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PubMed:18945288 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-72 Sentence denotes R58fs mutation in the HGD gene in a family with alkaptonuria in the UAE.
T2 73-217 Sentence denotes This study was conducted to determine the prevalence of alkaptonuria in the UAE population and to identify the genotype of affected individuals.
T3 218-402 Sentence denotes In a 3 stage sampling technique 2981 pupils from Government schools in Al Ain and private schools in Dubai were selected to take part in the study, of whom 2857 provided urine samples.
T4 403-494 Sentence denotes Urine collected was analysed for homogentisic acid by gas chromatography-mass spectrometry.
T5 495-631 Sentence denotes Genomic DNA was isolated from the white blood cells of all family members of the affected case following standard established protocols.
T6 632-780 Sentence denotes Specific PRC primers were designed to amplify all 14 exons of the HGD gene with the flanking intronic sequences including the splice site sequences.
T7 781-882 Sentence denotes 2857 children returned a viable urine sample, of which one was highly positive for homogentisic acid.
T8 883-990 Sentence denotes All 12 members of this girl's family were studied and one, a 22 year old brother, was found to excrete HGA.
T9 991-1080 Sentence denotes Another, a sister who had not provided a urine sample, was discovered by genetic testing.
T10 1081-1167 Sentence denotes There were no complaints of joint pain or other symptoms in any member of this family.
T11 1168-1195 Sentence denotes Parents were first cousins.
T12 1196-1344 Sentence denotes We found a single nucleotide deletion c.342delA, located in exon 3, which resulted in a frameshift at amino acid position 58 (p.Arg58fs or p.R58fs).
T13 1345-1474 Sentence denotes Alkaptonuria may be more common than it is thought to be with an allele prevalence estimated at 0.0107 (95% CI 0.000392-0.03473).
T14 1475-1600 Sentence denotes The R58fs mutation is old, perhaps having occurred several thousand years ago, and has spread over a large geographical area.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 289-295 OrganismTaxon denotes Al Ain NCBItxid:1912813

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
5523 0-5 SequenceVariant denotes R58fs p|FS|R|58||
5524 22-25 GeneOrGeneProduct denotes HGD NCBIGene:3081
5525 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria MESH:D000474
5526 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria MESH:D000474
5527 436-453 ChemicalEntity denotes homogentisic acid MESH:D006713
5528 698-701 GeneOrGeneProduct denotes HGD NCBIGene:3081
5529 864-881 ChemicalEntity denotes homogentisic acid MESH:D006713
5530 986-989 ChemicalEntity denotes HGA MESH:D006713
5531 1109-1119 DiseaseOrPhenotypicFeature denotes joint pain MESH:D018771
5532 1234-1243 SequenceVariant denotes c.342delA c|DEL|342|A
5533 1322-1331 SequenceVariant denotes p.Arg58fs p|FS|R|58||
5534 1335-1342 SequenceVariant denotes p.R58fs p|FS|R|58||
5535 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria MESH:D000474
5536 1479-1484 SequenceVariant denotes R58fs p|FS|R|58||

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria 0008753
T2 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria 0008753
T3 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria 0008753

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 0-5 SequenceVariant denotes R58fs
T2 1234-1243 SequenceVariant denotes c.342delA
T3 1322-1331 SequenceVariant denotes p.Arg58fs
T4 1335-1342 SequenceVariant denotes p.R58fs
T5 1479-1484 SequenceVariant denotes R58fs

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 48-60 GeneOrGeneProduct denotes alkaptonuria
T2 129-141 GeneOrGeneProduct denotes alkaptonuria
T3 449-453 GeneOrGeneProduct denotes acid
T4 529-534 GeneOrGeneProduct denotes white
T5 877-881 GeneOrGeneProduct denotes acid
T6 956-963 GeneOrGeneProduct denotes brother
T7 1115-1119 GeneOrGeneProduct denotes pain
T8 1123-1128 GeneOrGeneProduct denotes other
T9 1298-1308 GeneOrGeneProduct denotes amino acid
T10 1345-1357 GeneOrGeneProduct denotes Alkaptonuria
T11 1576-1581 GeneOrGeneProduct denotes large
T12 1595-1599 GeneOrGeneProduct denotes area

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 6-14 GeneOrGeneProduct denotes mutation
T2 26-35 GeneOrGeneProduct denotes gene in a
T3 48-60 GeneOrGeneProduct denotes alkaptonuria
T4 101-110 GeneOrGeneProduct denotes determine
T5 129-141 GeneOrGeneProduct denotes alkaptonuria
T6 221-224 GeneOrGeneProduct denotes a 3
T7 319-324 GeneOrGeneProduct denotes Dubai
T8 347-351 GeneOrGeneProduct denotes part
T9 449-453 GeneOrGeneProduct denotes acid
T10 476-480 GeneOrGeneProduct denotes mass
T11 529-534 GeneOrGeneProduct denotes white
T12 541-546 GeneOrGeneProduct denotes cells
T13 550-553 GeneOrGeneProduct denotes all
T14 585-589 GeneOrGeneProduct denotes case
T15 678-681 GeneOrGeneProduct denotes all
T16 758-764 GeneOrGeneProduct denotes splice
T17 844-850 GeneOrGeneProduct denotes highly
T18 877-881 GeneOrGeneProduct denotes acid
T19 883-889 GeneOrGeneProduct denotes All 12
T20 947-951 GeneOrGeneProduct denotes year
T21 956-963 GeneOrGeneProduct denotes brother
T22 1072-1079 GeneOrGeneProduct denotes testing
T23 1115-1119 GeneOrGeneProduct denotes pain
T24 1123-1128 GeneOrGeneProduct denotes other
T25 1279-1283 GeneOrGeneProduct denotes in a
T26 1298-1308 GeneOrGeneProduct denotes amino acid
T27 1345-1357 GeneOrGeneProduct denotes Alkaptonuria
T28 1485-1493 GeneOrGeneProduct denotes mutation
T29 1543-1548 GeneOrGeneProduct denotes years
T30 1576-1581 GeneOrGeneProduct denotes large
T31 1595-1599 GeneOrGeneProduct denotes area

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 289-295 OrganismTaxon denotes Al Ain

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T2 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T3 1109-1119 DiseaseOrPhenotypicFeature denotes joint pain D018771
T4 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria D000474

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 529-534 GeneOrGeneProduct denotes white
T2 956-963 GeneOrGeneProduct denotes brother

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria 0008753
T2 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria 0008753
T3 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria 0008753

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T2 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T3 1109-1119 DiseaseOrPhenotypicFeature denotes joint pain D018771
T4 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria D000474

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T2 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T3 1109-1119 DiseaseOrPhenotypicFeature denotes joint pain D018771
T4 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria D000474

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 436-453 ChemicalEntity denotes homogentisic acid D006713|http://purl.obolibrary.org/obo/CHEBI_44747
T3 670-677 ChemicalEntity denotes amplify http://purl.obolibrary.org/obo/CHEBI_145669
T4 864-881 ChemicalEntity denotes homogentisic acid D006713|http://purl.obolibrary.org/obo/CHEBI_44747
T6 986-989 ChemicalEntity denotes HGA ChemicalEntity

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T6 986-989 ChemicalEntity denotes HGA ChemicalEntity
T4 864-881 ChemicalEntity denotes homogentisic acid http://purl.obolibrary.org/obo/CHEBI_44747|D006713
T3 670-677 ChemicalEntity denotes amplify http://purl.obolibrary.org/obo/CHEBI_145669
T1 436-453 ChemicalEntity denotes homogentisic acid http://purl.obolibrary.org/obo/CHEBI_44747|D006713
T2 956-963 GeneOrGeneProduct denotes brother
T3165 529-534 GeneOrGeneProduct denotes white
T53894 1345-1357 DiseaseOrPhenotypicFeature denotes Alkaptonuria D000474
T90771 1109-1119 DiseaseOrPhenotypicFeature denotes joint pain D018771
T62351 129-141 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T63171 48-60 DiseaseOrPhenotypicFeature denotes alkaptonuria D000474
T50146 289-295 OrganismTaxon denotes Al Ain
T5 1479-1484 SequenceVariant denotes R58fs
T8153 1335-1342 SequenceVariant denotes p.R58fs
T60974 1322-1331 SequenceVariant denotes p.Arg58fs
T51009 1234-1243 SequenceVariant denotes c.342delA
T18244 0-5 SequenceVariant denotes R58fs

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
18945288-0#22#25#gene3081 22-25 gene3081 denotes HGD
18945288-0#48#60#diseaseC0002066 48-60 diseaseC0002066 denotes alkaptonuria
22#25#gene308148#60#diseaseC0002066 18945288-0#22#25#gene3081 18945288-0#48#60#diseaseC0002066 associated_with HGD,alkaptonuria

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 0-5 ProteinMutation:p|FS|R|58|| denotes R58fs
T2 1234-1243 DNAMutation:c|DEL|342|A denotes c.342delA
T3 1322-1331 ProteinMutation:p|FS|R|58|| denotes p.Arg58fs
T4 1335-1342 ProteinMutation:p|FS|R|58|| denotes p.R58fs
T5 1479-1484 ProteinMutation:p|FS|R|58|| denotes R58fs