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PubMed:10459348 JSONTXT

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PubmedHPO

Id Subject Object Predicate Lexical cue
T1 86-91 HP_0002664 denotes tumor
T2 171-185 HP_0100615 denotes ovarian cancer
T3 179-185 HP_0002664 denotes cancer
T4 420-433 HP_0100615 denotes ovarian tumor
T5 428-433 HP_0002664 denotes tumor
T6 454-468 HP_0100615 denotes ovarian cancer
T7 462-468 HP_0002664 denotes cancer
T8 573-578 HP_0002664 denotes tumor
T9 660-665 HP_0002664 denotes tumor
T10 1860-1865 HP_0002664 denotes tumor

jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 52-57 DNA denotes BRCA1
T2 86-107 DNA denotes tumor suppressor gene
T3 108-113 DNA denotes BRCA1
T4 281-287 DNA denotes allele
T5 324-337 DNA denotes normal allele
T6 353-358 DNA denotes BRCA1
T7 374-385 DNA denotes genomic DNA
T8 389-400 cell_type denotes lymphocytes
T9 405-439 cell_type denotes microdissected ovarian tumor cells
T10 573-614 DNA denotes tumor and constitutional (lymphocyte) DNA
T11 637-642 DNA denotes BRCA1
T12 752-757 DNA denotes BRCA1
T13 874-879 DNA denotes BRCA1
T14 938-958 DNA denotes premature stop codon
T15 1195-1200 DNA denotes BRCA1
T16 1248-1266 DNA denotes consensus sequence
T17 1273-1284 DNA denotes branch site
T18 1383-1388 DNA denotes BRCA1
T19 1447-1459 DNA denotes BRCA1 allele
T20 1561-1580 cell_line denotes lymphoid cell lines
T21 1671-1675 RNA denotes mRNA
T22 1710-1720 RNA denotes BRCA1 mRNA
T23 1759-1764 DNA denotes BRCA1
T24 1840-1852 DNA denotes BRCA1 allele
T25 1897-1902 DNA denotes BRCA1
T26 1970-1983 DNA denotes BRCA1 alleles
T27 2044-2057 DNA denotes normal allele

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
10459348-3#14#19#gene672 353-358 gene672 denotes BRCA1
10459348-3#115#129#diseaseC1140680 454-468 diseaseC1140680 denotes ovarian cancer
10459348-3#81#94#diseaseC0919267 420-433 diseaseC0919267 denotes ovarian tumor
14#19#gene672115#129#diseaseC1140680 10459348-3#14#19#gene672 10459348-3#115#129#diseaseC1140680 associated_with BRCA1,ovarian cancer
14#19#gene67281#94#diseaseC0919267 10459348-3#14#19#gene672 10459348-3#81#94#diseaseC0919267 associated_with BRCA1,ovarian tumor

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 52-57 NP denotes BRCA1
C2 82-113 NP denotes the tumor suppressor gene BRCA1
C38 277-287 NP denotes one allele
C39 320-337 NP denotes the normal allele
C8 353-358 NP denotes BRCA1
C21 443-476 NP denotes a familial ovarian cancer patient
C9 637-642 NP denotes BRCA1
C22 689-700 NP denotes the patient
C23 728-736 NP denotes 2418delA
C10 752-757 NP denotes BRCA1
C24 802-816 NP denotes The DNA change
C11 818-826 NP denotes 2418delA
C25 842-852 NP denotes a mutation
C26 853-857 NP denotes that
C27 895-897 NP denotes it
C28 1059-1076 NP denotes The DNA variation
C29 1078-1086 NP denotes 233G-->A
C32 1147-1168 NP denotes a benign polymorphism
C15 1186-1207 NP denotes a unique BRCA1 change
C30 1208-1212 NP denotes that
C37 1437-1459 NP denotes the other BRCA1 allele
C31 1584-1595 NP denotes the patient
C33 1793-1814 NP denotes a benign polymorphism
C40 1829-1852 NP denotes the normal BRCA1 allele
C34 1871-1911 NP denotes the heterozygous germline BRCA1 mutation
C35 1913-1921 NP denotes 2418delA
C36 1965-1983 NP denotes both BRCA1 alleles
C41 2040-2057 NP denotes the normal allele
R1 C2 C1 coref-ident the tumor suppressor gene BRCA1,BRCA1
R2 C8 C2 coref-ident BRCA1,the tumor suppressor gene BRCA1
R3 C9 C8 coref-ident BRCA1,BRCA1
R4 C22 C21 coref-ident the patient,a familial ovarian cancer patient
R5 C10 C9 coref-ident BRCA1,BRCA1
R6 C11 C24 coref-appos 2418delA,The DNA change
R7 C26 C25 coref-relat that,a mutation
R8 C27 C11 coref-pron it,2418delA
R9 C29 C28 coref-appos 233G-->A,The DNA variation
R10 C30 C15 coref-relat that,a unique BRCA1 change
R11 C31 C22 coref-ident the patient,the patient
R12 C33 C32 coref-other a benign polymorphism,a benign polymorphism
R13 C40 C39 coref-ident the normal BRCA1 allele,the normal allele
R14 C35 C34 coref-appos 2418delA,the heterozygous germline BRCA1 mutation
R15 C36 C38 coref-whole-part both BRCA1 alleles,one allele
R16 C41 C40 coref-ident the normal allele,the normal BRCA1 allele

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-58 Sentence denotes Classification of IVS1-10T-->C as a polymorphism of BRCA1.
S2 59-192 Sentence denotes Mutations inactivating the tumor suppressor gene BRCA1 may be responsible for disease for up to 80% of familial ovarian cancer cases.
S3 193-338 Sentence denotes In this syndrome, tumorigenesis classically initiates from an inherited mutation in one allele followed by somatic deletion of the normal allele.
S4 339-615 Sentence denotes Sequencing of BRCA1 amplified from genomic DNA of lymphocytes and microdissected ovarian tumor cells of a familial ovarian cancer patient revealed three, rare heterozygous DNA variations (2418delA, 233G-->A, and IVS1-10T-->C) in both tumor and constitutional (lymphocyte) DNA.
S5 616-666 Sentence denotes Thus, both copies of BRCA1 were retained in tumor.
S6 667-801 Sentence denotes Haplotype analysis of the patient and four siblings assigned 2418delA to one copy of BRCA1 and 233G-->A and IVS1-10T-->C to the other.
S7 802-1058 Sentence denotes The DNA change, 2418delA, is considered a mutation that inactivated one BRCA1 allele because it caused a frameshift and generation of a premature stop codon, resulting in synthesis of a truncated peptide as evidenced by an in vitro protein truncation test.
S8 1059-1169 Sentence denotes The DNA variation, 233G-->A, does not result in an amino acid change, and is considered a benign polymorphism.
S9 1170-1311 Sentence denotes IVS1-10T-->C is a unique BRCA1 change that occurs in the last nucleotide of a consensus sequence for a branch site critical for RNA splicing.
S10 1312-1460 Sentence denotes Therefore, we investigated whether IVS1-10T-->C deleteriously affected BRCA1 splicing or expression, and thereby inactivated the other BRCA1 allele.
S11 1461-1721 Sentence denotes Using the technique of reverse transcription-polymerase chain reaction (PCR) with RNA isolated from lymphoid cell lines of the patient and of controls, no evidence was found that IVS1-10TC abnormally disrupted mRNA splicing or caused the absence of BRCA1 mRNA.
S12 1722-1815 Sentence denotes Thus, IVS1-10T-->C is not harmful to BRCA1 function, and is classified a benign polymorphism.
S13 1816-2019 Sentence denotes Retention of the normal BRCA1 allele in the tumor with the heterozygous germline BRCA1 mutation, 2418delA, indicated that mutational inactivation of both BRCA1 alleles was not required for tumorigenesis.
S14 2020-2119 Sentence denotes It is possible that the normal allele may be functionally inactivated by a nonmutational mechanism.

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 18-28 other_name denotes IVS1-10T--
T2 28-29 other_name denotes >
T3 29-30 other_name denotes C
T4 36-48 other_name denotes polymorphism
T5 52-57 DNA_domain_or_region denotes BRCA1
T6 59-68 other_name denotes Mutations
T7 86-107 DNA_family_or_group denotes tumor suppressor gene
T8 108-113 DNA_domain_or_region denotes BRCA1
T9 162-191 other_name denotes familial ovarian cancer cases
T10 255-273 other_name denotes inherited mutation
T11 281-287 DNA_domain_or_region denotes allele
T12 300-316 other_name denotes somatic deletion
T13 324-337 DNA_domain_or_region denotes normal allele
T14 353-358 DNA_domain_or_region denotes BRCA1
T15 374-385 DNA_family_or_group denotes genomic DNA
T16 389-400 cell_type denotes lymphocytes
T17 405-439 cell_type denotes microdissected ovarian tumor cells
T18 445-476 multi_cell denotes familial ovarian cancer patient
T19 511-525 other_name denotes DNA variations
T20 527-535 other_name denotes 2418delA
T21 537-543 other_name denotes 233G--
T22 543-544 other_name denotes >
T23 544-545 other_name denotes A
T24 551-561 other_name denotes IVS1-10T--
T25 561-562 other_name denotes >
T26 562-563 other_name denotes C
T27 637-642 DNA_domain_or_region denotes BRCA1
T28 667-685 other_name denotes Haplotype analysis
T29 693-700 multi_cell denotes patient
T30 710-718 multi_cell denotes siblings
T31 728-736 other_name denotes 2418delA
T32 752-757 DNA_domain_or_region denotes BRCA1
T33 762-768 other_name denotes 233G--
T34 768-769 other_name denotes >
T35 769-770 other_name denotes A
T36 775-785 other_name denotes IVS1-10T--
T37 785-786 other_name denotes >
T38 786-787 other_name denotes C
T39 806-816 other_name denotes DNA change
T40 818-826 other_name denotes 2418delA
T41 844-852 other_name denotes mutation
T42 874-879 DNA_domain_or_region denotes BRCA1
T43 907-917 other_name denotes frameshift
T44 938-958 DNA_domain_or_region denotes premature stop codon
T45 988-1005 peptide denotes truncated peptide
T46 1063-1076 other_name denotes DNA variation
T47 1078-1084 other_name denotes 233G--
T48 1084-1085 other_name denotes >
T49 1085-1086 other_name denotes A
T50 1110-1127 other_name denotes amino acid change
T51 1149-1168 other_name denotes benign polymorphism
T52 1170-1180 other_name denotes IVS1-10T--
T53 1180-1181 other_name denotes >
T54 1181-1182 other_name denotes C
T55 1195-1200 DNA_domain_or_region denotes BRCA1
T56 1232-1242 nucleotide denotes nucleotide
T57 1248-1266 DNA_domain_or_region denotes consensus sequence
T58 1273-1284 DNA_domain_or_region denotes branch site
T59 1298-1310 other_name denotes RNA splicing
T60 1347-1357 other_name denotes IVS1-10T--
T61 1357-1358 other_name denotes >
T62 1358-1359 other_name denotes C
T63 1383-1388 DNA_domain_or_region denotes BRCA1
T64 1447-1452 DNA_domain_or_region denotes BRCA1
T65 1484-1531 other_name denotes reverse transcription-polymerase chain reaction
T66 1533-1536 other_name denotes PCR
T67 1561-1580 cell_line denotes lymphoid cell lines
T68 1640-1660 other_name denotes IVS1-10TC abnormally
T69 1671-1675 RNA_family_or_group denotes mRNA
T70 1710-1715 DNA_domain_or_region denotes BRCA1
T71 1728-1738 other_name denotes IVS1-10T--
T72 1738-1739 other_name denotes >
T73 1739-1740 other_name denotes C
T74 1759-1764 DNA_domain_or_region denotes BRCA1
T75 1795-1814 other_name denotes benign polymorphism
T76 1840-1845 DNA_domain_or_region denotes BRCA1
T77 1875-1896 other_name denotes heterozygous germline
T78 1897-1902 DNA_domain_or_region denotes BRCA1
T79 1913-1921 other_name denotes 2418delA
T80 1938-1961 other_name denotes mutational inactivation
T81 1970-1975 DNA_domain_or_region denotes BRCA1
T82 2005-2018 other_name denotes tumorigenesis
T83 2044-2057 DNA_domain_or_region denotes normal allele
T84 2095-2118 other_name denotes nonmutational mechanism

DisGeNET

Id Subject Object Predicate Lexical cue
T0 108-113 gene:672 denotes BRCA1
T1 171-185 disease:C1140680 denotes ovarian cancer
T2 108-113 gene:672 denotes BRCA1
T3 171-185 disease:C0029925 denotes ovarian cancer
T4 353-358 gene:672 denotes BRCA1
T5 420-433 disease:C0919267 denotes ovarian tumor
R1 T0 T1 associated_with BRCA1,ovarian cancer
R2 T2 T3 associated_with BRCA1,ovarian cancer
R3 T4 T5 associated_with BRCA1,ovarian tumor