRCA2
T3 470-475 GeneOrGeneProduct denotes BRCA2
T2 190-195 GeneOrGeneProduct denotes BRCA2
T1 7-12 GeneOrGeneProduct denotes BRCA2
T7 1447-1453 DiseaseOrPhenotypicFeature denotes cancer D009369
T6 965-979 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T5 875-888 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T4943 498-512 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T58027 343-349 DiseaseOrPhenotypicFeature denotes cancer D009369
T19450 291-305 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T16641 53-67 DiseaseOrPhenotypicFeature denotes ovarian cancer D010051
T72525 569-574 OrganismTaxon denotes women
T72018 1538-1543 SequenceVariant denotes N372H
T15227 1322-1327 SequenceVariant denotes N372H
T23613 1107-1111 SequenceVariant denotes 203A
T10040 1017-1022 SequenceVariant denotes N372H
T92662 453-457 SequenceVariant denotes 203G
T11899 381-386 SequenceVariant denotes N372H
T79781 177-182 SequenceVariant denotes N372H

DisGeNET5_variant_disease

Id Subject Object Predicate Lexical cue
15668505-7#66#71#geners144848 1017-1022 geners144848 denotes N372H
15668505-7#14#28#diseaseC0029925 965-979 diseaseC0029925 denotes ovarian cancer
15668505-7#14#28#diseaseC1140680 965-979 diseaseC1140680 denotes ovarian cancer
66#71#geners14484814#28#diseaseC0029925 15668505-7#66#71#geners144848 15668505-7#14#28#diseaseC0029925 associated_with N372H,ovarian cancer
66#71#geners14484814#28#diseaseC1140680 15668505-7#66#71#geners144848 15668505-7#14#28#diseaseC1140680 associated_with N372H,ovarian cancer

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
15668505-0#7#12#gene675 646-651 gene675 denotes BRCA2
15668505-0#76#81#gene672 1457-1462 gene672 denotes BRCA1
15668505-0#53#67#diseaseC0029925 1042-1262 diseaseC0029925 denotes observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar
15668505-0#53#67#diseaseC1140680 1042-1262 diseaseC1140680 denotes observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar
15668505-0#53#67#diseaseC0029925 1042-1262 diseaseC0029925 denotes observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar
15668505-0#53#67#diseaseC1140680 1042-1262 diseaseC1140680 denotes observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar
15668505-6#82#87#gene672 903-908 gene672 denotes BRCA1
15668505-6#54#67#diseaseC0006142 875-888 diseaseC0006142 denotes breast cancer
15668505-6#54#67#diseaseC0678222 875-888 diseaseC0678222 denotes breast cancer
7#12#gene67553#67#diseaseC0029925 15668505-0#7#12#gene675 15668505-0#53#67#diseaseC0029925 associated_with BRCA2,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
7#12#gene67553#67#diseaseC1140680 15668505-0#7#12#gene675 15668505-0#53#67#diseaseC1140680 associated_with BRCA2,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
7#12#gene67553#67#diseaseC0029925 15668505-0#7#12#gene675 15668505-0#53#67#diseaseC0029925 associated_with BRCA2,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
7#12#gene67553#67#diseaseC1140680 15668505-0#7#12#gene675 15668505-0#53#67#diseaseC1140680 associated_with BRCA2,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
76#81#gene67253#67#diseaseC0029925 15668505-0#76#81#gene672 15668505-0#53#67#diseaseC0029925 associated_with BRCA1,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
76#81#gene67253#67#diseaseC1140680 15668505-0#76#81#gene672 15668505-0#53#67#diseaseC1140680 associated_with BRCA1,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
76#81#gene67253#67#diseaseC0029925 15668505-0#76#81#gene672 15668505-0#53#67#diseaseC0029925 associated_with BRCA1,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
76#81#gene67253#67#diseaseC1140680 15668505-0#76#81#gene672 15668505-0#53#67#diseaseC1140680 associated_with BRCA1,"observe a borderline association with the 5'-untranslated region 203A allele (hazard ratio, 1.43; CI, 1.01-2.00). In contrast to the result of Healey et al. on newborn females and adult female controls, we found no depar"
82#87#gene67254#67#diseaseC0006142 15668505-6#82#87#gene672 15668505-6#54#67#diseaseC0006142 associated_with BRCA1,breast cancer
82#87#gene67254#67#diseaseC0678222 15668505-6#82#87#gene672 15668505-6#54#67#diseaseC0678222 associated_with BRCA1,breast cancer

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 177-182 ProteinMutation:p|SUB|N|372|H denotes N372H
T2 381-386 ProteinMutation:p|SUB|N|372|H denotes N372H
T3 453-461 DNAMutation:g|SUB|G|203|A denotes 203G > A
T4 1017-1022 ProteinMutation:p|SUB|N|372|H denotes N372H
T5 1322-1327 ProteinMutation:p|SUB|N|372|H denotes N372H
T6 1538-1543 ProteinMutation:p|SUB|N|372|H denotes N372H

DisGeNET

Id Subject Object Predicate Lexical cue
T0 470-475 gene:675 denotes BRCA2
T1 498-512 disease:C0029925 denotes ovarian cancer
T2 470-475 gene:675 denotes BRCA2
T3 498-512 disease:C1140680 denotes ovarian cancer
T4 521-526 gene:672 denotes BRCA1
T5 498-512 disease:C0029925 denotes ovarian cancer
T6 521-526 gene:672 denotes BRCA1
T7 498-512 disease:C1140680 denotes ovarian cancer
T8 903-908 gene:672 denotes BRCA1
T9 875-888 disease:C0006142 denotes breast cancer
T10 903-908 gene:672 denotes BRCA1
T11 875-888 disease:C0678222 denotes breast cancer
R1 T0 T1 associated_with BRCA2,ovarian cancer
R2 T2 T3 associated_with BRCA2,ovarian cancer
R3 T4 T5 associated_with BRCA1,ovarian cancer
R4 T6 T7 associated_with BRCA1,ovarian cancer
R5 T8 T9 associated_with BRCA1,breast cancer
R6 T10 T11 associated_with BRCA1,breast cancer