> top > docs > PubMed:20143913 > annotations

PubMed:20143913 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-132 Sentence denotes Large deletion involving exon 5 of the arylsulfatase B gene caused apparent homozygosity in a mucopolysaccharidosis type VI patient.
T2 133-342 Sentence denotes Apparent homozygosity for the mutation p.R315X present on exon 5 of the arylsulfatase B (ARSB) gene in a mucopolysaccharidosis type VI patient was solved in this study by further testing for a second mutation.
T3 343-477 Sentence denotes Patient cDNA analysis revealed that the entire exon 5 of the ARSB gene was lacking; this new mutation was identified as c.899-1142del.
T4 478-670 Sentence denotes As the genomic DNA sequencing excluded the presence of splicing mutations, polymerase chain reaction analysis was performed for polymorphisms listed in the NCBI SNP database for the ARSB gene.
T5 671-979 Sentence denotes This allowed the mutation at the genomic DNA level to be identified as g.99367-102002del; this gross deletion, involving the entire exon 5 of the gene and parts of introns 4 and 5 led to a frameshift starting at amino acid 300 and resulting in a protein with 39% amino acids different from the normal enzyme.
T6 980-1121 Sentence denotes We stress that extensive DNA analysis needs to be performed in case of apparent homozygosity to avoid potential errors in genetic counseling.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
7098 39-54 GeneOrGeneProduct denotes arylsulfatase B NCBIGene:411
7099 94-123 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI MESH:D009087
7100 124-131 OrganismTaxon denotes patient NCBITaxon:9606
7101 172-179 SequenceVariant denotes p.R315X p|SUB|R|315|X
7102 205-220 GeneOrGeneProduct denotes arylsulfatase B NCBIGene:411
7103 222-226 GeneOrGeneProduct denotes ARSB NCBIGene:411
7104 238-267 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI MESH:D009087
7105 268-275 OrganismTaxon denotes patient NCBITaxon:9606
7106 343-350 OrganismTaxon denotes Patient NCBITaxon:9606
7107 404-408 GeneOrGeneProduct denotes ARSB NCBIGene:411
7108 463-476 SequenceVariant denotes c.899-1142del c|DEL|899_1142|
7109 660-664 GeneOrGeneProduct denotes ARSB NCBIGene:411
7110 742-759 SequenceVariant denotes g.99367-102002del g|DEL|99367_102002|

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 94-115 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis 0019249
T2 238-259 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis 0019249

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 172-179 SequenceVariant denotes p.R315X
T2 463-476 SequenceVariant denotes c.899-1142del
T3 742-759 SequenceVariant denotes g.99367-102002del

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 0-5 GeneOrGeneProduct denotes Large
T2 39-54 GeneOrGeneProduct denotes arylsulfatase B
T3 89-93 GeneOrGeneProduct denotes in a
T4 163-171 GeneOrGeneProduct denotes mutation
T5 205-220 GeneOrGeneProduct denotes arylsulfatase B
T6 222-226 GeneOrGeneProduct denotes ARSB
T7 228-237 GeneOrGeneProduct denotes gene in a
T8 312-319 GeneOrGeneProduct denotes testing
T9 333-341 GeneOrGeneProduct denotes mutation
T10 351-355 GeneOrGeneProduct denotes cDNA
T11 383-389 GeneOrGeneProduct denotes entire
T12 404-408 GeneOrGeneProduct denotes ARSB
T13 418-425 GeneOrGeneProduct denotes lacking
T14 436-444 GeneOrGeneProduct denotes mutation
T15 533-541 GeneOrGeneProduct denotes splicing
T16 542-551 GeneOrGeneProduct denotes mutations
T17 553-563 GeneOrGeneProduct denotes polymerase
T18 564-569 GeneOrGeneProduct denotes chain
T19 620-626 GeneOrGeneProduct denotes listed
T20 660-664 GeneOrGeneProduct denotes ARSB
T21 688-696 GeneOrGeneProduct denotes mutation
T22 796-802 GeneOrGeneProduct denotes entire
T23 808-821 GeneOrGeneProduct denotes 5 of the gene
T24 826-831 GeneOrGeneProduct denotes parts
T25 843-848 GeneOrGeneProduct denotes 4 and
T26 871-879 GeneOrGeneProduct denotes starting
T27 883-893 GeneOrGeneProduct denotes amino acid
T28 917-924 GeneOrGeneProduct denotes protein
T29 934-945 GeneOrGeneProduct denotes amino acids
T30 972-978 GeneOrGeneProduct denotes enzyme
T31 995-1004 GeneOrGeneProduct denotes extensive
T32 1043-1047 GeneOrGeneProduct denotes case

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 0-5 GeneOrGeneProduct denotes Large
T2 39-54 GeneOrGeneProduct denotes arylsulfatase B
T3 205-220 GeneOrGeneProduct denotes arylsulfatase B
T4 222-226 GeneOrGeneProduct denotes ARSB
T5 351-355 GeneOrGeneProduct denotes cDNA
T6 404-408 GeneOrGeneProduct denotes ARSB
T7 553-563 GeneOrGeneProduct denotes polymerase
T8 564-569 GeneOrGeneProduct denotes chain
T9 660-664 GeneOrGeneProduct denotes ARSB
T10 883-893 GeneOrGeneProduct denotes amino acid
T11 917-924 GeneOrGeneProduct denotes protein
T12 934-945 GeneOrGeneProduct denotes amino acids
T13 972-978 GeneOrGeneProduct denotes enzyme

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 94-123 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087
T2 238-267 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 39-54 GeneOrGeneProduct denotes arylsulfatase B
T2 205-220 GeneOrGeneProduct denotes arylsulfatase B
T3 222-226 GeneOrGeneProduct denotes ARSB
T4 404-408 GeneOrGeneProduct denotes ARSB
T5 660-664 GeneOrGeneProduct denotes ARSB
T6 915-924 GeneOrGeneProduct denotes a protein

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 94-123 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI 0009661
T2 238-267 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI 0009661

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 94-123 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087
T2 238-267 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 94-123 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087
T2 238-267 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 124-131 OrganismTaxon denotes patient
T2 268-275 OrganismTaxon denotes patient
T3 343-350 OrganismTaxon denotes Patient

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 39-54 ChemicalEntity denotes arylsulfatase B D020051
T2 205-220 ChemicalEntity denotes arylsulfatase B D020051
T3 222-226 ChemicalEntity denotes ARSB D020051
T4 404-408 ChemicalEntity denotes ARSB D020051
T5 660-664 ChemicalEntity denotes ARSB D020051

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T5 660-664 ChemicalEntity denotes ARSB D020051
T4 404-408 ChemicalEntity denotes ARSB D020051
T3 222-226 ChemicalEntity denotes ARSB D020051
T2 205-220 ChemicalEntity denotes arylsulfatase B D020051
T1 39-54 ChemicalEntity denotes arylsulfatase B D020051
T6 915-924 GeneOrGeneProduct denotes a protein
T37447 660-664 GeneOrGeneProduct denotes ARSB
T8331 404-408 GeneOrGeneProduct denotes ARSB
T46094 222-226 GeneOrGeneProduct denotes ARSB
T22214 205-220 GeneOrGeneProduct denotes arylsulfatase B
T37591 39-54 GeneOrGeneProduct denotes arylsulfatase B
T95114 238-267 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087
T98066 94-123 DiseaseOrPhenotypicFeature denotes mucopolysaccharidosis type VI D009087
T16410 343-350 OrganismTaxon denotes Patient
T11111 268-275 OrganismTaxon denotes patient
T14962 124-131 OrganismTaxon denotes patient
T98771 742-759 SequenceVariant denotes g.99367-102002del
T87192 463-476 SequenceVariant denotes c.899-1142del
T47921 172-179 SequenceVariant denotes p.R315X

sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-132 Sentence denotes Large deletion involving exon 5 of the arylsulfatase B gene caused apparent homozygosity in a mucopolysaccharidosis type VI patient.
TextSentencer_T2 133-342 Sentence denotes Apparent homozygosity for the mutation p.R315X present on exon 5 of the arylsulfatase B (ARSB) gene in a mucopolysaccharidosis type VI patient was solved in this study by further testing for a second mutation.
TextSentencer_T3 343-477 Sentence denotes Patient cDNA analysis revealed that the entire exon 5 of the ARSB gene was lacking; this new mutation was identified as c.899-1142del.
TextSentencer_T4 478-670 Sentence denotes As the genomic DNA sequencing excluded the presence of splicing mutations, polymerase chain reaction analysis was performed for polymorphisms listed in the NCBI SNP database for the ARSB gene.
TextSentencer_T5 671-979 Sentence denotes This allowed the mutation at the genomic DNA level to be identified as g.99367-102002del; this gross deletion, involving the entire exon 5 of the gene and parts of introns 4 and 5 led to a frameshift starting at amino acid 300 and resulting in a protein with 39% amino acids different from the normal enzyme.
TextSentencer_T6 980-1121 Sentence denotes We stress that extensive DNA analysis needs to be performed in case of apparent homozygosity to avoid potential errors in genetic counseling.
T1 0-132 Sentence denotes Large deletion involving exon 5 of the arylsulfatase B gene caused apparent homozygosity in a mucopolysaccharidosis type VI patient.
T2 133-342 Sentence denotes Apparent homozygosity for the mutation p.R315X present on exon 5 of the arylsulfatase B (ARSB) gene in a mucopolysaccharidosis type VI patient was solved in this study by further testing for a second mutation.
T3 343-477 Sentence denotes Patient cDNA analysis revealed that the entire exon 5 of the ARSB gene was lacking; this new mutation was identified as c.899-1142del.
T4 478-670 Sentence denotes As the genomic DNA sequencing excluded the presence of splicing mutations, polymerase chain reaction analysis was performed for polymorphisms listed in the NCBI SNP database for the ARSB gene.
T5 671-979 Sentence denotes This allowed the mutation at the genomic DNA level to be identified as g.99367-102002del; this gross deletion, involving the entire exon 5 of the gene and parts of introns 4 and 5 led to a frameshift starting at amino acid 300 and resulting in a protein with 39% amino acids different from the normal enzyme.
T6 980-1121 Sentence denotes We stress that extensive DNA analysis needs to be performed in case of apparent homozygosity to avoid potential errors in genetic counseling.

DisGeNET

Id Subject Object Predicate Lexical cue
T0 39-54 gene:411 denotes arylsulfatase B
T1 94-123 disease:C0026709 denotes mucopolysaccharidosis type VI
T2 205-220 gene:411 denotes arylsulfatase B
T3 238-267 disease:C0026709 denotes mucopolysaccharidosis type VI
T4 222-226 gene:411 denotes ARSB
T5 238-267 disease:C0026709 denotes mucopolysaccharidosis type VI
R1 T0 T1 associated_with arylsulfatase B,mucopolysaccharidosis type VI
R2 T2 T3 associated_with arylsulfatase B,mucopolysaccharidosis type VI
R3 T4 T5 associated_with ARSB,mucopolysaccharidosis type VI

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 238-259 HP_0008155 denotes mucopolysaccharidosis

Allie

Id Subject Object Predicate Lexical cue
SS1_20143913_1_0 205-220 expanded denotes arylsulfatase B
SS2_20143913_1_0 222-226 abbr denotes ARSB
AE1_20143913_1_0 SS1_20143913_1_0 SS2_20143913_1_0 abbreviatedTo arylsulfatase B,ARSB

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
20143913-0#39#54#gene411 39-54 gene411 denotes arylsulfatase B
20143913-0#94#123#diseaseC0026709 94-123 diseaseC0026709 denotes mucopolysaccharidosis type VI
39#54#gene41194#123#diseaseC0026709 20143913-0#39#54#gene411 20143913-0#94#123#diseaseC0026709 associated_with arylsulfatase B,mucopolysaccharidosis type VI

UBERON-AE

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 995-1004 http://purl.obolibrary.org/obo/UBERON_2000106 denotes extensive

PubCasesORDO

Id Subject Object Predicate Lexical cue
TI1 94-123 ORDO:583 denotes mucopolysaccharidosis type VI
AB1 238-267 ORDO:583 denotes mucopolysaccharidosis type VI

performance-test

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 995-1004 http://purl.obolibrary.org/obo/UBERON_2000106 denotes extensive

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 172-179 ProteinMutation:p|SUB|R|315|X denotes p.R315X
T2 463-476 DNAMutation:c|DEL|899_1142| denotes c.899-1142del
T3 742-759 DNAMutation:g|DEL|99367_102002| denotes g.99367-102002del