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PubMed:17951029 JSONTXT

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LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
4432 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia MESH:D005489
4433 64-71 SequenceVariant denotes p.E300X p|SUB|E|300|X
4434 80-85 GeneOrGeneProduct denotes PORCN NCBIGene:64840
4435 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia MESH:D005489
4436 129-132 DiseaseOrPhenotypicFeature denotes FDH MESH:D005489
4437 135-146 DiseaseOrPhenotypicFeature denotes OMIM 305600 MESH:D005489
4438 154-180 DiseaseOrPhenotypicFeature denotes X-linked dominant disorder MESH:D040181
4439 227-241 DiseaseOrPhenotypicFeature denotes Goltz syndrome MESH:D005489
4440 243-246 DiseaseOrPhenotypicFeature denotes FDH MESH:D005489
4441 294-312 DiseaseOrPhenotypicFeature denotes hypoplastic dermis MESH:D005489
4442 408-411 DiseaseOrPhenotypicFeature denotes FDH MESH:D005489
4443 438-443 GeneOrGeneProduct denotes PORCN NCBIGene:64840
4444 633-636 DiseaseOrPhenotypicFeature denotes FDH MESH:D005489
4445 691-700 DiseaseOrPhenotypicFeature denotes depressed MESH:D003866
4446 814-827 DiseaseOrPhenotypicFeature denotes dental caries MESH:D003731
4447 997-1002 GeneOrGeneProduct denotes PORCN NCBIGene:64840
4448 1058-1094 SequenceVariant denotes G>T substitution at nucleotide c.898 c|SUB|G|898|T
4449 1138-1204 SequenceVariant denotes glutamic acid residue (GAA) to a premature termination codon (TAA) p|SUB|E||X
4450 1232-1239 SequenceVariant denotes p.E300X p|SUB|E|300|X
4451 1406-1409 DiseaseOrPhenotypicFeature denotes FDH MESH:D005489
4452 1466-1471 GeneOrGeneProduct denotes PORCN NCBIGene:64840

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-91 Sentence denotes Focal dermal hypoplasia resulting from a new nonsense mutation, p.E300X, in the PORCN gene.
T2 92-103 Sentence denotes BACKGROUND:
T3 104-212 Sentence denotes Focal dermal hypoplasia (FDH) (OMIM 305600) is an X-linked dominant disorder of ecto-mesodermal development.
T4 213-384 Sentence denotes Also known as Goltz syndrome, FDH presents with characteristic linear streaks of hypoplastic dermis and variable abnormalities of bone, nails, hair, limbs, teeth and eyes.
T5 385-582 Sentence denotes The molecular basis of FDH involves mutations in the PORCN gene, which encodes an enzyme that allows membrane targeting and secretion of several Wnt proteins critical for normal tissue development.
T6 583-594 Sentence denotes OBJECTIVES:
T7 595-877 Sentence denotes To investigate the molecular basis of FDH in a 2-year-old Thai girl who presented at birth with depressed, pale linear scars on the trunk and limbs, sparse brittle hair, syndactyly of the right middle and ring fingers, dental caries and radiological features of osteopathia striata.
T8 878-886 Sentence denotes METHODS:
T9 887-1008 Sentence denotes Sequencing of genomic DNA from the affected individual and both parents to search for pathogenic mutations in PORCN gene.
T10 1009-1205 Sentence denotes RESULTS: DNA sequencing disclosed a heterozygous G>T substitution at nucleotide c.898 within exon 10 (NM_203475.1), converting a glutamic acid residue (GAA) to a premature termination codon (TAA).
T11 1206-1314 Sentence denotes This mutation, designated p.E300X, was not detected in DNA from either parent or in 100 control chromosomes.
T12 1315-1326 Sentence denotes CONCLUSION:
T13 1327-1517 Sentence denotes Identification of this new de novo nonsense mutation confirms the diagnosis of FDH in this child and highlights the clinical importance of PORCN and Wnt signalling pathways in embryogenesis.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 1193-1198 OrganismTaxon denotes codon NCBItxid:79338

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia 0010592
T2 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia 0010592
T3 765-775 DiseaseOrPhenotypicFeature denotes syndactyly 0021002
T4 814-827 DiseaseOrPhenotypicFeature denotes dental caries 0005276

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 64-71 SequenceVariant denotes p.E300X
T2 1232-1239 SequenceVariant denotes p.E300X

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 54-62 GeneOrGeneProduct denotes mutation
T2 80-85 GeneOrGeneProduct denotes PORCN
T3 154-162 GeneOrGeneProduct denotes X-linked
T4 184-188 GeneOrGeneProduct denotes ecto
T5 233-241 GeneOrGeneProduct denotes syndrome
T6 283-290 GeneOrGeneProduct denotes streaks
T7 340-347 GeneOrGeneProduct denotes of bone
T8 349-354 GeneOrGeneProduct denotes nails
T9 356-360 GeneOrGeneProduct denotes hair
T10 362-367 GeneOrGeneProduct denotes limbs
T11 375-383 GeneOrGeneProduct denotes and eyes
T12 399-404 GeneOrGeneProduct denotes basis
T13 421-430 GeneOrGeneProduct denotes mutations
T14 438-443 GeneOrGeneProduct denotes PORCN
T15 467-473 GeneOrGeneProduct denotes enzyme
T16 509-518 GeneOrGeneProduct denotes secretion
T17 534-542 GeneOrGeneProduct denotes proteins
T18 624-629 GeneOrGeneProduct denotes basis
T19 640-643 GeneOrGeneProduct denotes a 2
T20 644-648 GeneOrGeneProduct denotes year
T21 691-700 GeneOrGeneProduct denotes depressed
T22 702-706 GeneOrGeneProduct denotes pale
T23 714-719 GeneOrGeneProduct denotes scars
T24 727-732 GeneOrGeneProduct denotes trunk
T25 737-742 GeneOrGeneProduct denotes limbs
T26 744-750 GeneOrGeneProduct denotes sparse
T27 759-763 GeneOrGeneProduct denotes hair
T28 783-788 GeneOrGeneProduct denotes right
T29 800-804 GeneOrGeneProduct denotes ring
T30 878-885 GeneOrGeneProduct denotes METHODS
T31 984-993 GeneOrGeneProduct denotes mutations
T32 997-1002 GeneOrGeneProduct denotes PORCN
T33 1138-1146 GeneOrGeneProduct denotes glutamic
T34 1147-1151 GeneOrGeneProduct denotes acid
T35 1211-1219 GeneOrGeneProduct denotes mutation
T36 1371-1379 GeneOrGeneProduct denotes mutation
T37 1466-1471 GeneOrGeneProduct denotes PORCN

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 80-85 GeneOrGeneProduct denotes PORCN
T2 154-162 GeneOrGeneProduct denotes X-linked
T3 184-188 GeneOrGeneProduct denotes ecto
T4 233-241 GeneOrGeneProduct denotes syndrome
T5 438-443 GeneOrGeneProduct denotes PORCN
T6 467-473 GeneOrGeneProduct denotes enzyme
T7 691-700 GeneOrGeneProduct denotes depressed
T8 702-706 GeneOrGeneProduct denotes pale
T9 727-732 GeneOrGeneProduct denotes trunk
T10 744-750 GeneOrGeneProduct denotes sparse
T11 800-804 GeneOrGeneProduct denotes ring
T12 997-1002 GeneOrGeneProduct denotes PORCN
T13 1147-1151 GeneOrGeneProduct denotes acid
T14 1466-1471 GeneOrGeneProduct denotes PORCN

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T2 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T3 129-132 DiseaseOrPhenotypicFeature denotes FDH D005489
T4 227-241 DiseaseOrPhenotypicFeature denotes Goltz syndrome D005489
T5 243-246 DiseaseOrPhenotypicFeature denotes FDH D005489
T6 408-411 DiseaseOrPhenotypicFeature denotes FDH D005489
T7 633-636 DiseaseOrPhenotypicFeature denotes FDH D005489
T8 691-700 DiseaseOrPhenotypicFeature denotes depressed DISEASE
T9 714-719 DiseaseOrPhenotypicFeature denotes scars D002921
T10 765-775 DiseaseOrPhenotypicFeature denotes syndactyly D013576
T11 814-827 DiseaseOrPhenotypicFeature denotes dental caries D003731
T12 1406-1409 DiseaseOrPhenotypicFeature denotes FDH D005489

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 80-85 GeneOrGeneProduct denotes PORCN
T2 184-188 GeneOrGeneProduct denotes ecto
T3 438-443 GeneOrGeneProduct denotes PORCN
T4 702-706 GeneOrGeneProduct denotes pale
T5 727-732 GeneOrGeneProduct denotes trunk
T6 744-750 GeneOrGeneProduct denotes sparse
T7 800-804 GeneOrGeneProduct denotes ring
T8 997-1002 GeneOrGeneProduct denotes PORCN
T9 1466-1471 GeneOrGeneProduct denotes PORCN

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia 0010592
T2 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia 0010592
T3 129-132 DiseaseOrPhenotypicFeature denotes FDH 0014448|0010592
T5 227-241 DiseaseOrPhenotypicFeature denotes Goltz syndrome 0010592
T6 243-246 DiseaseOrPhenotypicFeature denotes FDH 0014448|0010592
T8 408-411 DiseaseOrPhenotypicFeature denotes FDH 0014448|0010592
T10 633-636 DiseaseOrPhenotypicFeature denotes FDH 0014448|0010592
T12 702-706 DiseaseOrPhenotypicFeature denotes pale 0015595
T13 765-775 DiseaseOrPhenotypicFeature denotes syndactyly 0021002|0019530
T15 814-827 DiseaseOrPhenotypicFeature denotes dental caries 0005276
T16 1406-1409 DiseaseOrPhenotypicFeature denotes FDH 0014448|0010592
T18 1418-1423 DiseaseOrPhenotypicFeature denotes child 0017015

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T2 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T3 129-132 DiseaseOrPhenotypicFeature denotes FDH D005489
T4 135-146 DiseaseOrPhenotypicFeature denotes OMIM 305600 DISEASE
T5 154-180 DiseaseOrPhenotypicFeature denotes X-linked dominant disorder DISEASE
T6 227-241 DiseaseOrPhenotypicFeature denotes Goltz syndrome D005489
T7 243-246 DiseaseOrPhenotypicFeature denotes FDH D005489
T8 294-312 DiseaseOrPhenotypicFeature denotes hypoplastic dermis DISEASE
T9 408-411 DiseaseOrPhenotypicFeature denotes FDH D005489
T10 633-636 DiseaseOrPhenotypicFeature denotes FDH D005489
T11 691-700 DiseaseOrPhenotypicFeature denotes depressed DISEASE
T12 714-719 DiseaseOrPhenotypicFeature denotes scars D002921
T13 765-775 DiseaseOrPhenotypicFeature denotes syndactyly D013576
T14 814-827 DiseaseOrPhenotypicFeature denotes dental caries D003731
T15 1406-1409 DiseaseOrPhenotypicFeature denotes FDH D005489

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T2 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T3 129-132 DiseaseOrPhenotypicFeature denotes FDH D005489
T4 135-146 DiseaseOrPhenotypicFeature denotes OMIM 305600 DISEASE
T5 154-180 DiseaseOrPhenotypicFeature denotes X-linked dominant disorder DISEASE
T6 227-241 DiseaseOrPhenotypicFeature denotes Goltz syndrome D005489
T7 243-246 DiseaseOrPhenotypicFeature denotes FDH D005489
T8 294-312 DiseaseOrPhenotypicFeature denotes hypoplastic dermis DISEASE
T9 408-411 DiseaseOrPhenotypicFeature denotes FDH D005489
T10 633-636 DiseaseOrPhenotypicFeature denotes FDH D005489
T11 691-700 DiseaseOrPhenotypicFeature denotes depressed DISEASE
T12 714-719 DiseaseOrPhenotypicFeature denotes scars D002921
T13 765-775 DiseaseOrPhenotypicFeature denotes syndactyly D013576
T14 814-827 DiseaseOrPhenotypicFeature denotes dental caries D003731
T15 1406-1409 DiseaseOrPhenotypicFeature denotes FDH D005489

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 1138-1159 ChemicalEntity denotes glutamic acid residue http://purl.obolibrary.org/obo/CHEBI_32483
T2 1161-1164 ChemicalEntity denotes GAA http://purl.obolibrary.org/obo/CHEBI_144460|http://purl.obolibrary.org/obo/CHEBI_32483
T4 1200-1203 ChemicalEntity denotes TAA http://purl.obolibrary.org/obo/CHEBI_73654|http://purl.obolibrary.org/obo/CHEBI_32497

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T4 1200-1203 ChemicalEntity denotes TAA http://purl.obolibrary.org/obo/CHEBI_32497|http://purl.obolibrary.org/obo/CHEBI_73654
T2 1161-1164 ChemicalEntity denotes GAA http://purl.obolibrary.org/obo/CHEBI_32483|http://purl.obolibrary.org/obo/CHEBI_144460
T1 1138-1159 ChemicalEntity denotes glutamic acid residue http://purl.obolibrary.org/obo/CHEBI_32483
T9 1466-1471 GeneOrGeneProduct denotes PORCN
T8 997-1002 GeneOrGeneProduct denotes PORCN
T7 800-804 GeneOrGeneProduct denotes ring
T6 744-750 GeneOrGeneProduct denotes sparse
T5 727-732 GeneOrGeneProduct denotes trunk
T45332 702-706 GeneOrGeneProduct denotes pale
T3 438-443 GeneOrGeneProduct denotes PORCN
T37100 184-188 GeneOrGeneProduct denotes ecto
T52925 80-85 GeneOrGeneProduct denotes PORCN
T15 1406-1409 DiseaseOrPhenotypicFeature denotes FDH D005489
T14 814-827 DiseaseOrPhenotypicFeature denotes dental caries D003731
T13 765-775 DiseaseOrPhenotypicFeature denotes syndactyly D013576
T12 714-719 DiseaseOrPhenotypicFeature denotes scars D002921
T11 691-700 DiseaseOrPhenotypicFeature denotes depressed DISEASE
T10 633-636 DiseaseOrPhenotypicFeature denotes FDH D005489
T53621 408-411 DiseaseOrPhenotypicFeature denotes FDH D005489
T39803 294-312 DiseaseOrPhenotypicFeature denotes hypoplastic dermis DISEASE
T8929 243-246 DiseaseOrPhenotypicFeature denotes FDH D005489
T61636 227-241 DiseaseOrPhenotypicFeature denotes Goltz syndrome D005489
T3978 154-180 DiseaseOrPhenotypicFeature denotes X-linked dominant disorder DISEASE
T69872 135-146 DiseaseOrPhenotypicFeature denotes OMIM 305600 DISEASE
T3705 129-132 DiseaseOrPhenotypicFeature denotes FDH D005489
T43485 104-127 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T5661 0-23 DiseaseOrPhenotypicFeature denotes Focal dermal hypoplasia D005489
T23310 1232-1239 SequenceVariant denotes p.E300X
T95332 64-71 SequenceVariant denotes p.E300X

DisGeNET

Id Subject Object Predicate Lexical cue
T0 1466-1471 gene:64840 denotes PORCN
T1 1406-1409 disease:C0016395 denotes FDH
R1 T0 T1 associated_with PORCN,FDH

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 154-171 HP_0001423 denotes X-linked dominant
T2 154-162 HP_0001417 denotes X-linked
T1 154-171 HP_0001423 denotes X-linked dominant
T2 154-162 HP_0001417 denotes X-linked

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
17951029-8#139#144#gene64840 1466-1471 gene64840 denotes PORCN
17951029-8#79#82#diseaseC0016395 1406-1409 diseaseC0016395 denotes FDH
139#144#gene6484079#82#diseaseC0016395 17951029-8#139#144#gene64840 17951029-8#79#82#diseaseC0016395 associated_with PORCN,FDH

PubCasesHPO

Id Subject Object Predicate Lexical cue
AB1 714-719 HP:0100699 denotes scars
AB2 751-763 HP:0002299 denotes brittle hair
AB3 765-775 HP:0001159 denotes syndactyly
AB4 857-876 HP:0010740 denotes osteopathia striata

PubCasesORDO

Id Subject Object Predicate Lexical cue
TI1 0-23 ORDO:2092 denotes Focal dermal hypoplasia
AB1 227-241 ORDO:2092 denotes Goltz syndrome

sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-91 Sentence denotes Focal dermal hypoplasia resulting from a new nonsense mutation, p.E300X, in the PORCN gene.
TextSentencer_T2 92-103 Sentence denotes BACKGROUND:
TextSentencer_T3 104-212 Sentence denotes Focal dermal hypoplasia (FDH) (OMIM 305600) is an X-linked dominant disorder of ecto-mesodermal development.
TextSentencer_T4 213-384 Sentence denotes Also known as Goltz syndrome, FDH presents with characteristic linear streaks of hypoplastic dermis and variable abnormalities of bone, nails, hair, limbs, teeth and eyes.
TextSentencer_T5 385-582 Sentence denotes The molecular basis of FDH involves mutations in the PORCN gene, which encodes an enzyme that allows membrane targeting and secretion of several Wnt proteins critical for normal tissue development.
TextSentencer_T6 583-594 Sentence denotes OBJECTIVES:
TextSentencer_T7 595-877 Sentence denotes To investigate the molecular basis of FDH in a 2-year-old Thai girl who presented at birth with depressed, pale linear scars on the trunk and limbs, sparse brittle hair, syndactyly of the right middle and ring fingers, dental caries and radiological features of osteopathia striata.
TextSentencer_T8 878-886 Sentence denotes METHODS:
TextSentencer_T9 887-1008 Sentence denotes Sequencing of genomic DNA from the affected individual and both parents to search for pathogenic mutations in PORCN gene.
TextSentencer_T10 1009-1205 Sentence denotes RESULTS: DNA sequencing disclosed a heterozygous G>T substitution at nucleotide c.898 within exon 10 (NM_203475.1), converting a glutamic acid residue (GAA) to a premature termination codon (TAA).
TextSentencer_T11 1206-1314 Sentence denotes This mutation, designated p.E300X, was not detected in DNA from either parent or in 100 control chromosomes.
TextSentencer_T12 1315-1326 Sentence denotes CONCLUSION:
TextSentencer_T13 1327-1517 Sentence denotes Identification of this new de novo nonsense mutation confirms the diagnosis of FDH in this child and highlights the clinical importance of PORCN and Wnt signalling pathways in embryogenesis.
T1 0-91 Sentence denotes Focal dermal hypoplasia resulting from a new nonsense mutation, p.E300X, in the PORCN gene.
T2 92-103 Sentence denotes BACKGROUND:
T3 104-212 Sentence denotes Focal dermal hypoplasia (FDH) (OMIM 305600) is an X-linked dominant disorder of ecto-mesodermal development.
T4 213-384 Sentence denotes Also known as Goltz syndrome, FDH presents with characteristic linear streaks of hypoplastic dermis and variable abnormalities of bone, nails, hair, limbs, teeth and eyes.
T5 385-582 Sentence denotes The molecular basis of FDH involves mutations in the PORCN gene, which encodes an enzyme that allows membrane targeting and secretion of several Wnt proteins critical for normal tissue development.
T6 583-594 Sentence denotes OBJECTIVES:
T7 595-877 Sentence denotes To investigate the molecular basis of FDH in a 2-year-old Thai girl who presented at birth with depressed, pale linear scars on the trunk and limbs, sparse brittle hair, syndactyly of the right middle and ring fingers, dental caries and radiological features of osteopathia striata.
T8 878-886 Sentence denotes METHODS:
T9 887-1008 Sentence denotes Sequencing of genomic DNA from the affected individual and both parents to search for pathogenic mutations in PORCN gene.
T10 1009-1205 Sentence denotes RESULTS: DNA sequencing disclosed a heterozygous G>T substitution at nucleotide c.898 within exon 10 (NM_203475.1), converting a glutamic acid residue (GAA) to a premature termination codon (TAA).
T11 1206-1314 Sentence denotes This mutation, designated p.E300X, was not detected in DNA from either parent or in 100 control chromosomes.
T12 1315-1326 Sentence denotes CONCLUSION:
T13 1327-1517 Sentence denotes Identification of this new de novo nonsense mutation confirms the diagnosis of FDH in this child and highlights the clinical importance of PORCN and Wnt signalling pathways in embryogenesis.

performance-test

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 189-199 http://purl.obolibrary.org/obo/UBERON_0000926 denotes mesodermal
PD-UBERON-AE-B_T2 306-312 http://purl.obolibrary.org/obo/UBERON_0002067 denotes dermis
PD-UBERON-AE-B_T3 349-354 http://purl.obolibrary.org/obo/UBERON_0001705 denotes nails
PD-UBERON-AE-B_T4 362-367 http://purl.obolibrary.org/obo/UBERON_0002101 denotes limbs
PD-UBERON-AE-B_T5 737-742 http://purl.obolibrary.org/obo/UBERON_0002101 denotes limbs
PD-UBERON-AE-B_T6 379-383 http://purl.obolibrary.org/obo/UBERON_0000970 denotes eyes
PD-UBERON-AE-B_T7 563-569 http://purl.obolibrary.org/obo/UBERON_0000479 denotes tissue
PD-UBERON-AE-B_T8 727-732 http://purl.obolibrary.org/obo/UBERON_0002100 denotes trunk

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 64-71 ProteinMutation:p|SUB|E|300|X denotes p.E300X
T2 1058-1094 DNAMutation:c|SUB|G|898|T denotes G>T substitution at nucleotide c.898
T3 1232-1239 ProteinMutation:p|SUB|E|300|X denotes p.E300X