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stringlengths 15
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| passages
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|---|---|---|---|---|---|---|
split_0_train_0 | split_0_train_0 | [
{
"id": "split_0_train_0_passage",
"type": "progene_text",
"text": [
"NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae ."
],
"offsets": [
[
0,
118
]
]
}
] | [
{
"id": "split_0_train_0_entity",
"type": "progene_text",
"text": [
"NMD3"
],
"offsets": [
[
0,
4
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_1 | split_0_train_1 | [
{
"id": "split_0_train_1_passage",
"type": "progene_text",
"text": [
"A mutation in NMD3 was found to be lethal in the absence of XRN1 , which encodes the major cytoplasmic exoribonuclease responsible for mRNA turnover ."
],
"offsets": [
[
0,
150
]
]
}
] | [] | [] | [] | [] |
split_0_train_2 | split_0_train_2 | [
{
"id": "split_0_train_2_passage",
"type": "progene_text",
"text": [
"Molecular genetic analysis of NMD3 revealed that it is an essential gene required for stable 60S ribosomal subunits ."
],
"offsets": [
[
0,
117
]
]
}
] | [
{
"id": "split_0_train_1_entity",
"type": "progene_text",
"text": [
"NMD3"
],
"offsets": [
[
30,
34
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_3 | split_0_train_3 | [
{
"id": "split_0_train_3_passage",
"type": "progene_text",
"text": [
"Cells bearing a temperature - sensitive allele of NMD3 had decreased levels of 60S subunits at the nonpermissive temperature which resulted in the formation of half - mer polysomes ."
],
"offsets": [
[
0,
182
]
]
}
] | [
{
"id": "split_0_train_2_entity",
"type": "progene_text",
"text": [
"NMD3"
],
"offsets": [
[
50,
54
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_4 | split_0_train_4 | [
{
"id": "split_0_train_4_passage",
"type": "progene_text",
"text": [
"Pulse - chase analysis of rRNA biogenesis indicated that 25S rRNA was made and processed with kinetics similar to wild - type kinetics ."
],
"offsets": [
[
0,
136
]
]
}
] | [] | [] | [] | [] |
split_0_train_5 | split_0_train_5 | [
{
"id": "split_0_train_5_passage",
"type": "progene_text",
"text": [
"However , the mature RNA was rapidly degraded , with a half - life of 4 min ."
],
"offsets": [
[
0,
77
]
]
}
] | [] | [] | [] | [] |
split_0_train_6 | split_0_train_6 | [
{
"id": "split_0_train_6_passage",
"type": "progene_text",
"text": [
"Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients ."
],
"offsets": [
[
0,
118
]
]
}
] | [
{
"id": "split_0_train_3_entity",
"type": "progene_text",
"text": [
"Nmd3p"
],
"offsets": [
[
0,
5
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_7 | split_0_train_7 | [
{
"id": "split_0_train_7_passage",
"type": "progene_text",
"text": [
"These results suggest that Nmd3p is a cytoplasmic factor required for a late cytoplasmic assembly step of the 60S subunit but is not a ribosomal protein ."
],
"offsets": [
[
0,
154
]
]
}
] | [
{
"id": "split_0_train_4_entity",
"type": "progene_text",
"text": [
"Nmd3p"
],
"offsets": [
[
27,
32
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_8 | split_0_train_8 | [
{
"id": "split_0_train_8_passage",
"type": "progene_text",
"text": [
"Putative orthologs of Nmd3p exist in Drosophila , in nematodes , and in archaebacteria but not in eubacteria ."
],
"offsets": [
[
0,
110
]
]
}
] | [
{
"id": "split_0_train_5_entity",
"type": "progene_text",
"text": [
"Nmd3p"
],
"offsets": [
[
22,
27
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_9 | split_0_train_9 | [
{
"id": "split_0_train_9_passage",
"type": "progene_text",
"text": [
"The Nmd3 protein sequence does not contain readily recognizable motifs of known function ."
],
"offsets": [
[
0,
90
]
]
}
] | [
{
"id": "split_0_train_6_entity",
"type": "progene_text",
"text": [
"Nmd3"
],
"offsets": [
[
4,
8
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_10 | split_0_train_10 | [
{
"id": "split_0_train_10_passage",
"type": "progene_text",
"text": [
"However , these proteins all have an amino - terminal domain containing four repeats of Cx2C , reminiscent of zinc - binding proteins , implicated in nucleic acid binding or protein oligomerization ."
],
"offsets": [
[
0,
199
]
]
}
] | [] | [] | [] | [] |
split_0_train_11 | split_0_train_11 | [
{
"id": "split_0_train_11_passage",
"type": "progene_text",
"text": [
"Skeletal muscle type ryanodine receptor is involved in calcium signaling in human B lymphocytes ."
],
"offsets": [
[
0,
97
]
]
}
] | [
{
"id": "split_0_train_7_entity",
"type": "progene_text",
"text": [
"Skeletal muscle type ryanodine receptor"
],
"offsets": [
[
0,
39
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_12 | split_0_train_12 | [
{
"id": "split_0_train_12_passage",
"type": "progene_text",
"text": [
"The regulation of intracellular free Ca2+ concentration ( [ Ca2+ ] i ) in B cells remains poorly understood and is presently explained almost solely by inositol 1,4,5-triphosphate ( IP3 ) - mediated Ca2+ release , followed by activation of a store - operated channel mechanism ."
],
"offsets": [
[
0,
278
]
]
}
] | [] | [] | [] | [] |
split_0_train_13 | split_0_train_13 | [
{
"id": "split_0_train_13_passage",
"type": "progene_text",
"text": [
"In fact , there are reports indicating that IP3 production does not always correlate with the magnitude of Ca2+ release ."
],
"offsets": [
[
0,
121
]
]
}
] | [] | [] | [] | [] |
split_0_train_14 | split_0_train_14 | [
{
"id": "split_0_train_14_passage",
"type": "progene_text",
"text": [
"We demonstrate here that human B cells express a ryanodine receptor ( RYR ) that functions as a Ca2+ release channel during the B cell antigen receptor ( BCR ) - stimulated Ca2+ signaling process ."
],
"offsets": [
[
0,
197
]
]
}
] | [
{
"id": "split_0_train_8_entity",
"type": "progene_text",
"text": [
"ryanodine receptor"
],
"offsets": [
[
49,
67
]
],
"normalized": []
},
{
"id": "split_0_train_9_entity",
"type": "progene_text",
"text": [
"RYR"
],
"offsets": [
[
70,
73
]
],
"normalized": []
},
{
"id": "split_0_train_10_entity",
"type": "progene_text",
"text": [
"B cell antigen receptor"
],
"offsets": [
[
128,
151
]
],
"normalized": []
},
{
"id": "split_0_train_11_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
154,
157
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_15 | split_0_train_15 | [
{
"id": "split_0_train_15_passage",
"type": "progene_text",
"text": [
"Immunoblotting studies showed that both human primary CD19 ( + ) B and DAKIKI cells express a 565 - kDa immunoreactive protein that is indistinguishable in molecular size and immunoreactivity from the RYR ."
],
"offsets": [
[
0,
206
]
]
}
] | [
{
"id": "split_0_train_12_entity",
"type": "progene_text",
"text": [
"CD19"
],
"offsets": [
[
54,
58
]
],
"normalized": []
},
{
"id": "split_0_train_13_entity",
"type": "progene_text",
"text": [
"RYR"
],
"offsets": [
[
201,
204
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_16 | split_0_train_16 | [
{
"id": "split_0_train_16_passage",
"type": "progene_text",
"text": [
"Selective reverse transcription - polymerase chain reaction , restriction fragment length polymorphism , and sequencing of cloned cDNA indicated that the major isoform of the RYR expressed in primary CD19 ( + ) B and DAKIKI cells is identical to the skeletal muscle type ( RYR1 ) ."
],
"offsets": [
[
0,
281
]
]
}
] | [
{
"id": "split_0_train_14_entity",
"type": "progene_text",
"text": [
"RYR"
],
"offsets": [
[
175,
178
]
],
"normalized": []
},
{
"id": "split_0_train_15_entity",
"type": "progene_text",
"text": [
"CD19"
],
"offsets": [
[
200,
204
]
],
"normalized": []
},
{
"id": "split_0_train_16_entity",
"type": "progene_text",
"text": [
"skeletal muscle type"
],
"offsets": [
[
250,
270
]
],
"normalized": []
},
{
"id": "split_0_train_17_entity",
"type": "progene_text",
"text": [
"RYR1"
],
"offsets": [
[
273,
277
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_17 | split_0_train_17 | [
{
"id": "split_0_train_17_passage",
"type": "progene_text",
"text": [
"Saturation analysis of [3H]ryanodine binding yielded Bmax = 150 fmol / mg of protein and Kd = 110 nM in DAKIKI cells ."
],
"offsets": [
[
0,
118
]
]
}
] | [] | [] | [] | [] |
split_0_train_18 | split_0_train_18 | [
{
"id": "split_0_train_18_passage",
"type": "progene_text",
"text": [
"In fluo-3-loaded CD19 ( + ) B and DAKIKI cells , 4-chloro-m-cresol , a potent activator of Ca2+ release mediated by the ryanodine - sensitive Ca2+ release channel , induced Ca2+ release in a dose - dependent and ryanodine - sensitive fashion ."
],
"offsets": [
[
0,
243
]
]
}
] | [
{
"id": "split_0_train_18_entity",
"type": "progene_text",
"text": [
"CD19"
],
"offsets": [
[
17,
21
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_19 | split_0_train_19 | [
{
"id": "split_0_train_19_passage",
"type": "progene_text",
"text": [
"Furthermore , BCR - mediated Ca2+ release in CD19 ( + ) B cells was significantly altered by 4-chloro-m-cresol and ryanodine ."
],
"offsets": [
[
0,
126
]
]
}
] | [
{
"id": "split_0_train_19_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
14,
17
]
],
"normalized": []
},
{
"id": "split_0_train_20_entity",
"type": "progene_text",
"text": [
"CD19"
],
"offsets": [
[
45,
49
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_20 | split_0_train_20 | [
{
"id": "split_0_train_20_passage",
"type": "progene_text",
"text": [
"These results indicate that RYR1 functions as a Ca2+ release channel during BCR - stimulated Ca2+ signaling and suggest that complex Ca2+ signals that control the cellular activities of B cells may be generated by cooperation of the IP3 receptor and RYR1 ."
],
"offsets": [
[
0,
256
]
]
}
] | [
{
"id": "split_0_train_21_entity",
"type": "progene_text",
"text": [
"RYR1"
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"offsets": [
[
28,
32
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],
"normalized": []
},
{
"id": "split_0_train_22_entity",
"type": "progene_text",
"text": [
"BCR"
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"offsets": [
[
76,
79
]
],
"normalized": []
},
{
"id": "split_0_train_23_entity",
"type": "progene_text",
"text": [
"IP3 receptor"
],
"offsets": [
[
233,
245
]
],
"normalized": []
},
{
"id": "split_0_train_24_entity",
"type": "progene_text",
"text": [
"RYR1"
],
"offsets": [
[
250,
254
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_21 | split_0_train_21 | [
{
"id": "split_0_train_21_passage",
"type": "progene_text",
"text": [
"Myofibroblasts in schistosomal portal fibrosis of man ."
],
"offsets": [
[
0,
55
]
]
}
] | [] | [] | [] | [] |
split_0_train_22 | split_0_train_22 | [
{
"id": "split_0_train_22_passage",
"type": "progene_text",
"text": [
"Myofibroblasts , cells with intermediate features between smooth muscle cells and fibroblasts , have been described as an important cellular component of schistosomal portal fibrosis ."
],
"offsets": [
[
0,
184
]
]
}
] | [] | [] | [] | [] |
split_0_train_23 | split_0_train_23 | [
{
"id": "split_0_train_23_passage",
"type": "progene_text",
"text": [
"The origin , distribution and fate of myofibroblasts were investigated by means of light , fluorescent , immunoenzymatic and ultrastructural techniques in wedge liver biopsies from 68 patients with the hepatosplenic form of schistosomiasis ."
],
"offsets": [
[
0,
241
]
]
}
] | [] | [] | [] | [] |
split_0_train_24 | split_0_train_24 | [
{
"id": "split_0_train_24_passage",
"type": "progene_text",
"text": [
"Results demonstrated that the presence of myofibroblasts varied considerably from case to case and was always related to smooth muscle cell dispersion , which occurred around medium - sized damaged portal vein branches ."
],
"offsets": [
[
0,
220
]
]
}
] | [] | [] | [] | [] |
split_0_train_25 | split_0_train_25 | [
{
"id": "split_0_train_25_passage",
"type": "progene_text",
"text": [
"By sequential observation of several cases , it was evident that myofibroblasts derived by differentiation of vascular smooth muscle and gradually tended to disappear , some of them further differentiating into fibroblasts ."
],
"offsets": [
[
0,
224
]
]
}
] | [] | [] | [] | [] |
split_0_train_26 | split_0_train_26 | [
{
"id": "split_0_train_26_passage",
"type": "progene_text",
"text": [
"Thus , in schistosomal pipestem fibrosis myofibroblasts appear as transient cells , focally accumulated around damaged portal vein branches , and do not seem to have by themselves any important participation in the pathogenesis of hepatosplenic schistosomiasis ."
],
"offsets": [
[
0,
262
]
]
}
] | [] | [] | [] | [] |
split_0_train_27 | split_0_train_27 | [
{
"id": "split_0_train_27_passage",
"type": "progene_text",
"text": [
"Ski is a component of the histone deacetylase complex required for transcriptional repression by Mad and thyroid hormone receptor ."
],
"offsets": [
[
0,
131
]
]
}
] | [
{
"id": "split_0_train_25_entity",
"type": "progene_text",
"text": [
"Ski"
],
"offsets": [
[
0,
3
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],
"normalized": []
},
{
"id": "split_0_train_26_entity",
"type": "progene_text",
"text": [
"histone deacetylase"
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"offsets": [
[
26,
45
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],
"normalized": []
},
{
"id": "split_0_train_27_entity",
"type": "progene_text",
"text": [
"Mad"
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"offsets": [
[
97,
100
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],
"normalized": []
},
{
"id": "split_0_train_28_entity",
"type": "progene_text",
"text": [
"thyroid hormone receptor"
],
"offsets": [
[
105,
129
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_28 | split_0_train_28 | [
{
"id": "split_0_train_28_passage",
"type": "progene_text",
"text": [
"The N-CoR / SMRT complex containing mSin3 and histone deacetylase ( HDAC ) mediates transcriptional repression by nuclear hormone receptors and Mad ."
],
"offsets": [
[
0,
149
]
]
}
] | [
{
"id": "split_0_train_29_entity",
"type": "progene_text",
"text": [
"N-CoR"
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"offsets": [
[
4,
9
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],
"normalized": []
},
{
"id": "split_0_train_30_entity",
"type": "progene_text",
"text": [
"SMRT"
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"offsets": [
[
12,
16
]
],
"normalized": []
},
{
"id": "split_0_train_31_entity",
"type": "progene_text",
"text": [
"mSin3"
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"offsets": [
[
36,
41
]
],
"normalized": []
},
{
"id": "split_0_train_32_entity",
"type": "progene_text",
"text": [
"histone deacetylase"
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"offsets": [
[
46,
65
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],
"normalized": []
},
{
"id": "split_0_train_33_entity",
"type": "progene_text",
"text": [
"HDAC"
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68,
72
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],
"normalized": []
},
{
"id": "split_0_train_34_entity",
"type": "progene_text",
"text": [
"nuclear hormone receptors"
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114,
139
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],
"normalized": []
},
{
"id": "split_0_train_35_entity",
"type": "progene_text",
"text": [
"Mad"
],
"offsets": [
[
144,
147
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_29 | split_0_train_29 | [
{
"id": "split_0_train_29_passage",
"type": "progene_text",
"text": [
"The proteins encoded by the ski proto - oncogene family directly bind to N-CoR / SMRT and mSin3A , and forms a complex with HDAC ."
],
"offsets": [
[
0,
130
]
]
}
] | [
{
"id": "split_0_train_36_entity",
"type": "progene_text",
"text": [
"ski proto - oncogene family"
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28,
55
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},
{
"id": "split_0_train_37_entity",
"type": "progene_text",
"text": [
"N-CoR"
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[
73,
78
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],
"normalized": []
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{
"id": "split_0_train_38_entity",
"type": "progene_text",
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"SMRT"
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81,
85
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],
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},
{
"id": "split_0_train_39_entity",
"type": "progene_text",
"text": [
"mSin3A"
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90,
96
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},
{
"id": "split_0_train_40_entity",
"type": "progene_text",
"text": [
"HDAC"
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"offsets": [
[
124,
128
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_30 | split_0_train_30 | [
{
"id": "split_0_train_30_passage",
"type": "progene_text",
"text": [
"c-Ski and its related gene product Sno are required for transcriptional repression by Mad and thyroid hormone receptor ( TRbeta ) ."
],
"offsets": [
[
0,
131
]
]
}
] | [
{
"id": "split_0_train_41_entity",
"type": "progene_text",
"text": [
"c-Ski"
],
"offsets": [
[
0,
5
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],
"normalized": []
},
{
"id": "split_0_train_42_entity",
"type": "progene_text",
"text": [
"Sno"
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"offsets": [
[
35,
38
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],
"normalized": []
},
{
"id": "split_0_train_43_entity",
"type": "progene_text",
"text": [
"Mad"
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[
86,
89
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},
{
"id": "split_0_train_44_entity",
"type": "progene_text",
"text": [
"thyroid hormone receptor"
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94,
118
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},
{
"id": "split_0_train_45_entity",
"type": "progene_text",
"text": [
"TRbeta"
],
"offsets": [
[
121,
127
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_31 | split_0_train_31 | [
{
"id": "split_0_train_31_passage",
"type": "progene_text",
"text": [
"The oncogenic form , v-Ski , which lacks the mSin3A - binding domain , acts in a dominant - negative fashion , and abrogates transcriptional repression by Mad and TRbeta ."
],
"offsets": [
[
0,
171
]
]
}
] | [
{
"id": "split_0_train_46_entity",
"type": "progene_text",
"text": [
"v-Ski"
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21,
26
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],
"normalized": []
},
{
"id": "split_0_train_47_entity",
"type": "progene_text",
"text": [
"mSin3A"
],
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[
45,
51
]
],
"normalized": []
},
{
"id": "split_0_train_48_entity",
"type": "progene_text",
"text": [
"Mad"
],
"offsets": [
[
155,
158
]
],
"normalized": []
},
{
"id": "split_0_train_49_entity",
"type": "progene_text",
"text": [
"TRbeta"
],
"offsets": [
[
163,
169
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_32 | split_0_train_32 | [
{
"id": "split_0_train_32_passage",
"type": "progene_text",
"text": [
"In ski - deficient mouse embryos , the ornithine decarboxylase gene , whose expression is normally repressed by Mad - Max , is expressed ectopically ."
],
"offsets": [
[
0,
150
]
]
}
] | [
{
"id": "split_0_train_50_entity",
"type": "progene_text",
"text": [
"ski"
],
"offsets": [
[
3,
6
]
],
"normalized": []
},
{
"id": "split_0_train_51_entity",
"type": "progene_text",
"text": [
"ornithine decarboxylase"
],
"offsets": [
[
39,
62
]
],
"normalized": []
},
{
"id": "split_0_train_52_entity",
"type": "progene_text",
"text": [
"Mad"
],
"offsets": [
[
112,
115
]
],
"normalized": []
},
{
"id": "split_0_train_53_entity",
"type": "progene_text",
"text": [
"Max"
],
"offsets": [
[
118,
121
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_33 | split_0_train_33 | [
{
"id": "split_0_train_33_passage",
"type": "progene_text",
"text": [
"These results show that Ski is a component of the HDAC complex and that Ski is required for the transcriptional repression mediated by this complex ."
],
"offsets": [
[
0,
149
]
]
}
] | [
{
"id": "split_0_train_54_entity",
"type": "progene_text",
"text": [
"Ski"
],
"offsets": [
[
24,
27
]
],
"normalized": []
},
{
"id": "split_0_train_55_entity",
"type": "progene_text",
"text": [
"HDAC"
],
"offsets": [
[
50,
54
]
],
"normalized": []
},
{
"id": "split_0_train_56_entity",
"type": "progene_text",
"text": [
"Ski"
],
"offsets": [
[
72,
75
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_34 | split_0_train_34 | [
{
"id": "split_0_train_34_passage",
"type": "progene_text",
"text": [
"The involvement of c-Ski in the HDAC complex indicates that the function of the HDAC complex is important for oncogenesis ."
],
"offsets": [
[
0,
123
]
]
}
] | [
{
"id": "split_0_train_57_entity",
"type": "progene_text",
"text": [
"c-Ski"
],
"offsets": [
[
19,
24
]
],
"normalized": []
},
{
"id": "split_0_train_58_entity",
"type": "progene_text",
"text": [
"HDAC"
],
"offsets": [
[
32,
36
]
],
"normalized": []
},
{
"id": "split_0_train_59_entity",
"type": "progene_text",
"text": [
"HDAC"
],
"offsets": [
[
80,
84
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_35 | split_0_train_35 | [
{
"id": "split_0_train_35_passage",
"type": "progene_text",
"text": [
"Physical and transcriptional map of a 3-Mb region of mouse chromosome 1 containing the gene for the neural tube defect mutant loop - tail ( Lp ) ."
],
"offsets": [
[
0,
146
]
]
}
] | [] | [] | [] | [] |
split_0_train_36 | split_0_train_36 | [
{
"id": "split_0_train_36_passage",
"type": "progene_text",
"text": [
"The Lp mouse mutant provides a model for the severe human neural tube defect ( NTD ) , cranio - rachischisis ."
],
"offsets": [
[
0,
110
]
]
}
] | [] | [] | [] | [] |
split_0_train_37 | split_0_train_37 | [
{
"id": "split_0_train_37_passage",
"type": "progene_text",
"text": [
"To identify the Lp gene , a positional cloning approach has been adopted ."
],
"offsets": [
[
0,
74
]
]
}
] | [] | [] | [] | [] |
split_0_train_38 | split_0_train_38 | [
{
"id": "split_0_train_38_passage",
"type": "progene_text",
"text": [
"Previously , linkage analysis in a large intraspecific backcross was used to map the Lp locus to distal mouse chromosome 1 ."
],
"offsets": [
[
0,
124
]
]
}
] | [] | [] | [] | [] |
split_0_train_39 | split_0_train_39 | [
{
"id": "split_0_train_39_passage",
"type": "progene_text",
"text": [
"Here we report a detailed physical map of this region ."
],
"offsets": [
[
0,
55
]
]
}
] | [] | [] | [] | [] |
split_0_train_40 | split_0_train_40 | [
{
"id": "split_0_train_40_passage",
"type": "progene_text",
"text": [
"The interval surrounding Lp has been cloned in a yeast artificial chromosome ( YAC ) contig consisting of 63 clones spanning approximately 3.2 Mb ."
],
"offsets": [
[
0,
147
]
]
}
] | [] | [] | [] | [] |
split_0_train_41 | split_0_train_41 | [
{
"id": "split_0_train_41_passage",
"type": "progene_text",
"text": [
"Fifty sequence tagged sites ( STSs ) have been used to construct the contig and establish marker order across the interval ."
],
"offsets": [
[
0,
124
]
]
}
] | [] | [] | [] | [] |
split_0_train_42 | split_0_train_42 | [
{
"id": "split_0_train_42_passage",
"type": "progene_text",
"text": [
"Based on the high level of conserved synteny between distal mouse chromosome 1 and human 1q21 - q24 , many of these STSs were designed from expressed sequences identified by cross - screening human and mouse databases of expressed sequence tags ."
],
"offsets": [
[
0,
246
]
]
}
] | [] | [] | [] | [] |
split_0_train_43 | split_0_train_43 | [
{
"id": "split_0_train_43_passage",
"type": "progene_text",
"text": [
"Added to other known genes in the region , a total of 29 genes were located and ordered within the contig ."
],
"offsets": [
[
0,
107
]
]
}
] | [] | [] | [] | [] |
split_0_train_44 | split_0_train_44 | [
{
"id": "split_0_train_44_passage",
"type": "progene_text",
"text": [
"Seven novel polymorphisms were identified within the region , allowing refinement of the genetic map and a reduction in the size of the physical interval containing the Lp gene ."
],
"offsets": [
[
0,
178
]
]
}
] | [] | [] | [] | [] |
split_0_train_45 | split_0_train_45 | [
{
"id": "split_0_train_45_passage",
"type": "progene_text",
"text": [
"The Lp interval , between D1Mit113 and Tagln2 , can be spanned by two nonchimeric overlapping YACs that define a physical distance of approximately 1 Mb ."
],
"offsets": [
[
0,
154
]
]
}
] | [] | [] | [] | [] |
split_0_train_46 | split_0_train_46 | [
{
"id": "split_0_train_46_passage",
"type": "progene_text",
"text": [
"Within this region , 10 potential candidate genes have been mapped ."
],
"offsets": [
[
0,
68
]
]
}
] | [] | [] | [] | [] |
split_0_train_47 | split_0_train_47 | [
{
"id": "split_0_train_47_passage",
"type": "progene_text",
"text": [
"The materials and genes described here will provide a resource for the identification and further study of the mutated Lp gene that causes this severe neural tube defect and will provide candidates for other defects known to map to the homologous region on human chromosome 1q ."
],
"offsets": [
[
0,
278
]
]
}
] | [] | [] | [] | [] |
split_0_train_48 | split_0_train_48 | [
{
"id": "split_0_train_48_passage",
"type": "progene_text",
"text": [
"The SH2 domain - containing inositol 5'-phosphatase ( SHIP ) recruits the p85 subunit of phosphoinositide 3-kinase during FcgammaRIIb1 - mediated inhibition of B cell receptor signaling ."
],
"offsets": [
[
0,
187
]
]
}
] | [
{
"id": "split_0_train_60_entity",
"type": "progene_text",
"text": [
"SH2 domain - containing inositol 5'-phosphatase"
],
"offsets": [
[
4,
51
]
],
"normalized": []
},
{
"id": "split_0_train_61_entity",
"type": "progene_text",
"text": [
"SHIP"
],
"offsets": [
[
54,
58
]
],
"normalized": []
},
{
"id": "split_0_train_62_entity",
"type": "progene_text",
"text": [
"p85 subunit of phosphoinositide 3-kinase"
],
"offsets": [
[
74,
114
]
],
"normalized": []
},
{
"id": "split_0_train_63_entity",
"type": "progene_text",
"text": [
"FcgammaRIIb1"
],
"offsets": [
[
122,
134
]
],
"normalized": []
},
{
"id": "split_0_train_64_entity",
"type": "progene_text",
"text": [
"B cell receptor"
],
"offsets": [
[
160,
175
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_49 | split_0_train_49 | [
{
"id": "split_0_train_49_passage",
"type": "progene_text",
"text": [
"Coligation of FcgammaRIIb1 with the B cell receptor ( BCR ) or FcepsilonRI on mast cells inhibits B cell or mast cell activation ."
],
"offsets": [
[
0,
130
]
]
}
] | [
{
"id": "split_0_train_65_entity",
"type": "progene_text",
"text": [
"FcgammaRIIb1"
],
"offsets": [
[
14,
26
]
],
"normalized": []
},
{
"id": "split_0_train_66_entity",
"type": "progene_text",
"text": [
"B cell receptor"
],
"offsets": [
[
36,
51
]
],
"normalized": []
},
{
"id": "split_0_train_67_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
54,
57
]
],
"normalized": []
},
{
"id": "split_0_train_68_entity",
"type": "progene_text",
"text": [
"FcepsilonRI"
],
"offsets": [
[
63,
74
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_50 | split_0_train_50 | [
{
"id": "split_0_train_50_passage",
"type": "progene_text",
"text": [
"Activity of the inositol phosphatase SHIP is required for this negative signal ."
],
"offsets": [
[
0,
80
]
]
}
] | [
{
"id": "split_0_train_69_entity",
"type": "progene_text",
"text": [
"inositol phosphatase"
],
"offsets": [
[
16,
36
]
],
"normalized": []
},
{
"id": "split_0_train_70_entity",
"type": "progene_text",
"text": [
"SHIP"
],
"offsets": [
[
37,
41
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_51 | split_0_train_51 | [
{
"id": "split_0_train_51_passage",
"type": "progene_text",
"text": [
"In vitro , SHIP catalyzes the conversion of the phosphoinositide 3-kinase ( PI3K ) product phosphatidylinositol 3,4 , 5-trisphosphate ( PIP3 ) into phosphatidylinositol 3,4-bisphosphate ."
],
"offsets": [
[
0,
187
]
]
}
] | [
{
"id": "split_0_train_71_entity",
"type": "progene_text",
"text": [
"SHIP"
],
"offsets": [
[
11,
15
]
],
"normalized": []
},
{
"id": "split_0_train_72_entity",
"type": "progene_text",
"text": [
"phosphoinositide 3-kinase"
],
"offsets": [
[
48,
73
]
],
"normalized": []
},
{
"id": "split_0_train_73_entity",
"type": "progene_text",
"text": [
"PI3K"
],
"offsets": [
[
76,
80
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_52 | split_0_train_52 | [
{
"id": "split_0_train_52_passage",
"type": "progene_text",
"text": [
"Recent data demonstrate that coligation of FcgammaRIIb1 with BCR inhibits PIP3 - dependent Btk ( Bruton 's tyrosine kinase ) activation and the Btk - dependent generation of inositol trisphosphate that regulates sustained calcium influx ."
],
"offsets": [
[
0,
238
]
]
}
] | [
{
"id": "split_0_train_74_entity",
"type": "progene_text",
"text": [
"FcgammaRIIb1"
],
"offsets": [
[
43,
55
]
],
"normalized": []
},
{
"id": "split_0_train_75_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
61,
64
]
],
"normalized": []
},
{
"id": "split_0_train_76_entity",
"type": "progene_text",
"text": [
"Btk"
],
"offsets": [
[
91,
94
]
],
"normalized": []
},
{
"id": "split_0_train_77_entity",
"type": "progene_text",
"text": [
"Bruton 's tyrosine kinase"
],
"offsets": [
[
97,
122
]
],
"normalized": []
},
{
"id": "split_0_train_78_entity",
"type": "progene_text",
"text": [
"Btk"
],
"offsets": [
[
144,
147
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_53 | split_0_train_53 | [
{
"id": "split_0_train_53_passage",
"type": "progene_text",
"text": [
"In this study , we provide evidence that coligation of FcgammaRIIb1 with BCR induces binding of PI3K to SHIP ."
],
"offsets": [
[
0,
110
]
]
}
] | [
{
"id": "split_0_train_79_entity",
"type": "progene_text",
"text": [
"FcgammaRIIb1"
],
"offsets": [
[
55,
67
]
],
"normalized": []
},
{
"id": "split_0_train_80_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
73,
76
]
],
"normalized": []
},
{
"id": "split_0_train_81_entity",
"type": "progene_text",
"text": [
"PI3K"
],
"offsets": [
[
96,
100
]
],
"normalized": []
},
{
"id": "split_0_train_82_entity",
"type": "progene_text",
"text": [
"SHIP"
],
"offsets": [
[
104,
108
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_54 | split_0_train_54 | [
{
"id": "split_0_train_54_passage",
"type": "progene_text",
"text": [
"This interaction is mediated by the binding of the SH2 domains of the p85 subunit of PI3K to a tyrosine - based motif in the C - terminal region of SHIP ."
],
"offsets": [
[
0,
154
]
]
}
] | [
{
"id": "split_0_train_83_entity",
"type": "progene_text",
"text": [
"p85 subunit of PI3K"
],
"offsets": [
[
70,
89
]
],
"normalized": []
},
{
"id": "split_0_train_84_entity",
"type": "progene_text",
"text": [
"SHIP"
],
"offsets": [
[
148,
152
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_55 | split_0_train_55 | [
{
"id": "split_0_train_55_passage",
"type": "progene_text",
"text": [
"Furthermore , the generation of phosphatidylinositol 3,4-bisphosphate was only partially reduced during coligation of BCR with FcgammaRIIb1 despite a drastic reduction in PIP3 ."
],
"offsets": [
[
0,
177
]
]
}
] | [
{
"id": "split_0_train_85_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
118,
121
]
],
"normalized": []
},
{
"id": "split_0_train_86_entity",
"type": "progene_text",
"text": [
"FcgammaRIIb1"
],
"offsets": [
[
127,
139
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_56 | split_0_train_56 | [
{
"id": "split_0_train_56_passage",
"type": "progene_text",
"text": [
"In contrast to the complete inhibition of Tec kinase - dependent calcium signaling , activation of the serine / threonine kinase Akt was partially preserved during BCR and FcgammaRIIb1 coligation ."
],
"offsets": [
[
0,
197
]
]
}
] | [
{
"id": "split_0_train_87_entity",
"type": "progene_text",
"text": [
"Tec"
],
"offsets": [
[
42,
45
]
],
"normalized": []
},
{
"id": "split_0_train_88_entity",
"type": "progene_text",
"text": [
"kinase"
],
"offsets": [
[
46,
52
]
],
"normalized": []
},
{
"id": "split_0_train_89_entity",
"type": "progene_text",
"text": [
"serine / threonine kinase"
],
"offsets": [
[
103,
128
]
],
"normalized": []
},
{
"id": "split_0_train_90_entity",
"type": "progene_text",
"text": [
"Akt"
],
"offsets": [
[
129,
132
]
],
"normalized": []
},
{
"id": "split_0_train_91_entity",
"type": "progene_text",
"text": [
"BCR"
],
"offsets": [
[
164,
167
]
],
"normalized": []
},
{
"id": "split_0_train_92_entity",
"type": "progene_text",
"text": [
"FcgammaRIIb1"
],
"offsets": [
[
172,
184
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_57 | split_0_train_57 | [
{
"id": "split_0_train_57_passage",
"type": "progene_text",
"text": [
"The association of PI3K with SHIP may serve to activate PI3K and to regulate downstream events such as B cell activation - induced apoptosis ."
],
"offsets": [
[
0,
142
]
]
}
] | [
{
"id": "split_0_train_93_entity",
"type": "progene_text",
"text": [
"PI3K"
],
"offsets": [
[
19,
23
]
],
"normalized": []
},
{
"id": "split_0_train_94_entity",
"type": "progene_text",
"text": [
"SHIP"
],
"offsets": [
[
29,
33
]
],
"normalized": []
},
{
"id": "split_0_train_95_entity",
"type": "progene_text",
"text": [
"PI3K"
],
"offsets": [
[
56,
60
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_58 | split_0_train_58 | [
{
"id": "split_0_train_58_passage",
"type": "progene_text",
"text": [
"Non-LTR retrotransposons ( LINEs ) as ubiquitous components of plant genomes ."
],
"offsets": [
[
0,
78
]
]
}
] | [] | [] | [] | [] |
split_0_train_59 | split_0_train_59 | [
{
"id": "split_0_train_59_passage",
"type": "progene_text",
"text": [
"During the course of work aimed at isolating a rice gene from Oryza australiensis by PCR , the oligonucleotide primers used were found to generate a fragment that showed sequence homology to the endonuclease ( EN ) region of the maize non - LTR retrotransposon ( LINE ) Cin4 ."
],
"offsets": [
[
0,
276
]
]
}
] | [
{
"id": "split_0_train_96_entity",
"type": "progene_text",
"text": [
"endonuclease"
],
"offsets": [
[
195,
207
]
],
"normalized": []
},
{
"id": "split_0_train_97_entity",
"type": "progene_text",
"text": [
"EN"
],
"offsets": [
[
210,
212
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_60 | split_0_train_60 | [
{
"id": "split_0_train_60_passage",
"type": "progene_text",
"text": [
"We carried out further PCRs using oligonucleotide primers that hybridized to these sequences , and found that they amplified several fragments , each with homology to the EN regions , from Oryza sativa cv. Nipponbare as well as O. australiensis ."
],
"offsets": [
[
0,
246
]
]
}
] | [
{
"id": "split_0_train_98_entity",
"type": "progene_text",
"text": [
"EN"
],
"offsets": [
[
171,
173
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_61 | split_0_train_61 | [
{
"id": "split_0_train_61_passage",
"type": "progene_text",
"text": [
"We mapped the approximate locations of two rice LINE homologues by screening clones in a YAC library made from a rice ( O. sativa ) genome , and found that each homologue was present in a low copy number apparently at nonspecific regions on rice chromosomes ."
],
"offsets": [
[
0,
259
]
]
}
] | [] | [] | [] | [] |
split_0_train_62 | split_0_train_62 | [
{
"id": "split_0_train_62_passage",
"type": "progene_text",
"text": [
"We then carried out PCR using degenerate oligonucleotide primers which hybridized to the rice LINE homologues and Cin4 to ascertain whether LINE homologues are present in a variety of members of the plant kingdom , including angiosperms , gymnosperms , bracken , horsetail and liverwort ."
],
"offsets": [
[
0,
288
]
]
}
] | [] | [] | [] | [] |
split_0_train_63 | split_0_train_63 | [
{
"id": "split_0_train_63_passage",
"type": "progene_text",
"text": [
"Cloning and nucleotide sequencing revealed that 53 clones obtained from 27 out of 33 plant species contained LINE homologues ."
],
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[
0,
126
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]
}
] | [] | [] | [] | [] |
split_0_train_64 | split_0_train_64 | [
{
"id": "split_0_train_64_passage",
"type": "progene_text",
"text": [
"In addition to these homologues , we identified four homologues with EN regions in the Arabidopsis thaliana genome by a computer search of databases ."
],
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[
0,
150
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]
}
] | [
{
"id": "split_0_train_99_entity",
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"text": [
"EN"
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[
69,
71
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_65 | split_0_train_65 | [
{
"id": "split_0_train_65_passage",
"type": "progene_text",
"text": [
"The nucleotide sequences of almost all the LINE homologues were greatly diverged , but the derived amino acid sequences were well conserved , and all contained glutamic acid and tyrosine residues at almost the same relative positions as in the the active site regions of AP ( apurinic / apyrimidinic ) - endonucleases ."
],
"offsets": [
[
0,
319
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]
}
] | [
{
"id": "split_0_train_100_entity",
"type": "progene_text",
"text": [
"AP ( apurinic / apyrimidinic ) - endonucleases"
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[
271,
317
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_66 | split_0_train_66 | [
{
"id": "split_0_train_66_passage",
"type": "progene_text",
"text": [
"The EN regions in the LINE homologues from closely related plant species show a closer phylogenetic relationship , indicating that sequence divergence during vertical transmission has been a major influence upon the evolution of plant LINEs ."
],
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[
0,
242
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]
}
] | [
{
"id": "split_0_train_101_entity",
"type": "progene_text",
"text": [
"EN"
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[
4,
6
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_67 | split_0_train_67 | [
{
"id": "split_0_train_67_passage",
"type": "progene_text",
"text": [
"[ The effect of NO - like relaxing factor on vascular reactivity in tourniquet shock rat ]"
],
"offsets": [
[
0,
90
]
]
}
] | [] | [] | [] | [] |
split_0_train_68 | split_0_train_68 | [
{
"id": "split_0_train_68_passage",
"type": "progene_text",
"text": [
"This work was done on rat tourniquet shock ( ToS ) model ."
],
"offsets": [
[
0,
58
]
]
}
] | [] | [] | [] | [] |
split_0_train_69 | split_0_train_69 | [
{
"id": "split_0_train_69_passage",
"type": "progene_text",
"text": [
"It was found that reactivity of isolated perfused aortic ring to noradrenaline decreased , while cGMP content of the aortic tissue increased ."
],
"offsets": [
[
0,
142
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]
}
] | [] | [] | [] | [] |
split_0_train_70 | split_0_train_70 | [
{
"id": "split_0_train_70_passage",
"type": "progene_text",
"text": [
"These changes could be potentiated by perfusion with L-arginine ( NO-precursor ) ."
],
"offsets": [
[
0,
82
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]
}
] | [] | [] | [] | [] |
split_0_train_71 | split_0_train_71 | [
{
"id": "split_0_train_71_passage",
"type": "progene_text",
"text": [
"On the other side , when the aortic ring was perfused with L-NNA ( NO-synthesis inhibitor ) or methylene blue ( soluble cGMPase inhibitor ) , the changes could be attenuated ."
],
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[
0,
175
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}
] | [
{
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"type": "progene_text",
"text": [
"cGMPase"
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[
120,
127
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_72 | split_0_train_72 | [
{
"id": "split_0_train_72_passage",
"type": "progene_text",
"text": [
"The effect of these drugs are independent of the presence of vascular endothelium ."
],
"offsets": [
[
0,
83
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]
}
] | [] | [] | [] | [] |
split_0_train_73 | split_0_train_73 | [
{
"id": "split_0_train_73_passage",
"type": "progene_text",
"text": [
"The results suggest that non - endothelium - derived NO - like relaxing factor may be one of the factors causing low vascular reactivity of the ToS animals ."
],
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[
0,
157
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]
}
] | [] | [] | [] | [] |
split_0_train_74 | split_0_train_74 | [
{
"id": "split_0_train_74_passage",
"type": "progene_text",
"text": [
"Systematic identification , classification , and characterization of the open reading frames which encode novel helicase - related proteins in Saccharomyces cerevisiae by gene disruption and Northern analysis ."
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"offsets": [
[
0,
210
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]
}
] | [
{
"id": "split_0_train_103_entity",
"type": "progene_text",
"text": [
"helicase"
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[
112,
120
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_75 | split_0_train_75 | [
{
"id": "split_0_train_75_passage",
"type": "progene_text",
"text": [
"Helicase - related proteins play important roles in various cellular processes incuding DNA replication , DNA repair , RNA processing and so on ."
],
"offsets": [
[
0,
145
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]
}
] | [
{
"id": "split_0_train_104_entity",
"type": "progene_text",
"text": [
"Helicase"
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"offsets": [
[
0,
8
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_76 | split_0_train_76 | [
{
"id": "split_0_train_76_passage",
"type": "progene_text",
"text": [
"It has been well known that the amino acid sequences of these proteins contain several conserved motifs , and that the open reading frames ( ORFs ) which encode helicase - related proteins make up several gene families ."
],
"offsets": [
[
0,
220
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}
] | [
{
"id": "split_0_train_105_entity",
"type": "progene_text",
"text": [
"helicase"
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[
161,
169
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],
"normalized": []
}
] | [] | [] | [] |
split_0_train_77 | split_0_train_77 | [
{
"id": "split_0_train_77_passage",
"type": "progene_text",
"text": [
"In this study , we have identified 134 ORFs that encode helicase - like proteins in the Saccharomyces genome , based on similarity with the ORFs of authentic helicase and helicase - related proteins ."
],
"offsets": [
[
0,
200
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]
}
] | [
{
"id": "split_0_train_106_entity",
"type": "progene_text",
"text": [
"helicase"
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56,
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{
"id": "split_0_train_107_entity",
"type": "progene_text",
"text": [
"helicase"
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158,
166
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{
"id": "split_0_train_108_entity",
"type": "progene_text",
"text": [
"helicase"
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"offsets": [
[
171,
179
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_78 | split_0_train_78 | [
{
"id": "split_0_train_78_passage",
"type": "progene_text",
"text": [
"Multiple alignment of the ORF sequences resulted in the 134 ORFs being classified to 11 clusters ."
],
"offsets": [
[
0,
98
]
]
}
] | [] | [] | [] | [] |
split_0_train_79 | split_0_train_79 | [
{
"id": "split_0_train_79_passage",
"type": "progene_text",
"text": [
"Seven out of 21 previously uncharacterized ORFs ( YDL031w , YDL070w , YDL084w , YGL150c , YKL078w , YLR276c , and YMR128w ) were identified by systematic gene disruption , to be essential for vegetative growth ."
],
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0,
211
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]
}
] | [
{
"id": "split_0_train_109_entity",
"type": "progene_text",
"text": [
"YDL031w"
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50,
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{
"id": "split_0_train_110_entity",
"type": "progene_text",
"text": [
"YDL070w"
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60,
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{
"id": "split_0_train_111_entity",
"type": "progene_text",
"text": [
"YDL084w"
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70,
77
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{
"id": "split_0_train_112_entity",
"type": "progene_text",
"text": [
"YGL150c"
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80,
87
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{
"id": "split_0_train_113_entity",
"type": "progene_text",
"text": [
"YKL078w"
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90,
97
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{
"id": "split_0_train_114_entity",
"type": "progene_text",
"text": [
"YLR276c"
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100,
107
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],
"normalized": []
},
{
"id": "split_0_train_115_entity",
"type": "progene_text",
"text": [
"YMR128w"
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"offsets": [
[
114,
121
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_80 | split_0_train_80 | [
{
"id": "split_0_train_80_passage",
"type": "progene_text",
"text": [
"Three ( YDR332w , YGL064c , and YOL095c ) out of the remaining 14 dispensable ORFs exhibited the slow - growth phenotype at 30 degrees C and 37 degrees C ."
],
"offsets": [
[
0,
155
]
]
}
] | [
{
"id": "split_0_train_116_entity",
"type": "progene_text",
"text": [
"YDR332w"
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"offsets": [
[
8,
15
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],
"normalized": []
},
{
"id": "split_0_train_117_entity",
"type": "progene_text",
"text": [
"YGL064c"
],
"offsets": [
[
18,
25
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],
"normalized": []
},
{
"id": "split_0_train_118_entity",
"type": "progene_text",
"text": [
"YOL095c"
],
"offsets": [
[
32,
39
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_81 | split_0_train_81 | [
{
"id": "split_0_train_81_passage",
"type": "progene_text",
"text": [
"Furthermore , the expression profiles of transcripts from 43 ORFs were examined under seven different growth conditions by Northern analysis and reverse transcription - polymerase chain reaction , indicating that all of the 43 tested ORFs were transcribed ."
],
"offsets": [
[
0,
257
]
]
}
] | [] | [] | [] | [] |
split_0_train_82 | split_0_train_82 | [
{
"id": "split_0_train_82_passage",
"type": "progene_text",
"text": [
"Interestingly , we found that the level of transcript from 34 helicase - like genes was markedly increased by heat shock ."
],
"offsets": [
[
0,
122
]
]
}
] | [
{
"id": "split_0_train_119_entity",
"type": "progene_text",
"text": [
"helicase"
],
"offsets": [
[
62,
70
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_83 | split_0_train_83 | [
{
"id": "split_0_train_83_passage",
"type": "progene_text",
"text": [
"This suggests that helicase - like genes may be involved in the biosynthesis of nucleic acids and proteins , and that the genes can be transcriptionally activated by heat shock to compensate for the repressed synthesis of mRNA and protein ."
],
"offsets": [
[
0,
240
]
]
}
] | [
{
"id": "split_0_train_120_entity",
"type": "progene_text",
"text": [
"helicase"
],
"offsets": [
[
19,
27
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_84 | split_0_train_84 | [
{
"id": "split_0_train_84_passage",
"type": "progene_text",
"text": [
"A novel ubiquitin - specific protease , UBP43 , cloned from leukemia fusion protein AML1 - ETO - expressing mice , functions in hematopoietic cell differentiation ."
],
"offsets": [
[
0,
164
]
]
}
] | [
{
"id": "split_0_train_121_entity",
"type": "progene_text",
"text": [
"ubiquitin"
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"offsets": [
[
8,
17
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],
"normalized": []
},
{
"id": "split_0_train_122_entity",
"type": "progene_text",
"text": [
"protease"
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"offsets": [
[
29,
37
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],
"normalized": []
},
{
"id": "split_0_train_123_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
40,
45
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],
"normalized": []
},
{
"id": "split_0_train_124_entity",
"type": "progene_text",
"text": [
"AML1"
],
"offsets": [
[
84,
88
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],
"normalized": []
},
{
"id": "split_0_train_125_entity",
"type": "progene_text",
"text": [
"ETO"
],
"offsets": [
[
91,
94
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_85 | split_0_train_85 | [
{
"id": "split_0_train_85_passage",
"type": "progene_text",
"text": [
"Using PCR - coupled subtractive screening - representational difference analysis , we have cloned a novel gene from AML1 - ETO knockin mice ."
],
"offsets": [
[
0,
141
]
]
}
] | [
{
"id": "split_0_train_126_entity",
"type": "progene_text",
"text": [
"AML1"
],
"offsets": [
[
116,
120
]
],
"normalized": []
},
{
"id": "split_0_train_127_entity",
"type": "progene_text",
"text": [
"ETO"
],
"offsets": [
[
123,
126
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_86 | split_0_train_86 | [
{
"id": "split_0_train_86_passage",
"type": "progene_text",
"text": [
"This gene is highly expressed in the yolk sac and fetal liver of the knockin mice ."
],
"offsets": [
[
0,
83
]
]
}
] | [] | [] | [] | [] |
split_0_train_87 | split_0_train_87 | [
{
"id": "split_0_train_87_passage",
"type": "progene_text",
"text": [
"Nucleotide sequence analysis indicates that its cDNA contains an 1,107-bp open reading frame encoding a 368 - amino - acid polypeptide ."
],
"offsets": [
[
0,
136
]
]
}
] | [] | [] | [] | [] |
split_0_train_88 | split_0_train_88 | [
{
"id": "split_0_train_88_passage",
"type": "progene_text",
"text": [
"Further protein sequence and protein translation analysis shows that it belongs to a family of ubiquitin - specific proteases ( UBP ) , and its molecular mass is 43 kDa ."
],
"offsets": [
[
0,
170
]
]
}
] | [
{
"id": "split_0_train_128_entity",
"type": "progene_text",
"text": [
"family of ubiquitin - specific proteases"
],
"offsets": [
[
85,
125
]
],
"normalized": []
},
{
"id": "split_0_train_129_entity",
"type": "progene_text",
"text": [
"UBP"
],
"offsets": [
[
128,
131
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_89 | split_0_train_89 | [
{
"id": "split_0_train_89_passage",
"type": "progene_text",
"text": [
"Therefore , we have named this gene UBP43 ."
],
"offsets": [
[
0,
43
]
]
}
] | [
{
"id": "split_0_train_130_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
36,
41
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_90 | split_0_train_90 | [
{
"id": "split_0_train_90_passage",
"type": "progene_text",
"text": [
"Like other ubiquitin proteases , the UBP43 protein has deubiquitinating enzyme activity ."
],
"offsets": [
[
0,
89
]
]
}
] | [
{
"id": "split_0_train_131_entity",
"type": "progene_text",
"text": [
"ubiquitin proteases"
],
"offsets": [
[
11,
30
]
],
"normalized": []
},
{
"id": "split_0_train_132_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
37,
42
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_91 | split_0_train_91 | [
{
"id": "split_0_train_91_passage",
"type": "progene_text",
"text": [
"Protein ubiquitination has been implicated in many important cellular events ."
],
"offsets": [
[
0,
78
]
]
}
] | [] | [] | [] | [] |
split_0_train_92 | split_0_train_92 | [
{
"id": "split_0_train_92_passage",
"type": "progene_text",
"text": [
"In wild - type adult mice , UBP43 is highly expressed in the thymus and in peritoneal macrophages ."
],
"offsets": [
[
0,
99
]
]
}
] | [
{
"id": "split_0_train_133_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
28,
33
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_93 | split_0_train_93 | [
{
"id": "split_0_train_93_passage",
"type": "progene_text",
"text": [
"Among nine different murine hematopoietic cell lines analyzed , UBP43 expression is detectable only in cell lines related to the monocytic lineage ."
],
"offsets": [
[
0,
148
]
]
}
] | [
{
"id": "split_0_train_134_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
64,
69
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_94 | split_0_train_94 | [
{
"id": "split_0_train_94_passage",
"type": "progene_text",
"text": [
"Furthermore , its expression is regulated during cytokine - induced monocytic cell differentiation ."
],
"offsets": [
[
0,
100
]
]
}
] | [
{
"id": "split_0_train_135_entity",
"type": "progene_text",
"text": [
"cytokine"
],
"offsets": [
[
49,
57
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_95 | split_0_train_95 | [
{
"id": "split_0_train_95_passage",
"type": "progene_text",
"text": [
"We have investigated its function in the hematopoietic myeloid cell line M1 ."
],
"offsets": [
[
0,
77
]
]
}
] | [] | [] | [] | [] |
split_0_train_96 | split_0_train_96 | [
{
"id": "split_0_train_96_passage",
"type": "progene_text",
"text": [
"UBP43 was introduced into M1 cells by retroviral gene transfer , and several high - expressing UBP43 clones were obtained for further study ."
],
"offsets": [
[
0,
141
]
]
}
] | [
{
"id": "split_0_train_136_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
0,
5
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],
"normalized": []
},
{
"id": "split_0_train_137_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
95,
100
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_97 | split_0_train_97 | [
{
"id": "split_0_train_97_passage",
"type": "progene_text",
"text": [
"Morphologic and cell surface marker examination of UBP43 / M1 cells reveals that overexpression of UBP43 blocks cytokine - induced terminal differentiation of monocytic cells ."
],
"offsets": [
[
0,
176
]
]
}
] | [
{
"id": "split_0_train_138_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
51,
56
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],
"normalized": []
},
{
"id": "split_0_train_139_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
99,
104
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_98 | split_0_train_98 | [
{
"id": "split_0_train_98_passage",
"type": "progene_text",
"text": [
"These data suggest that UBP43 plays an important role in hematopoiesis by modulating either the ubiquitin - dependent proteolytic pathway or the ubiquitination state of another regulatory factor(s) during myeloid cell differentiation ."
],
"offsets": [
[
0,
235
]
]
}
] | [
{
"id": "split_0_train_140_entity",
"type": "progene_text",
"text": [
"UBP43"
],
"offsets": [
[
24,
29
]
],
"normalized": []
},
{
"id": "split_0_train_141_entity",
"type": "progene_text",
"text": [
"ubiquitin"
],
"offsets": [
[
96,
105
]
],
"normalized": []
}
] | [] | [] | [] |
split_0_train_99 | split_0_train_99 | [
{
"id": "split_0_train_99_passage",
"type": "progene_text",
"text": [
"Reduced inotropic support after aprotinin therapy during pediatric cardiac operations ."
],
"offsets": [
[
0,
87
]
]
}
] | [] | [] | [] | [] |
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Dataset Card for ProGene
The Protein/Gene corpus was developed at the JULIE Lab Jena under supervision of Prof. Udo Hahn. The executing scientist was Dr. Joachim Wermter. The main annotator was Dr. Rico Pusch who is an expert in biology. The corpus was developed in the context of the StemNet project (http://www.stemnet.de/).
Citation Information
@inproceedings{faessler-etal-2020-progene,
title = "{P}ro{G}ene - A Large-scale, High-Quality Protein-Gene Annotated Benchmark Corpus",
author = "Faessler, Erik and
Modersohn, Luise and
Lohr, Christina and
Hahn, Udo",
booktitle = "Proceedings of the 12th Language Resources and Evaluation Conference",
month = may,
year = "2020",
address = "Marseille, France",
publisher = "European Language Resources Association",
url = "https://aclanthology.org/2020.lrec-1.564",
pages = "4585--4596",
abstract = "Genes and proteins constitute the fundamental entities of molecular genetics. We here introduce ProGene (formerly called FSU-PRGE), a corpus that reflects our efforts to cope with this important class of named entities within the framework of a long-lasting large-scale annotation campaign at the Jena University Language {\&} Information Engineering (JULIE) Lab. We assembled the entire corpus from 11 subcorpora covering various biological domains to achieve an overall subdomain-independent corpus. It consists of 3,308 MEDLINE abstracts with over 36k sentences and more than 960k tokens annotated with nearly 60k named entity mentions. Two annotators strove for carefully assigning entity mentions to classes of genes/proteins as well as families/groups, complexes, variants and enumerations of those where genes and proteins are represented by a single class. The main purpose of the corpus is to provide a large body of consistent and reliable annotations for supervised training and evaluation of machine learning algorithms in this relevant domain. Furthermore, we provide an evaluation of two state-of-the-art baseline systems {---} BioBert and flair {---} on the ProGene corpus. We make the evaluation datasets and the trained models available to encourage comparable evaluations of new methods in the future.",
language = "English",
ISBN = "979-10-95546-34-4",
}
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