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|---|---|---|---|---|---|---|
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HPRD50.d1 | 10529171 | [
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HPRD50.d2 | 10563789 | [
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HPRD50.d3 | 10579793 | [
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HPRD50.d4 | 10736564 | [
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HPRD50.d5 | 10835351 | [
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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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HPRD50.d12 | 11779129 | [
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HPRD50.d13 | 11940666 | [
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HPRD50.d14 | 11994745 | [
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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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HPRD50.d23 | 12852857 | [
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"id": "HPRD50.d23.s0",
"type": "sentence",
"text": [
"A role for Plk1 phosphorylation of NudC in cytokinesis"
],
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0,
54
]
]
},
{
"id": "HPRD50.d23.s1",
"type": "sentence",
"text": [
"Here, we characterize the interaction... | [
{
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"type": "protein",
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]
},
{
"id": "HPRD50.d23.s0.e1",
"type": "protein",
... | [] | [] | [
{
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{
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"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d24 | 12947119 | [
{
"id": "HPRD50.d24.s0",
"type": "sentence",
"text": [
"Specific interaction of Egr1 and c/EBPbeta leads to the transcriptional activation of the human low density lipoprotein receptor gene"
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0,
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]
},
{
"id": "HPRD50.d24.s1",
... | [
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]
},
{
"id": "HPRD50.d24.s0.e1",
"type": "protein",
... | [] | [] | [
{
"id": "HPRD50.d24.s0.i0",
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"arg2_id": "HPRD50.d24.s1.e2",
"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d25 | 12949936 | [
{
"id": "HPRD50.d25.s0",
"type": "sentence",
"text": [
"TR2 orphan receptor functions as negative modulator for androgen receptor in prostate cancer cells PC-3"
],
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[
0,
103
]
]
},
{
"id": "HPRD50.d25.s1",
"type": "sentence",
"tex... | [
{
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"type": "protein",
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"TR2"
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3
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],
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"db_id": "pm0104071||pm0107975||pm0108440||pm0116348||pm0122716"
}
]
},
{
"id": "HPRD5... | [] | [] | [
{
"id": "HPRD50.d25.s0.i0",
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"normalized": []
}
] |
HPRD50.d26 | 14556007 | [
{
"id": "HPRD50.d26.s0",
"type": "sentence",
"text": [
"The protein pVHL functions in a multi-subunit E3 ubiquitin ligase that targets the hypoxia-inducible transcription factor Hif1 alpha for proteasomal degradation during normoxia"
],
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[
0,
176
]
... | [
{
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]
},
{
"id": "HPRD50.d26.s0.e1",
"type": "protein",
... | [] | [] | [
{
"id": "HPRD50.d26.s0.i0",
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"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d27 | 14578391 | [
{
"id": "HPRD50.d27.s0",
"type": "sentence",
"text": [
"Pinin/DRS/memA interacts with SRp75, SRm300 and SRrp130 in corneal epithelial cells"
],
"offsets": [
[
0,
83
]
]
},
{
"id": "HPRD50.d27.s1",
"type": "sentence",
"text": [
"Three SR... | [
{
"id": "HPRD50.d27.s0.e0",
"type": "protein",
"text": [
"Pinin"
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0,
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],
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]
},
{
"id": "HPRD50.d27.s0.e1",
"type": "protein",
"... | [] | [] | [
{
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},
{
"id": "HPRD50.d27.s0.i1",
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"arg2_id": "HPRD50.d27.s0.e3",
"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d29 | 14752048 | [
{
"id": "HPRD50.d29.s0",
"type": "sentence",
"text": [
"Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription"
],
"offsets": [
[
0,
169
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]
... | [
{
"id": "HPRD50.d29.s0.e0",
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},
{
"id": "HPRD50.d29.s0.e1",
"type": "protein",
... | [] | [] | [
{
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},
{
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"arg2_id": "HPRD50.d29.s1.e1",
"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d30 | 7629131 | [
{
"id": "HPRD50.d30.s0",
"type": "sentence",
"text": [
"The tyrosine kinase Tyk-2 is physically associated with the Type I interferon (IFN) receptor complex and is rapidly activated during IFN alpha stimulation"
],
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[
0,
154
]
]
}
] | [
{
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"Tyk-2"
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},
{
"id": "HPRD50.d30.s0.e1",
"type": "protein",
... | [] | [] | [
{
"id": "HPRD50.d30.s0.i0",
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"arg2_id": "HPRD50.d30.s0.e2",
"normalized": []
}
] |
HPRD50.d31 | 7744247 | [
{
"id": "HPRD50.d31.s0",
"type": "sentence",
"text": [
"Raf1 interaction with Cdc25 phosphatase ties mitogenic signal transduction to cell cycle activation"
],
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0,
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]
},
{
"id": "HPRD50.d31.s1",
"type": "sentence",
"text": [... | [
{
"id": "HPRD50.d31.s0.e0",
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"Raf1"
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0,
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}
]
},
{
"id": "HPRD50.d31.s0.e1",
"type": "protein",
"t... | [] | [] | [
{
"id": "HPRD50.d31.s0.i0",
"type": "PPI",
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{
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"arg2_id": "HPRD50.d31.s1.e1",
"normalized": []
}
] |
HPRD50.d32 | 7793988 | [
{
"id": "HPRD50.d32.s0",
"type": "sentence",
"text": [
"Differential binding of vascular cell-derived proteoglycans (perlecan, biglycan, decorin, and versican) to the beta-amyloid protein of Alzheimer's disease"
],
"offsets": [
[
0,
154
]
]
},
{
"id"... | [
{
"id": "HPRD50.d32.s0.e0",
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"perlecan"
],
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61,
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],
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}
]
},
{
"id": "HPRD50.d32.s0.e1",
"type": "protein",
... | [] | [] | [
{
"id": "HPRD50.d32.s1.i0",
"type": "PPI",
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"arg2_id": "HPRD50.d32.s1.e2",
"normalized": []
},
{
"id": "HPRD50.d32.s1.i1",
"type": "PPI",
"arg1_id": "HPRD50.d32.s1.e0",
"arg2_id": "HPRD50.d32.s1.e3",
"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d33 | 7963560 | [
{
"id": "HPRD50.d33.s0",
"type": "sentence",
"text": [
"Cross-linking of CD53 with the use of the mAb MEM-53 and a polyclonal sheep anti-mouse Ig promoted activation of resting B cells into the G1 phase of the cell cycle as judged by increased expression of the early activation Ag CD69, increases ... | [
{
"id": "HPRD50.d33.s0.e0",
"type": "protein",
"text": [
"CD53"
],
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17,
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],
"normalized": [
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"db_id": "pm0107494"
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]
},
{
"id": "HPRD50.d33.s0.e1",
"type": "protein",
... | [] | [] | [
{
"id": "HPRD50.d33.s0.i0",
"type": "PPI",
"arg1_id": "HPRD50.d33.s0.e0",
"arg2_id": "HPRD50.d33.s0.e1",
"normalized": []
},
{
"id": "HPRD50.d33.s0.i1",
"type": "PPI",
"arg1_id": "HPRD50.d33.s0.e0",
"arg2_id": "HPRD50.d33.s0.e2",
"normalized": []
},
{
"id": "HPRD5... |
HPRD50.d34 | 8078915 | [
{
"id": "HPRD50.d34.s0",
"type": "sentence",
"text": [
"The human apoB mRNA editing protein is a cytidine deaminase showing structural homology to some known mammalian and bacteriophage deoxycytidylate deaminases"
],
"offsets": [
[
0,
156
]
]
},
{
"i... | [
{
"id": "HPRD50.d34.s0.e0",
"type": "protein",
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"apoB"
],
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10,
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],
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"db_id": "pm0126272"
}
]
},
{
"id": "HPRD50.d34.s0.e1",
"type": "protein",
... | [] | [] | [] |
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.d... | [
{
"id": "HPRD50.d35.s0.e0",
"type": "protein",
"text": [
"Etfdh"
],
"offsets": [
[
14,
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]
],
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"db_name": "HPRD",
"db_id": "pm0103481"
}
]
},
{
"id": "HPRD50.d35.s0.e1",
"type": "protein",
... | [] | [] | [] |
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 pro... | [
{
"id": "HPRD50.d38.s0.e0",
"type": "protein",
"text": [
"involucrin"
],
"offsets": [
[
66,
76
]
],
"normalized": [
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"db_id": "pm0104308"
}
]
},
{
"id": "HPRD50.d38.s0.e1",
"type": "protein"... | [] | [] | [
{
"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": "HPRD5... |
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": "senten... | [
{
"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",
... | [] | [] | [
{
"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.s... | [
{
"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",
... | [] | [] | [
{
"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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