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PubMed:3108247 JSONTXT

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Glycosmos6-MAT

Id Subject Object Predicate Lexical cue
T1 425-429 http://purl.obolibrary.org/obo/MAT_0000299 denotes bone
T2 1227-1231 http://purl.obolibrary.org/obo/MAT_0000299 denotes bone

DisGeNET

Id Subject Object Predicate Lexical cue
T0 111-118 gene:146 denotes alpha 1
T1 17-40 disease:C0029434 denotes osteogenesis imperfecta
T2 278-296 gene:1278 denotes type I procollagen
T3 189-212 disease:C0029434 denotes osteogenesis imperfecta
T4 258-265 gene:146 denotes alpha 1
T5 189-212 disease:C0029434 denotes osteogenesis imperfecta
R1 T0 T1 associated_with alpha 1,osteogenesis imperfecta
R2 T2 T3 associated_with type I procollagen,osteogenesis imperfecta
R3 T4 T5 associated_with alpha 1,osteogenesis imperfecta

bionlp-st-epi-2011-training

Id Subject Object Predicate Lexical cue
T1 111-121 Protein denotes alpha 1(I)
T2 258-268 Protein denotes alpha 1(I)
T3 316-326 Protein denotes alpha 1(I)
T4 387-397 Protein denotes alpha 1(I)
T5 497-507 Protein denotes alpha 1(I)
T6 575-585 Protein denotes alpha 1(I)
T7 912-922 Protein denotes alpha 1(I)
T8 1438-1448 Protein denotes alpha 1(I)

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
3108247-1#130#148#gene1278 278-296 gene1278 denotes type I procollagen
3108247-1#41#64#diseaseC0029434 189-212 diseaseC0029434 denotes osteogenesis imperfecta
130#148#gene127841#64#diseaseC0029434 3108247-1#130#148#gene1278 3108247-1#41#64#diseaseC0029434 associated_with type I procollagen,osteogenesis imperfecta

performance-test

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 1116-1121 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix
PD-UBERON-AE-B_T2 806-813 http://purl.obolibrary.org/obo/UBERON_0000479 denotes tissues

UBERON-AE

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 806-813 http://purl.obolibrary.org/obo/UBERON_0000479 denotes tissues
PD-UBERON-AE-B_T2 1116-1121 http://purl.obolibrary.org/obo/UBERON_0002488 denotes helix

sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-147 Sentence denotes Lethal perinatal osteogenesis imperfecta due to the substitution of arginine for glycine at residue 391 of the alpha 1(I) chain of type I collagen.
TextSentencer_T2 148-297 Sentence denotes A baby with the lethal perinatal form of osteogenesis imperfecta was shown to have a structural defect in the alpha 1(I) chain of type I procollagen.
TextSentencer_T3 298-430 Sentence denotes Normal and mutant alpha 1(I) CB8 cyanogen bromide peptides, from the helical part of the alpha 1(I) chains, were purified from bone.
TextSentencer_T4 431-633 Sentence denotes Amino acid sequencing of tryptic peptides derived from the mutant alpha 1(I) CB8 peptide showed that the glycine residue at position 391 of the alpha 1(I) chain had been replaced by an arginine residue.
TextSentencer_T5 634-814 Sentence denotes This substitution accounted for the more basic charged form of this peptide that was observed on two-dimensional electrophoresis of the collagen peptides obtained from the tissues.
TextSentencer_T6 815-1012 Sentence denotes The substitution was associated with increased enzymatic hydroxylation of lysine residues in the alpha 1(I) CB8 and the adjoining CB3 peptides but not in the carboxyl-terminal CB6 and CB7 peptides.
TextSentencer_T7 1013-1147 Sentence denotes This finding suggested that the sequence abnormality had interfered with the propagation of the triple helix across the mutant region.
TextSentencer_T8 1148-1241 Sentence denotes The abnormal collagen was not incorporated into the more insoluble fraction of bone collagen.
TextSentencer_T9 1242-1454 Sentence denotes The baby appeared to be heterozygous for the sequence abnormality and as the parents did not show any evidence of the defect it is likely that the baby had a new mutation of one allele of the pro-alpha 1(I) gene.
TextSentencer_T10 1455-1593 Sentence denotes The amino acid substitution could result from a single nucleotide mutation in the codon GGC (glycine) to produce the codon CGC (arginine).
T1 0-147 Sentence denotes Lethal perinatal osteogenesis imperfecta due to the substitution of arginine for glycine at residue 391 of the alpha 1(I) chain of type I collagen.
T2 148-297 Sentence denotes A baby with the lethal perinatal form of osteogenesis imperfecta was shown to have a structural defect in the alpha 1(I) chain of type I procollagen.
T3 298-430 Sentence denotes Normal and mutant alpha 1(I) CB8 cyanogen bromide peptides, from the helical part of the alpha 1(I) chains, were purified from bone.
T4 431-633 Sentence denotes Amino acid sequencing of tryptic peptides derived from the mutant alpha 1(I) CB8 peptide showed that the glycine residue at position 391 of the alpha 1(I) chain had been replaced by an arginine residue.
T5 634-814 Sentence denotes This substitution accounted for the more basic charged form of this peptide that was observed on two-dimensional electrophoresis of the collagen peptides obtained from the tissues.
T6 815-1012 Sentence denotes The substitution was associated with increased enzymatic hydroxylation of lysine residues in the alpha 1(I) CB8 and the adjoining CB3 peptides but not in the carboxyl-terminal CB6 and CB7 peptides.
T7 1013-1147 Sentence denotes This finding suggested that the sequence abnormality had interfered with the propagation of the triple helix across the mutant region.
T8 1148-1241 Sentence denotes The abnormal collagen was not incorporated into the more insoluble fraction of bone collagen.
T9 1242-1454 Sentence denotes The baby appeared to be heterozygous for the sequence abnormality and as the parents did not show any evidence of the defect it is likely that the baby had a new mutation of one allele of the pro-alpha 1(I) gene.
T10 1455-1593 Sentence denotes The amino acid substitution could result from a single nucleotide mutation in the codon GGC (glycine) to produce the codon CGC (arginine).

PubCasesORDO

Id Subject Object Predicate Lexical cue
TI1 17-40 ORDO:666 denotes osteogenesis imperfecta
AB1 189-212 ORDO:666 denotes osteogenesis imperfecta

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 17-40 Disease denotes osteogenesis imperfecta http://purl.obolibrary.org/obo/MONDO_0019019
T2 189-212 Disease denotes osteogenesis imperfecta http://purl.obolibrary.org/obo/MONDO_0019019

Anatomy-MAT

Id Subject Object Predicate Lexical cue mat_id
T1 425-429 Body_part denotes bone http://purl.obolibrary.org/obo/MAT_0000299
T2 1227-1231 Body_part denotes bone http://purl.obolibrary.org/obo/MAT_0000299

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 81-88 OrganismTaxon denotes glycine 3846
T2 536-543 OrganismTaxon denotes glycine 3846
T3 1548-1555 OrganismTaxon denotes glycine 3846

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 425-429 Body_part denotes bone http://purl.obolibrary.org/obo/UBERON_0001474|http://purl.obolibrary.org/obo/UBERON_0002481
T3 1116-1121 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T4 1227-1231 Body_part denotes bone http://purl.obolibrary.org/obo/UBERON_0001474|http://purl.obolibrary.org/obo/UBERON_0002481

CL-cell

Id Subject Object Predicate Lexical cue cl_id
T1 131-137 Cell denotes type I http://purl.obolibrary.org/obo/CL:0004120|http://purl.obolibrary.org/obo/CL:0004138
T3 278-284 Cell denotes type I http://purl.obolibrary.org/obo/CL:0004120|http://purl.obolibrary.org/obo/CL:0004138