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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 1199-1206 cell_type denotes B cells
T2 1348-1355 cell_type denotes B cells
T3 1412-1449 DNA denotes immunoglobulin heavy chain (IgH) gene

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
10385650-2#73#90#gene29760 589-606 gene29760 denotes B-cell activation
10385650-2#152#171#diseaseC0524910 668-687 diseaseC0524910 denotes chronic hepatitis C
10385650-4#112#116#gene2208 1021-1025 gene2208 denotes CD23
10385650-4#121#126#gene596 1030-1035 gene596 denotes bcl-2
10385650-4#131#136#gene604 1040-1045 gene604 denotes bcl-6
10385650-4#531#534#gene3492 1440-1443 gene3492 denotes IgH
10385650-4#393#412#diseaseC0524910 1302-1321 diseaseC0524910 denotes chronic hepatitis C
10385650-4#216#235#diseaseC0524910 1125-1144 diseaseC0524910 denotes chronic hepatitis C
10385650-4#393#412#diseaseC0524910 1302-1321 diseaseC0524910 denotes chronic hepatitis C
10385650-4#216#235#diseaseC0524910 1125-1144 diseaseC0524910 denotes chronic hepatitis C
10385650-4#393#412#diseaseC0524910 1302-1321 diseaseC0524910 denotes chronic hepatitis C
73#90#gene29760152#171#diseaseC0524910 10385650-2#73#90#gene29760 10385650-2#152#171#diseaseC0524910 associated_with B-cell activation,chronic hepatitis C
112#116#gene2208393#412#diseaseC0524910 10385650-4#112#116#gene2208 10385650-4#393#412#diseaseC0524910 associated_with CD23,chronic hepatitis C
112#116#gene2208216#235#diseaseC0524910 10385650-4#112#116#gene2208 10385650-4#216#235#diseaseC0524910 associated_with CD23,chronic hepatitis C
112#116#gene2208393#412#diseaseC0524910 10385650-4#112#116#gene2208 10385650-4#393#412#diseaseC0524910 associated_with CD23,chronic hepatitis C
112#116#gene2208216#235#diseaseC0524910 10385650-4#112#116#gene2208 10385650-4#216#235#diseaseC0524910 associated_with CD23,chronic hepatitis C
112#116#gene2208393#412#diseaseC0524910 10385650-4#112#116#gene2208 10385650-4#393#412#diseaseC0524910 associated_with CD23,chronic hepatitis C
121#126#gene596393#412#diseaseC0524910 10385650-4#121#126#gene596 10385650-4#393#412#diseaseC0524910 associated_with bcl-2,chronic hepatitis C
121#126#gene596216#235#diseaseC0524910 10385650-4#121#126#gene596 10385650-4#216#235#diseaseC0524910 associated_with bcl-2,chronic hepatitis C
121#126#gene596393#412#diseaseC0524910 10385650-4#121#126#gene596 10385650-4#393#412#diseaseC0524910 associated_with bcl-2,chronic hepatitis C
121#126#gene596216#235#diseaseC0524910 10385650-4#121#126#gene596 10385650-4#216#235#diseaseC0524910 associated_with bcl-2,chronic hepatitis C
121#126#gene596393#412#diseaseC0524910 10385650-4#121#126#gene596 10385650-4#393#412#diseaseC0524910 associated_with bcl-2,chronic hepatitis C
131#136#gene604393#412#diseaseC0524910 10385650-4#131#136#gene604 10385650-4#393#412#diseaseC0524910 associated_with bcl-6,chronic hepatitis C
131#136#gene604216#235#diseaseC0524910 10385650-4#131#136#gene604 10385650-4#216#235#diseaseC0524910 associated_with bcl-6,chronic hepatitis C
131#136#gene604393#412#diseaseC0524910 10385650-4#131#136#gene604 10385650-4#393#412#diseaseC0524910 associated_with bcl-6,chronic hepatitis C
131#136#gene604216#235#diseaseC0524910 10385650-4#131#136#gene604 10385650-4#216#235#diseaseC0524910 associated_with bcl-6,chronic hepatitis C
131#136#gene604393#412#diseaseC0524910 10385650-4#131#136#gene604 10385650-4#393#412#diseaseC0524910 associated_with bcl-6,chronic hepatitis C
531#534#gene3492393#412#diseaseC0524910 10385650-4#531#534#gene3492 10385650-4#393#412#diseaseC0524910 associated_with IgH,chronic hepatitis C
531#534#gene3492216#235#diseaseC0524910 10385650-4#531#534#gene3492 10385650-4#216#235#diseaseC0524910 associated_with IgH,chronic hepatitis C
531#534#gene3492393#412#diseaseC0524910 10385650-4#531#534#gene3492 10385650-4#393#412#diseaseC0524910 associated_with IgH,chronic hepatitis C
531#534#gene3492216#235#diseaseC0524910 10385650-4#531#534#gene3492 10385650-4#216#235#diseaseC0524910 associated_with IgH,chronic hepatitis C
531#534#gene3492393#412#diseaseC0524910 10385650-4#531#534#gene3492 10385650-4#393#412#diseaseC0524910 associated_with IgH,chronic hepatitis C

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 65-84 NP denotes chronic hepatitis C
C3 228-247 NP denotes chronic hepatitis C
C2 214-247 NP denotes patients with chronic hepatitis C
C4 360-367 NP denotes B cells
C7 668-687 NP denotes chronic hepatitis C
C6 654-687 NP denotes patients with chronic hepatitis C
C5 559-687 NP denotes the expression of markers for B-cell activation, differentiation, and proliferation in ILFs in patients with chronic hepatitis C
C8 738-742 NP denotes them
C9 856-864 NP denotes the ILFs
C10 909-1059 NP denotes The distribution of immunoglobulin M (IgM)-, IgD-, and IgG-positive cells and the expression patterns of Ki-67, CD23, or bcl-2 and bcl-6 gene products
C11 1082-1094 NP denotes GC formation
C13 1125-1144 NP denotes chronic hepatitis C
C12 1111-1144 NP denotes patients with chronic hepatitis C
C14 1161-1166 NP denotes those
C15 1170-1181 NP denotes lymph nodes
C16 1199-1206 NP denotes B cells
C17 1272-1284 NP denotes GC formation
C19 1302-1321 NP denotes chronic hepatitis C
C18 1288-1321 NP denotes patients with chronic hepatitis C
C20 1348-1355 NP denotes B cells
C21 1375-1379 NP denotes ILFs
C23 1554-1566 NP denotes GC formation
C22 1544-1566 NP denotes ILFs with GC formation
C24 1568-1573 NP denotes which
C26 1612-1631 NP denotes chronic hepatitis C
C25 1598-1631 NP denotes patients with chronic hepatitis C
C27 1665-1670 NP denotes those
C28 1680-1691 NP denotes lymph nodes
R1 C3 C1 coref-ident chronic hepatitis C,chronic hepatitis C
R2 C7 C3 coref-ident chronic hepatitis C,chronic hepatitis C
R3 C6 C2 coref-ident patients with chronic hepatitis C,patients with chronic hepatitis C
R4 C8 C5 coref-pron them,"the expression of markers for B-cell activation, differentiation, and proliferation in ILFs in patients with chronic hepatitis C"
R5 C13 C7 coref-ident chronic hepatitis C,chronic hepatitis C
R6 C12 C6 coref-ident patients with chronic hepatitis C,patients with chronic hepatitis C
R7 C14 C10 coref-pron those,"The distribution of immunoglobulin M (IgM)-, IgD-, and IgG-positive cells and the expression patterns of Ki-67, CD23, or bcl-2 and bcl-6 gene products"
R8 C16 C4 coref-ident B cells,B cells
R9 C17 C11 coref-ident GC formation,GC formation
R10 C19 C13 coref-ident chronic hepatitis C,chronic hepatitis C
R11 C18 C12 coref-ident patients with chronic hepatitis C,patients with chronic hepatitis C
R12 C20 C16 coref-ident B cells,B cells
R13 C21 C9 coref-ident ILFs,the ILFs
R14 C23 C17 coref-ident GC formation,GC formation
R15 C24 C22 coref-relat which,ILFs with GC formation
R16 C26 C19 coref-ident chronic hepatitis C,chronic hepatitis C
R17 C25 C18 coref-ident patients with chronic hepatitis C,patients with chronic hepatitis C
R18 C27 C22 coref-pron those,ILFs with GC formation
R19 C28 C15 coref-ident lymph nodes,lymph nodes

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-85 Sentence denotes Functional B-cell response in intrahepatic lymphoid follicles in chronic hepatitis C.
S2 86-248 Sentence denotes Intrahepatic lymphoid follicle (ILF) formation is one of the most characteristic and commonly observed histological features in patients with chronic hepatitis C.
S3 249-515 Sentence denotes However, little is known regarding whether follicles in the liver belong to functional lymphoid tissues, where B cells are activated, differentiated, and proliferated, or if the lymphocytes are merely infiltrated after recruitment from the secondary lymphoid organs.
S4 516-821 Sentence denotes To ascertain this possibility, we examined the expression of markers for B-cell activation, differentiation, and proliferation in ILFs in patients with chronic hepatitis C using surgically resected specimens, and compared them with specimens of perihepatic lymph nodes by an immunohistochemical technique.
S5 822-908 Sentence denotes Germinal center (GC) formation in the ILFs was frequently found in HCV-positive cases.
S6 909-1322 Sentence denotes The distribution of immunoglobulin M (IgM)-, IgD-, and IgG-positive cells and the expression patterns of Ki-67, CD23, or bcl-2 and bcl-6 gene products in the follicles with GC formation in the liver of patients with chronic hepatitis C were similar to those of lymph nodes, indicating that B cells are activated, proliferated, and differentiated in the ILFs with GC formation in patients with chronic hepatitis C.
S7 1323-1510 Sentence denotes Oligoclonal expansion of B cells in the livers with ILFs was confirmed by an analysis of immunoglobulin heavy chain (IgH) gene rearrangement determined by polymerase chain reaction (PCR).
S8 1511-1740 Sentence denotes These data strongly suggest that ILFs with GC formation, which are frequently found in patients with chronic hepatitis C, may functionally be the same as those found in lymph nodes with respect to B-cell expansion and maturation.

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 11-26 other_name denotes B-cell response
T2 30-61 tissue denotes intrahepatic lymphoid follicles
T3 65-84 other_name denotes chronic hepatitis C
T4 86-116 tissue denotes Intrahepatic lymphoid follicle
T5 118-121 tissue denotes ILF
T6 189-210 other_name denotes histological features
T7 214-222 multi_cell denotes patients
T8 228-247 other_name denotes chronic hepatitis C
T9 292-301 tissue denotes follicles
T10 646-650 tissue denotes ILFs
T11 654-662 multi_cell denotes patients
T12 668-687 other_name denotes chronic hepatitis C
T13 761-784 body_part denotes perihepatic lymph nodes
T14 791-820 other_name denotes immunohistochemical technique
T15 822-837 tissue denotes Germinal center
T16 839-841 tissue denotes GC
T17 860-864 tissue denotes ILFs
T18 1067-1076 tissue denotes follicles
T19 1082-1084 tissue denotes GC
T20 1102-1107 body_part denotes liver
T21 1111-1119 multi_cell denotes patients
T22 1125-1144 other_name denotes chronic hepatitis C
T23 1170-1181 body_part denotes lymph nodes
T24 1199-1206 cell_type denotes B cells
T25 1262-1266 tissue denotes ILFs
T26 1272-1274 tissue denotes GC
T27 1288-1296 multi_cell denotes patients
T28 1302-1321 other_name denotes chronic hepatitis C
T29 1323-1344 other_name denotes Oligoclonal expansion
T30 1348-1355 cell_type denotes B cells
T31 1363-1369 body_part denotes livers
T32 1375-1379 tissue denotes ILFs
T33 1412-1438 protein_family_or_group denotes immunoglobulin heavy chain
T34 1440-1443 protein_family_or_group denotes IgH
T35 1478-1503 other_name denotes polymerase chain reaction
T36 1505-1508 other_name denotes PCR
T37 1544-1548 tissue denotes ILFs
T38 1554-1556 tissue denotes GC
T39 1598-1606 multi_cell denotes patients
T40 1612-1631 other_name denotes chronic hepatitis C
T41 1680-1691 body_part denotes lymph nodes

DisGeNET

Id Subject Object Predicate Lexical cue
T0 1021-1025 gene:2208 denotes CD23
T1 1302-1321 disease:C0524910 denotes chronic hepatitis C
T2 1030-1035 gene:596 denotes bcl-2
T3 1125-1144 disease:C0524910 denotes chronic hepatitis C
T4 1030-1035 gene:596 denotes bcl-2
T5 1302-1321 disease:C0524910 denotes chronic hepatitis C
T6 1040-1045 gene:604 denotes bcl-6
T7 1125-1144 disease:C0524910 denotes chronic hepatitis C
T8 1040-1045 gene:604 denotes bcl-6
T9 1302-1321 disease:C0524910 denotes chronic hepatitis C
T10 1440-1443 gene:3492 denotes IgH
T11 1125-1144 disease:C0524910 denotes chronic hepatitis C
T12 1440-1443 gene:3492 denotes IgH
T13 1302-1321 disease:C0524910 denotes chronic hepatitis C
R1 T0 T1 associated_with CD23,chronic hepatitis C
R2 T2 T3 associated_with bcl-2,chronic hepatitis C
R3 T4 T5 associated_with bcl-2,chronic hepatitis C
R4 T6 T7 associated_with bcl-6,chronic hepatitis C
R5 T8 T9 associated_with bcl-6,chronic hepatitis C
R6 T10 T11 associated_with IgH,chronic hepatitis C
R7 T12 T13 associated_with IgH,chronic hepatitis C