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PubMed:19365571 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-84 Sentence denotes Macular corneal dystrophy in a Chinese family related with novel mutations of CHST6.
T2 85-93 Sentence denotes PURPOSE:
T3 94-296 Sentence denotes To identify mutations in the carbohydrate sulfotransferase gene (CHST6) for a Chinese family with macular corneal dystrophy (MCD) and to investigate the histopathological changes in the affected cornea.
T4 297-305 Sentence denotes METHODS:
T5 306-379 Sentence denotes A corneal button of the proband was obtained by penetrating keratoplasty.
T7 554-715 Sentence denotes Genomic DNA was extracted from peripheral blood of 11 family members, and the coding region of CHST6 was amplified by the polymerase chain reaction (PCR) method.
T6 380-553 Sentence denotes The half button and ultrathin sections from the other half button were examined with special stains under a light microscope (LM) and an electron microscope (EM) separately.
T8 716-801 Sentence denotes The PCR products were analyzed by direct sequencing and restriction enzyme digestion.
T9 802-810 Sentence denotes RESULTS:
T10 811-942 Sentence denotes The positive reaction to colloidal iron stain (extracellular blue accumulations in the stroma) was detected under light microscopy.
T11 943-1079 Sentence denotes Transmission electron microscopy revealed the enlargement of smooth endoplasmic reticulum and the presence of intracytoplasmic vacuoles.
T12 1080-1194 Sentence denotes The compound heterozygous mutations, c.892C>T and c.1072T>C, were identified in exon 3 of CHST6 in three patients.
T13 1195-1369 Sentence denotes The two transversions resulted in the substitution of a stop codon for glutamine at codon 298 (p.Q298X) and a missense mutation at codon 358, tyrosine to histidine (p.Y358H).
T14 1370-1451 Sentence denotes The six unaffected family individuals carried alternative heterozygous mutations.
T15 1452-1525 Sentence denotes These two mutations were not detected in any of the 100 control subjects.
T16 1526-1538 Sentence denotes CONCLUSIONS:
T17 1539-1740 Sentence denotes Those novel compound heterozygous mutations were thought to contribute to the loss of CHST6 function, which induced the abnormal metabolism of keratan sulfate (KS) that deposited in the corneal stroma.
T18 1741-1895 Sentence denotes It could be proved by the observation of a positive stain reaction and the enlarged collagen fibers as well as hyperplastic fibroblasts under microscopes.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 1256-1261 OrganismTaxon denotes codon NCBItxid:79338
T2 1279-1284 OrganismTaxon denotes codon NCBItxid:79338
T3 1326-1331 OrganismTaxon denotes codon NCBItxid:79338

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
5968 0-25 DiseaseOrPhenotypicFeature denotes Macular corneal dystrophy MESH:D003317
5969 78-83 GeneOrGeneProduct denotes CHST6 NCBIGene:4166
5970 123-157 GeneOrGeneProduct denotes carbohydrate sulfotransferase gene NCBIGene:4166
5971 159-164 GeneOrGeneProduct denotes CHST6 NCBIGene:4166
5972 192-217 DiseaseOrPhenotypicFeature denotes macular corneal dystrophy MESH:D003317
5973 219-222 DiseaseOrPhenotypicFeature denotes MCD MESH:D003317
5974 649-654 GeneOrGeneProduct denotes CHST6 NCBIGene:4166
5975 846-850 ChemicalEntity denotes iron MESH:D007501
5976 1117-1125 SequenceVariant denotes c.892C>T c|SUB|C|892|T
5977 1130-1139 SequenceVariant denotes c.1072T>C c|SUB|T|1072|C
5978 1170-1175 GeneOrGeneProduct denotes CHST6 NCBIGene:4166
5979 1185-1193 OrganismTaxon denotes patients NCBITaxon:9606
5980 1251-1288 SequenceVariant denotes stop codon for glutamine at codon 298 p|SUB|Q|298|X
5981 1290-1297 SequenceVariant denotes p.Q298X p|SUB|Q|298|X
5982 1326-1358 SequenceVariant denotes codon 358, tyrosine to histidine p|SUB|Y|358|H
5983 1360-1367 SequenceVariant denotes p.Y358H p|SUB|Y|358|H
5984 1625-1630 GeneOrGeneProduct denotes CHST6 NCBIGene:4166
5985 1682-1697 ChemicalEntity denotes keratan sulfate MESH:D007632
5986 1699-1701 ChemicalEntity denotes KS MESH:D007632
5987 1825-1833 GeneOrGeneProduct denotes collagen NCBIGene:1277

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 0-25 DiseaseOrPhenotypicFeature denotes Macular corneal dystrophy 0009020
T2 8-25 DiseaseOrPhenotypicFeature denotes corneal dystrophy 0018102
T3 192-217 DiseaseOrPhenotypicFeature denotes macular corneal dystrophy 0009020
T4 200-217 DiseaseOrPhenotypicFeature denotes corneal dystrophy 0018102

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 1117-1125 SequenceVariant denotes c.892C>T
T2 1130-1139 SequenceVariant denotes c.1072T>C
T3 1290-1297 SequenceVariant denotes p.Q298X
T4 1360-1367 SequenceVariant denotes p.Y358H

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 26-30 GeneOrGeneProduct denotes in a
T2 59-64 GeneOrGeneProduct denotes novel
T3 65-74 GeneOrGeneProduct denotes mutations
T4 78-83 GeneOrGeneProduct denotes CHST6
T5 106-115 GeneOrGeneProduct denotes mutations
T6 123-152 GeneOrGeneProduct denotes carbohydrate sulfotransferase
T7 159-164 GeneOrGeneProduct denotes CHST6
T8 297-304 GeneOrGeneProduct denotes METHODS
T9 428-433 GeneOrGeneProduct denotes other
T10 488-493 GeneOrGeneProduct denotes light
T11 542-552 GeneOrGeneProduct denotes separately
T12 649-654 GeneOrGeneProduct denotes CHST6
T13 676-686 GeneOrGeneProduct denotes polymerase
T14 687-692 GeneOrGeneProduct denotes chain
T15 708-714 GeneOrGeneProduct denotes method
T16 724-732 GeneOrGeneProduct denotes products
T17 784-790 GeneOrGeneProduct denotes enzyme
T18 846-850 GeneOrGeneProduct denotes iron
T19 858-871 GeneOrGeneProduct denotes extracellular
T20 872-876 GeneOrGeneProduct denotes blue
T21 925-930 GeneOrGeneProduct denotes light
T22 1004-1010 GeneOrGeneProduct denotes smooth
T23 1011-1032 GeneOrGeneProduct denotes endoplasmic reticulum
T24 1070-1078 GeneOrGeneProduct denotes vacuoles
T25 1106-1115 GeneOrGeneProduct denotes mutations
T26 1170-1175 GeneOrGeneProduct denotes CHST6
T27 1251-1255 GeneOrGeneProduct denotes stop
T28 1266-1275 GeneOrGeneProduct denotes glutamine
T29 1305-1313 GeneOrGeneProduct denotes missense
T30 1314-1322 GeneOrGeneProduct denotes mutation
T31 1337-1345 GeneOrGeneProduct denotes tyrosine
T32 1441-1450 GeneOrGeneProduct denotes mutations
T33 1462-1471 GeneOrGeneProduct denotes mutations
T34 1545-1550 GeneOrGeneProduct denotes novel
T35 1573-1582 GeneOrGeneProduct denotes mutations
T36 1625-1630 GeneOrGeneProduct denotes CHST6
T37 1647-1658 GeneOrGeneProduct denotes induced the
T38 1690-1697 GeneOrGeneProduct denotes sulfate
T39 1825-1833 GeneOrGeneProduct denotes collagen
T40 1834-1840 GeneOrGeneProduct denotes fibers

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 59-64 GeneOrGeneProduct denotes novel
T2 78-83 GeneOrGeneProduct denotes CHST6
T3 123-152 GeneOrGeneProduct denotes carbohydrate sulfotransferase
T4 159-164 GeneOrGeneProduct denotes CHST6
T5 428-433 GeneOrGeneProduct denotes other
T6 488-493 GeneOrGeneProduct denotes light
T7 649-654 GeneOrGeneProduct denotes CHST6
T8 676-686 GeneOrGeneProduct denotes polymerase
T9 687-692 GeneOrGeneProduct denotes chain
T10 708-714 GeneOrGeneProduct denotes method
T11 784-790 GeneOrGeneProduct denotes enzyme
T12 858-871 GeneOrGeneProduct denotes extracellular
T13 872-876 GeneOrGeneProduct denotes blue
T14 925-930 GeneOrGeneProduct denotes light
T15 1004-1010 GeneOrGeneProduct denotes smooth
T16 1011-1032 GeneOrGeneProduct denotes endoplasmic reticulum
T17 1170-1175 GeneOrGeneProduct denotes CHST6
T18 1251-1255 GeneOrGeneProduct denotes stop
T19 1266-1275 GeneOrGeneProduct denotes glutamine
T20 1337-1345 GeneOrGeneProduct denotes tyrosine
T21 1545-1550 GeneOrGeneProduct denotes novel
T22 1625-1630 GeneOrGeneProduct denotes CHST6
T23 1825-1833 GeneOrGeneProduct denotes collagen

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 8-25 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317
T2 200-217 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317
T3 219-222 DiseaseOrPhenotypicFeature denotes MCD C537834

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 78-83 GeneOrGeneProduct denotes CHST6
T2 123-152 GeneOrGeneProduct denotes carbohydrate sulfotransferase
T3 159-164 GeneOrGeneProduct denotes CHST6
T4 649-654 GeneOrGeneProduct denotes CHST6
T5 1004-1010 GeneOrGeneProduct denotes smooth
T6 1170-1175 GeneOrGeneProduct denotes CHST6
T7 1625-1630 GeneOrGeneProduct denotes CHST6
T8 1825-1833 GeneOrGeneProduct denotes collagen

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 0-25 DiseaseOrPhenotypicFeature denotes Macular corneal dystrophy 0009020
T2 192-217 DiseaseOrPhenotypicFeature denotes macular corneal dystrophy 0009020
T3 219-222 DiseaseOrPhenotypicFeature denotes MCD 0019754|0015454|0009020
T6 506-508 DiseaseOrPhenotypicFeature denotes LM 0002013
T7 538-540 DiseaseOrPhenotypicFeature denotes EM 0006545
T8 1699-1701 DiseaseOrPhenotypicFeature denotes KS 0008260|0005055
T10 1852-1864 DiseaseOrPhenotypicFeature denotes hyperplastic 0005043

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 8-25 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317
T2 200-217 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 8-25 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317
T2 200-217 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 123-152 ChemicalEntity denotes carbohydrate sulfotransferase C118929
T2 846-850 ChemicalEntity denotes iron D007501|http://purl.obolibrary.org/obo/CHEBI_18248
T4 1266-1275 ChemicalEntity denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T5 1337-1345 ChemicalEntity denotes tyrosine http://purl.obolibrary.org/obo/CHEBI_18186
T6 1349-1358 ChemicalEntity denotes histidine http://purl.obolibrary.org/obo/CHEBI_27570
T7 1682-1697 ChemicalEntity denotes keratan sulfate D007632|http://purl.obolibrary.org/obo/CHEBI_60924
T9 1699-1701 ChemicalEntity denotes KS D007632
T10 1825-1833 ChemicalEntity denotes collagen http://purl.obolibrary.org/obo/CHEBI_3815

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 1185-1193 OrganismTaxon denotes patients

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T10 1825-1833 ChemicalEntity denotes collagen http://purl.obolibrary.org/obo/CHEBI_3815
T9 1699-1701 ChemicalEntity denotes KS D007632
T7 1682-1697 ChemicalEntity denotes keratan sulfate http://purl.obolibrary.org/obo/CHEBI_60924|D007632
T6 1349-1358 ChemicalEntity denotes histidine http://purl.obolibrary.org/obo/CHEBI_27570
T5 1337-1345 ChemicalEntity denotes tyrosine http://purl.obolibrary.org/obo/CHEBI_18186
T4 1266-1275 ChemicalEntity denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T2 846-850 ChemicalEntity denotes iron http://purl.obolibrary.org/obo/CHEBI_18248|D007501
T1 123-152 ChemicalEntity denotes carbohydrate sulfotransferase C118929
T8 1825-1833 GeneOrGeneProduct denotes collagen
T82028 1625-1630 GeneOrGeneProduct denotes CHST6
T64079 1170-1175 GeneOrGeneProduct denotes CHST6
T34089 1004-1010 GeneOrGeneProduct denotes smooth
T11618 649-654 GeneOrGeneProduct denotes CHST6
T3 159-164 GeneOrGeneProduct denotes CHST6
T69046 123-152 GeneOrGeneProduct denotes carbohydrate sulfotransferase
T96841 78-83 GeneOrGeneProduct denotes CHST6
T59049 200-217 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317
T78325 8-25 DiseaseOrPhenotypicFeature denotes corneal dystrophy D003317
T91872 1185-1193 OrganismTaxon denotes patients
T15391 1360-1367 SequenceVariant denotes p.Y358H
T35403 1290-1297 SequenceVariant denotes p.Q298X
T37064 1130-1139 SequenceVariant denotes c.1072T>C
T59375 1117-1125 SequenceVariant denotes c.892C>T

PMID_GLOBAL

Id Subject Object Predicate Lexical cue mondo_id
T1 0-25 DiseaseOrPhenotypicFeature denotes Macular corneal dystrophy 0009020
T2 192-217 DiseaseOrPhenotypicFeature denotes macular corneal dystrophy 0009020
T3 219-222 DiseaseOrPhenotypicFeature denotes MCD 0009020|0015454|0019754
T6 506-508 DiseaseOrPhenotypicFeature denotes LM 0002013
T7 538-540 DiseaseOrPhenotypicFeature denotes EM 0006545
T8 1699-1701 DiseaseOrPhenotypicFeature denotes KS 0005055|0008260
T10 1852-1864 DiseaseOrPhenotypicFeature denotes hyperplastic 0005043

DisGeNET

Id Subject Object Predicate Lexical cue
T0 159-164 gene:4166 denotes CHST6
T1 192-217 disease:C0024439 denotes macular corneal dystrophy
T2 159-164 gene:4166 denotes CHST6
T3 219-222 disease:C0342793 denotes MCD
T4 159-164 gene:4166 denotes CHST6
T5 219-222 disease:C1636149 denotes MCD
R1 T0 T1 associated_with CHST6,macular corneal dystrophy
R2 T2 T3 associated_with CHST6,MCD
R3 T4 T5 associated_with CHST6,MCD

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
19365571-0#78#83#gene4166 1625-1630 gene4166 denotes CHST6
19365571-0#0#25#diseaseC0024439 297-680 diseaseC0024439 denotes METHODS: A corneal button of the proband was obtained by penetrating keratoplasty. The half button and ultrathin sections from the other half button were examined with special stains under a light microscope (LM) and an electron microscope (EM) separately. Genomic DNA was extracted from peripheral blood of 11 family members, and the coding region of CHST6 was amplified by the poly
19365571-1#65#70#gene4166 159-164 gene4166 denotes CHST6
19365571-1#125#128#diseaseC1636149 219-222 diseaseC1636149 denotes MCD
78#83#gene41660#25#diseaseC0024439 19365571-0#78#83#gene4166 19365571-0#0#25#diseaseC0024439 associated_with CHST6,"METHODS: A corneal button of the proband was obtained by penetrating keratoplasty. The half button and ultrathin sections from the other half button were examined with special stains under a light microscope (LM) and an electron microscope (EM) separately. Genomic DNA was extracted from peripheral blood of 11 family members, and the coding region of CHST6 was amplified by the poly"
65#70#gene4166125#128#diseaseC1636149 19365571-1#65#70#gene4166 19365571-1#125#128#diseaseC1636149 associated_with CHST6,MCD

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 1117-1125 DNAMutation:c|SUB|C|892|T denotes c.892C>T
T2 1130-1139 DNAMutation:c|SUB|T|1072|C denotes c.1072T>C
T3 1290-1297 ProteinMutation:p|SUB|Q|298|X denotes p.Q298X
T4 1360-1367 ProteinMutation:p|SUB|Y|358|H denotes p.Y358H