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1.0alpha7.train.20 | 23310850 | [
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1.0alpha7.train.29 | 15179628 | [
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1.0alpha7.train.30 | 16352875 | [
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1.0alpha7.train.31 | 3737303 | [
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1.0alpha7.train.32 | 3737303 | [
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1.0alpha7.train.33 | 11560304 | [
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1.0alpha7.train.34 | 15685147 | [
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1.0alpha7.train.35 | 24566933 | [
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1.0alpha7.train.36 | 15862392 | [
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1.0alpha7.train.37 | 3573748 | [
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1.0alpha7.train.38 | 1380101 | [
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1.0alpha7.train.39 | 2712406 | [
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1.0alpha7.train.40 | 2528920 | [
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1.0alpha7.train.41 | 15213790 | [
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1.0alpha7.train.42 | 15178756 | [
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1.0alpha7.train.43 | 1989374 | [
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1.0alpha7.train.63 | 17880851 | [
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1.0alpha7.train.78 | 1778453 | [
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1.0alpha7.train.79 | 15268259 | [
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1.0alpha7.train.81 | 11949602 | [
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1.0alpha7.train.83 | 8934428 | [
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1.0alpha7.train.84 | 9849106 | [
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1.0alpha7.train.85 | 2164892 | [
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1.0alpha7.train.86 | 3548985 | [
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1.0alpha7.train.87 | 11828384 | [
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"arg2_id": "1.0alpha7.train.87.ent1_0",
"normalized": []
}
] |
1.0alpha7.train.88 | 2450060 | [
{
"id": "1.0alpha7.train.88.sent",
"type": "sentence",
"text": [
"A mutant form of Pyk2 (Pyk2-Y402F) that is unable to bind and activate Src is impaired in its ability to induce association of Grb2 with Shc, binding of Crk to p130Cas and stimulation of the ERK and JNK cascades."
],
"offset... | [
{
"id": "1.0alpha7.train.88.ent0_0",
"type": "protein",
"text": [
"Src"
],
"offsets": [
[
71,
74
]
],
"normalized": [
{
"db_name": "NCBI gene",
"db_id": "6714"
},
{
"db_name": "hgnc",
"db_id": "SRC"
... | [] | [
{
"id": "1.0alpha7.train.88.coref0",
"entity_ids": [
"1.0alpha7.train.88.ent0_0"
]
},
{
"id": "1.0alpha7.train.88.coref1",
"entity_ids": [
"1.0alpha7.train.88.ent1_0",
"1.0alpha7.train.88.ent2_1"
]
},
{
"id": "1.0alpha7.train.88.coref2",
"entity_ids": [
... | [
{
"id": "1.0alpha7.train.88.rel0s1.0alpha7.train.88.ent0_0.o1.0alpha7.train.88.ent1_0",
"type": "bind",
"arg1_id": "1.0alpha7.train.88.ent0_0",
"arg2_id": "1.0alpha7.train.88.ent1_0",
"normalized": []
},
{
"id": "1.0alpha7.train.88.rel0s1.0alpha7.train.88.ent0_0.o1.0alpha7.train.88.ent2_... |
1.0alpha7.train.89 | 8949357 | [
{
"id": "1.0alpha7.train.89.sent",
"type": "sentence",
"text": [
"These results indicate that LIN-7 binds to LIN-2 and that LIN-2 binds to LIN-10 in vivo."
],
"offsets": [
[
0,
88
]
]
}
] | [
{
"id": "1.0alpha7.train.89.ent0_0",
"type": "protein",
"text": [
"LIN-7"
],
"offsets": [
[
28,
33
]
],
"normalized": [
{
"db_name": "NCBI gene",
"db_id": "8825"
},
{
"db_name": "hgnc",
"db_id": "LIN7A"
... | [] | [
{
"id": "1.0alpha7.train.89.coref0",
"entity_ids": [
"1.0alpha7.train.89.ent0_0"
]
},
{
"id": "1.0alpha7.train.89.coref1",
"entity_ids": [
"1.0alpha7.train.89.ent1_0",
"1.0alpha7.train.89.ent2_1"
]
},
{
"id": "1.0alpha7.train.89.coref2",
"entity_ids": [
... | [
{
"id": "1.0alpha7.train.89.rel0s1.0alpha7.train.89.ent0_0.o1.0alpha7.train.89.ent1_0",
"type": "bind",
"arg1_id": "1.0alpha7.train.89.ent0_0",
"arg2_id": "1.0alpha7.train.89.ent1_0",
"normalized": []
},
{
"id": "1.0alpha7.train.89.rel0s1.0alpha7.train.89.ent0_0.o1.0alpha7.train.89.ent2_... |
1.0alpha7.train.90 | 24605299 | [
{
"id": "1.0alpha7.train.90.sent",
"type": "sentence",
"text": [
"Binding of GMP to the GK domain of PSD-95 did not induce large conformational changes in the nucleoside binding domain, in contrast to yeast guanylate kinase (Blaszczyk et al., 2001 )."
],
"offsets": [
[
0,
... | [
{
"id": "1.0alpha7.train.90.ent0_0",
"type": "chemical",
"text": [
"GMP"
],
"offsets": [
[
11,
14
]
],
"normalized": [
{
"db_name": "pubchem:compound",
"db_id": "135398631"
}
]
},
{
"id": "1.0alpha7.train.90.ent1_0... | [] | [
{
"id": "1.0alpha7.train.90.coref0",
"entity_ids": [
"1.0alpha7.train.90.ent0_0"
]
},
{
"id": "1.0alpha7.train.90.coref1",
"entity_ids": [
"1.0alpha7.train.90.ent1_0"
]
},
{
"id": "1.0alpha7.train.90.coref2",
"entity_ids": [
"1.0alpha7.train.90.ent2_0"
]... | [
{
"id": "1.0alpha7.train.90.rel0s1.0alpha7.train.90.ent0_0.o1.0alpha7.train.90.ent2_0",
"type": "bind",
"arg1_id": "1.0alpha7.train.90.ent0_0",
"arg2_id": "1.0alpha7.train.90.ent2_0",
"normalized": []
},
{
"id": "1.0alpha7.train.90.rel1s1.0alpha7.train.90.ent0_0.o1.0alpha7.train.90.ent1_... |
1.0alpha7.train.91 | 305922 | [
{
"id": "1.0alpha7.train.91.sent",
"type": "sentence",
"text": [
"In this model calcium stabilizes the binding of PKC to PS containing membranes (see also ( 2 , 3 , 4 , 6 ) )."
],
"offsets": [
[
0,
109
]
]
}
] | [
{
"id": "1.0alpha7.train.91.ent0_0",
"type": "chemical",
"text": [
"calcium"
],
"offsets": [
[
14,
21
]
],
"normalized": [
{
"db_name": "pubchem:compound",
"db_id": "5460341"
}
]
},
{
"id": "1.0alpha7.train.91.ent1... | [] | [
{
"id": "1.0alpha7.train.91.coref0",
"entity_ids": [
"1.0alpha7.train.91.ent0_0"
]
},
{
"id": "1.0alpha7.train.91.coref1",
"entity_ids": [
"1.0alpha7.train.91.ent1_0"
]
},
{
"id": "1.0alpha7.train.91.coref2",
"entity_ids": [
"1.0alpha7.train.91.ent2_0"
]... | [] |
1.0alpha7.train.92 | 1570410 | [
{
"id": "1.0alpha7.train.92.sent",
"type": "sentence",
"text": [
"It is now apparent that 4E-BP1 inhibits the function of eIF4E in cap-dependent translation by blocking the binding of eIF4E to eIF4G, another component of the eIF4F complex."
],
"offsets": [
[
0,
173
... | [
{
"id": "1.0alpha7.train.92.ent0_0",
"type": "protein",
"text": [
"eIF4E"
],
"offsets": [
[
56,
61
]
],
"normalized": [
{
"db_name": "NCBI gene",
"db_id": "1977"
},
{
"db_name": "hgnc",
"db_id": "EIF4E"
... | [] | [
{
"id": "1.0alpha7.train.92.coref0",
"entity_ids": [
"1.0alpha7.train.92.ent0_0",
"1.0alpha7.train.92.ent1_1"
]
},
{
"id": "1.0alpha7.train.92.coref1",
"entity_ids": [
"1.0alpha7.train.92.ent2_0"
]
},
{
"id": "1.0alpha7.train.92.coref2",
"entity_ids": [
... | [
{
"id": "1.0alpha7.train.92.rel0s1.0alpha7.train.92.ent0_0.o1.0alpha7.train.92.ent2_0",
"type": "bind",
"arg1_id": "1.0alpha7.train.92.ent0_0",
"arg2_id": "1.0alpha7.train.92.ent2_0",
"normalized": []
},
{
"id": "1.0alpha7.train.92.rel0s1.0alpha7.train.92.ent1_1.o1.0alpha7.train.92.ent2_... |
1.0alpha7.train.93 | 25350899 | [
{
"id": "1.0alpha7.train.93.sent",
"type": "sentence",
"text": [
"ADF/ cofilin can directly bind to actin filaments and promote their disassembly (Carlier et al., 1999 ; Bamburg, 1999 )."
],
"offsets": [
[
0,
120
]
]
}
] | [
{
"id": "1.0alpha7.train.93.ent0_0",
"type": "protein-family",
"text": [
"ADF/ cofilin"
],
"offsets": [
[
0,
12
]
],
"normalized": [
{
"db_name": "interpro",
"db_id": "IPR017904"
}
]
},
{
"id": "1.0alpha7.train.93.... | [] | [
{
"id": "1.0alpha7.train.93.coref0",
"entity_ids": [
"1.0alpha7.train.93.ent0_0"
]
},
{
"id": "1.0alpha7.train.93.coref1",
"entity_ids": [
"1.0alpha7.train.93.ent1_0"
]
}
] | [
{
"id": "1.0alpha7.train.93.rel0s1.0alpha7.train.93.ent0_0.o1.0alpha7.train.93.ent1_0",
"type": "bind",
"arg1_id": "1.0alpha7.train.93.ent0_0",
"arg2_id": "1.0alpha7.train.93.ent1_0",
"normalized": []
}
] |
End of preview. Expand
in Data Studio
Dataset Card for BioRelEx
BioRelEx is a biological relation extraction dataset. Version 1.0 contains 2010 annotated sentences that describe binding interactions between various biological entities (proteins, chemicals, etc.). 1405 sentences are for training, another 201 sentences are for validation. They are publicly available at https://github.com/YerevaNN/BioRelEx/releases. Another 404 sentences are for testing which are kept private for at this Codalab competition https://competitions.codalab.org/competitions/20468. All sentences contain words "bind", "bound" or "binding". For every sentence we provide: 1) Complete annotations of all biological entities that appear in the sentence 2) Entity types (32 types) and grounding information for most of the proteins and families (links to uniprot, interpro and other databases) 3) Coreference between entities in the same sentence (e.g. abbreviations and synonyms) 4) Binding interactions between the annotated entities 5) Binding interaction types: positive, negative (A does not bind B) and neutral (A may bind to B)
Citation Information
@inproceedings{khachatrian2019biorelex,
title = "{B}io{R}el{E}x 1.0: Biological Relation Extraction Benchmark",
author = "Khachatrian, Hrant and
Nersisyan, Lilit and
Hambardzumyan, Karen and
Galstyan, Tigran and
Hakobyan, Anna and
Arakelyan, Arsen and
Rzhetsky, Andrey and
Galstyan, Aram",
booktitle = "Proceedings of the 18th BioNLP Workshop and Shared Task",
month = aug,
year = "2019",
address = "Florence, Italy",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/W19-5019",
doi = "10.18653/v1/W19-5019",
pages = "176--190"
}
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