id
stringlengths 9
10
| document_id
stringlengths 7
8
| passages
list | entities
list | events
list | coreferences
list | relations
list |
|---|---|---|---|---|---|---|
HPRD50.d0 | 10373544 | [
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"id": "HPRD50.d0.s0",
"type": "sentence",
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"Cloning and characterization of two evolutionarily conserved subunits (TFIIIC102 and TFIIIC63) of human TFIIIC and their involvement in functional interactions with TFIIIB and RNA polymerase III"
],
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0,
194
]
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85,
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{
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104,
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{
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"db_id": "pm0120026"
}
]
}
] | [] | [] | [] |
HPRD50.d1 | 10529171 | [
{
"id": "HPRD50.d1.s0",
"type": "sentence",
"text": [
"Identification of residues in the monocyte chemotactic protein-1 that contact the MCP-1 receptor, CCR2"
],
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[
0,
102
]
]
},
{
"id": "HPRD50.d1.s1",
"type": "sentence",
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"The receptor binding site of MCP-1 also is significantly different from the binding sites of RANTES and IL-8, providing insight into the issue of receptor specificity"
],
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103,
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{
"id": "HPRD50.d1.s2",
"type": "sentence",
"text": [
"It was previously shown that the N-terminus of CCR2 is critical for binding MCP-1"
],
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270,
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},
{
"id": "HPRD50.d1.s3",
"type": "sentence",
"text": [
"To identify the regions of MCP-1 that contact its receptor, CCR2, we substituted all surface-exposed residues with alanine"
],
"offsets": [
[
352,
474
]
]
}
] | [
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"CCR2"
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"RANTES"
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"text": [
"IL-8"
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"MCP-1"
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},
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"CCR2"
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],
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"db_id": "pm0111607"
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]
}
] | [] | [] | [
{
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"arg2_id": "HPRD50.d1.s3.e1",
"normalized": []
}
] |
HPRD50.d2 | 10563789 | [
{
"id": "HPRD50.d2.s0",
"type": "sentence",
"text": [
"We tested this point by cotransfecting CHO cells with the genes encoding F beta alpha and the CG beta subunit or the CG beta alpha and FSH beta monomer"
],
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[
0,
151
]
]
},
{
"id": "HPRD50.d2.s1",
"type": "sentence",
"text": [
"The formation of a functional single chain/subunit complex was not restricted to the FSH single chain/CG beta subunit since CG single chain interacts with the monomeric FSH beta subunit and exhibits FSH activity"
],
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152,
363
]
]
},
{
"id": "HPRD50.d2.s2",
"type": "sentence",
"text": [
"This is relevant for the case of LH and FSH, because both are synthesized in the same cell (i.e., pituitary gonadotrophs) and several of the alpha subunit sequences required for association with either the LH beta or FSH beta subunits are different"
],
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364,
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]
]
},
{
"id": "HPRD50.d2.s3",
"type": "sentence",
"text": [
"Previously, we showed that the CG beta or FSH beta subunit genes can be genetically fused to the alpha gene to produce biologically active single chains, CG beta alpha and F beta alpha, respectively"
],
"offsets": [
[
613,
811
]
]
}
] | [
{
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"CG beta"
],
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94,
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],
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]
},
{
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"text": [
"CG beta alpha"
],
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117,
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]
],
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]
},
{
"id": "HPRD50.d2.s0.e2",
"type": "protein",
"text": [
"FSH beta"
],
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135,
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]
],
"normalized": [
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}
]
},
{
"id": "HPRD50.d2.s1.e0",
"type": "protein",
"text": [
"CG beta"
],
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102,
109
]
],
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]
},
{
"id": "HPRD50.d2.s1.e1",
"type": "protein",
"text": [
"FSH beta"
],
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169,
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]
],
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}
]
},
{
"id": "HPRD50.d2.s2.e0",
"type": "protein",
"text": [
"LH beta"
],
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206,
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]
],
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}
]
},
{
"id": "HPRD50.d2.s2.e1",
"type": "protein",
"text": [
"FSH beta"
],
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217,
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]
],
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}
]
},
{
"id": "HPRD50.d2.s3.e0",
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"CG beta"
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31,
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]
},
{
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"FSH beta"
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42,
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},
{
"id": "HPRD50.d2.s3.e2",
"type": "protein",
"text": [
"CG beta alpha"
],
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154,
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]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0125097"
}
]
}
] | [] | [] | [] |
HPRD50.d3 | 10579793 | [
{
"id": "HPRD50.d3.s0",
"type": "sentence",
"text": [
"Interleukin-6 activates phosphatidylinositol-3 kinase, which inhibits apoptosis in human prostate cancer cell lines"
],
"offsets": [
[
0,
115
]
]
},
{
"id": "HPRD50.d3.s1",
"type": "sentence",
"text": [
"RESULTS: Tyrosine phosphorylation of p85 is upregulated by IL-6 in both LNCaP and PC-3"
],
"offsets": [
[
116,
202
]
]
},
{
"id": "HPRD50.d3.s2",
"type": "sentence",
"text": [
"IL-6 promotes coprecipitation of p85 with gp130, the signal-transducing component of the IL-6 receptor"
],
"offsets": [
[
203,
305
]
]
}
] | [
{
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"Interleukin-6"
],
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0,
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],
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"db_id": "pm0110911"
}
]
},
{
"id": "HPRD50.d3.s0.e1",
"type": "protein",
"text": [
"phosphatidylinositol-3 kinase"
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24,
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]
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}
]
},
{
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]
},
{
"id": "HPRD50.d3.s1.e1",
"type": "protein",
"text": [
"PC-3"
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},
{
"id": "HPRD50.d3.s2.e0",
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"text": [
"IL-6"
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},
{
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"gp130"
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42,
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},
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],
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"db_name": "HPRD",
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]
}
] | [] | [] | [
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}
] |
HPRD50.d4 | 10736564 | [
{
"id": "HPRD50.d4.s0",
"type": "sentence",
"text": [
"In solution, FGFR4ed formed complexes with acidic FGF (FGF-1) and basic FGF (FGF-2), both in the presence and absence of heparin"
],
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0,
128
]
]
},
{
"id": "HPRD50.d4.s1",
"type": "sentence",
"text": [
"Immobilized FGFR4 also bound FGF-8 besides FGF-1 and FGF-2"
],
"offsets": [
[
129,
187
]
]
}
] | [
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}
] | [] | [] | [
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}
] |
HPRD50.d5 | 10835351 | [
{
"id": "HPRD50.d5.s0",
"type": "sentence",
"text": [
"Cytohesin-1 regulates beta-2 integrin-mediated adhesion through both ARF-GEF function and interaction with LFA-1"
],
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0,
112
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},
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],
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113,
271
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]
},
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"id": "HPRD50.d5.s2",
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"Mutational analyses of the beta-2 cytoplasmic domain revealed that the adhesive function of LFA-1 depends on its interaction with cytohesin-1, unless the integrin is activated by exogenous divalent cations"
],
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272,
477
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"id": "HPRD50.d5.s3",
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],
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478,
635
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},
{
"id": "HPRD50.d5.s4",
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"In contrast, LFA-1-mediated cell adhesion and spreading on intercellular cell adhesion molecule 1 is strongly inhibited by a cytohesin-1 mutant, which fails to catalyze ARF GDP-GTP exchange in vitro"
],
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636,
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"id": "HPRD50.d5.s5",
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"Thus, cytohesin-1 is involved in the activation of LFA-1, most probably through direct interaction with the integrin, and induces cell spreading by its ARF-GEF activity"
],
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] |
HPRD50.d7 | 10930400 | [
{
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] |
HPRD50.d8 | 10995457 | [
{
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}
] | [] | [] | [] |
HPRD50.d9 | 11171101 | [
{
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}
] | [] | [] | [] |
HPRD50.d11 | 11313349 | [
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],
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] |
HPRD50.d12 | 11779129 | [
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] |
HPRD50.d13 | 11940666 | [
{
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300,
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] |
HPRD50.d14 | 11994745 | [
{
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],
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57,
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}
] | [] | [] | [
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HPRD50.d16 | 12124778 | [
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HPRD50.d18 | 12370829 | [
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HPRD50.d19 | 12371907 | [
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HPRD50.d20 | 12655004 | [
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HPRD50.d21 | 12690115 | [
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HPRD50.d22 | 12819203 | [
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] | [] | [] | [
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] |
HPRD50.d23 | 12852857 | [
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] |
HPRD50.d24 | 12947119 | [
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] | [] | [] | [
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] |
HPRD50.d25 | 12949936 | [
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104,
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],
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284,
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]
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}
] | [] | [] | [
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] |
HPRD50.d26 | 14556007 | [
{
"id": "HPRD50.d26.s0",
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HPRD50.d27 | 14578391 | [
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HPRD50.d29 | 14752048 | [
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] |
HPRD50.d30 | 7629131 | [
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HPRD50.d31 | 7744247 | [
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HPRD50.d32 | 7793988 | [
{
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}
] | [] | [] | [
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] |
HPRD50.d33 | 7963560 | [
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HPRD50.d34 | 8078915 | [
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},
{
"id": "HPRD50.d34.s1.e1",
"type": "protein",
"text": [
"homodimer"
],
"offsets": [
[
61,
70
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0125626"
}
]
},
{
"id": "HPRD50.d34.s1.e2",
"type": "protein",
"text": [
"apoB"
],
"offsets": [
[
119,
123
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0126272"
}
]
}
] | [] | [] | [] |
HPRD50.d35 | 8617498 | [
{
"id": "HPRD50.d35.s0",
"type": "sentence",
"text": [
"Assignment of Etfdh, Etfb, and Etfa to chromosomes 3, 7, and 13: the mouse homologs of genes responsible for glutaric acidemia type II in human"
],
"offsets": [
[
0,
143
]
]
},
{
"id": "HPRD50.d35.s1",
"type": "sentence",
"text": [
"We used cDNA probes for the Etfdh, Etfb, and Etfa genes to determine localization of these mouse genes to chromosomes 3, 7, and 13"
],
"offsets": [
[
144,
274
]
]
}
] | [
{
"id": "HPRD50.d35.s0.e0",
"type": "protein",
"text": [
"Etfdh"
],
"offsets": [
[
14,
19
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0103481"
}
]
},
{
"id": "HPRD50.d35.s0.e1",
"type": "protein",
"text": [
"Etfb"
],
"offsets": [
[
21,
25
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110405"
}
]
},
{
"id": "HPRD50.d35.s1.e0",
"type": "protein",
"text": [
"Etfdh"
],
"offsets": [
[
28,
33
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0103481"
}
]
},
{
"id": "HPRD50.d35.s1.e1",
"type": "protein",
"text": [
"Etfb"
],
"offsets": [
[
35,
39
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110405"
}
]
}
] | [] | [] | [] |
HPRD50.d38 | 8999895 | [
{
"id": "HPRD50.d38.s0",
"type": "sentence",
"text": [
"Subsequent amino acid sequencing revealed many peptides involving involucrin cross-linked either to itself or to a variety of other known CE protein components, including cystatin alpha, desmoplakin, elafin, keratins, members of the small proline-rich superfamily, loricrin, and unknown proteins related to the desmoplakin family"
],
"offsets": [
[
0,
329
]
]
},
{
"id": "HPRD50.d38.s1",
"type": "sentence",
"text": [
"Specific glutamines or lysines of involucrin were used to cross-link the different proteins, such as glutamines 495 and 496 to desmoplakin, glutamine 288 to keratins, and lysines 468, 485, and 508 and glutamines 465 and 489 for interchain involucrin cross-links"
],
"offsets": [
[
330,
591
]
]
}
] | [
{
"id": "HPRD50.d38.s0.e0",
"type": "protein",
"text": [
"involucrin"
],
"offsets": [
[
66,
76
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0104308"
}
]
},
{
"id": "HPRD50.d38.s0.e1",
"type": "protein",
"text": [
"cystatin alpha"
],
"offsets": [
[
171,
185
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0104526"
}
]
},
{
"id": "HPRD50.d38.s0.e2",
"type": "protein",
"text": [
"desmoplakin"
],
"offsets": [
[
187,
198
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110549"
}
]
},
{
"id": "HPRD50.d38.s0.e3",
"type": "protein",
"text": [
"elafin"
],
"offsets": [
[
200,
206
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0114270"
}
]
},
{
"id": "HPRD50.d38.s0.e4",
"type": "protein",
"text": [
"loricrin"
],
"offsets": [
[
265,
273
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0103809"
}
]
},
{
"id": "HPRD50.d38.s0.e5",
"type": "protein",
"text": [
"desmoplakin"
],
"offsets": [
[
311,
322
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110549"
}
]
},
{
"id": "HPRD50.d38.s1.e0",
"type": "protein",
"text": [
"involucrin"
],
"offsets": [
[
34,
44
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0104308"
}
]
},
{
"id": "HPRD50.d38.s1.e1",
"type": "protein",
"text": [
"desmoplakin"
],
"offsets": [
[
127,
138
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110549"
}
]
},
{
"id": "HPRD50.d38.s1.e2",
"type": "protein",
"text": [
"involucrin"
],
"offsets": [
[
239,
249
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0104308"
}
]
}
] | [] | [] | [
{
"id": "HPRD50.d38.s0.i0",
"type": "PPI",
"arg1_id": "HPRD50.d38.s0.e0",
"arg2_id": "HPRD50.d38.s0.e1",
"normalized": []
},
{
"id": "HPRD50.d38.s0.i1",
"type": "PPI",
"arg1_id": "HPRD50.d38.s0.e0",
"arg2_id": "HPRD50.d38.s0.e2",
"normalized": []
},
{
"id": "HPRD50.d38.s0.i2",
"type": "PPI",
"arg1_id": "HPRD50.d38.s0.e0",
"arg2_id": "HPRD50.d38.s0.e3",
"normalized": []
},
{
"id": "HPRD50.d38.s0.i3",
"type": "PPI",
"arg1_id": "HPRD50.d38.s0.e0",
"arg2_id": "HPRD50.d38.s0.e4",
"normalized": []
},
{
"id": "HPRD50.d38.s0.i4",
"type": "PPI",
"arg1_id": "HPRD50.d38.s0.e0",
"arg2_id": "HPRD50.d38.s0.e5",
"normalized": []
}
] |
HPRD50.d39 | 9153302 | [
{
"id": "HPRD50.d39.s0",
"type": "sentence",
"text": [
"A prominent isolate, designated SRcyp/CASP10, specifically interacts with the CTD not only in vivo but also in vitro"
],
"offsets": [
[
0,
116
]
]
},
{
"id": "HPRD50.d39.s1",
"type": "sentence",
"text": [
"SRcyp is a nuclear protein with a characteristic distribution in large irregularly shaped nuclear speckles and co-localizes perfectly with the SR domain-containing splicing factor SC35"
],
"offsets": [
[
117,
301
]
]
}
] | [
{
"id": "HPRD50.d39.s0.e0",
"type": "protein",
"text": [
"SRcyp"
],
"offsets": [
[
32,
37
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0120029"
}
]
},
{
"id": "HPRD50.d39.s0.e1",
"type": "protein",
"text": [
"CASP10"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0122990"
}
]
},
{
"id": "HPRD50.d39.s0.e2",
"type": "protein",
"text": [
"CTD"
],
"offsets": [
[
78,
81
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0113359"
}
]
},
{
"id": "HPRD50.d39.s1.e0",
"type": "protein",
"text": [
"SRcyp"
],
"offsets": [
[
0,
5
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0120029"
}
]
},
{
"id": "HPRD50.d39.s1.e1",
"type": "protein",
"text": [
"splicing factor SC35"
],
"offsets": [
[
164,
184
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0120690"
}
]
}
] | [] | [] | [
{
"id": "HPRD50.d39.s0.i0",
"type": "PPI",
"arg1_id": "HPRD50.d39.s0.e0",
"arg2_id": "HPRD50.d39.s0.e2",
"normalized": []
},
{
"id": "HPRD50.d39.s0.i1",
"type": "PPI",
"arg1_id": "HPRD50.d39.s0.e1",
"arg2_id": "HPRD50.d39.s0.e2",
"normalized": []
}
] |
HPRD50.d40 | 9668116 | [
{
"id": "HPRD50.d40.s0",
"type": "sentence",
"text": [
"Transient expression of the full-length E2-2 without RSRS in U1240MG glioblastoma cells resulted in repression of FGF-1.B promoter activity"
],
"offsets": [
[
0,
139
]
]
},
{
"id": "HPRD50.d40.s1",
"type": "sentence",
"text": [
"These results suggest that the relative abundance of the two splice variants of E2-2 in brain could be an important determinant for the expression of FGF-1"
],
"offsets": [
[
140,
295
]
]
}
] | [
{
"id": "HPRD50.d40.s0.e0",
"type": "protein",
"text": [
"E2-2"
],
"offsets": [
[
40,
44
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110165"
}
]
},
{
"id": "HPRD50.d40.s0.e1",
"type": "protein",
"text": [
"FGF-1.B"
],
"offsets": [
[
114,
121
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0124654-1.B"
}
]
},
{
"id": "HPRD50.d40.s1.e0",
"type": "protein",
"text": [
"E2-2"
],
"offsets": [
[
80,
84
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0110165"
}
]
},
{
"id": "HPRD50.d40.s1.e1",
"type": "protein",
"text": [
"FGF-1"
],
"offsets": [
[
150,
155
]
],
"normalized": [
{
"db_name": "HPRD",
"db_id": "pm0124654"
}
]
}
] | [] | [] | [
{
"id": "HPRD50.d40.s0.i0",
"type": "PPI",
"arg1_id": "HPRD50.d40.s0.e0",
"arg2_id": "HPRD50.d40.s0.e1",
"normalized": []
},
{
"id": "HPRD50.d40.s1.i0",
"type": "PPI",
"arg1_id": "HPRD50.d40.s1.e0",
"arg2_id": "HPRD50.d40.s1.e1",
"normalized": []
}
] |
Dataset Card for HPRD50
HPRD50 is a dataset of randomly selected, hand-annotated abstracts of biomedical papers referenced by the Human Protein Reference Database (HPRD). It is parsed in XML format, splitting each abstract into sentences, and in each sentence there may be entities and interactions between those entities. In this particular dataset, entities are all proteins and interactions are thus protein-protein interactions.
Moreover, all entities are normalized to the HPRD database. These normalized terms are stored in each entity's 'type' attribute in the source XML. This means the dataset can determine e.g. that "Janus kinase 2" and "Jak2" are referencing the same normalized entity.
Because the dataset contains entities and relations, it is suitable for Named Entity Recognition and Relation Extraction.
Citation Information
@article{fundel2007relex,
title={RelEx—Relation extraction using dependency parse trees},
author={Fundel, Katrin and K{"u}ffner, Robert and Zimmer, Ralf},
journal={Bioinformatics},
volume={23},
number={3},
pages={365--371},
year={2007},
publisher={Oxford University Press}
}
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