id stringlengths 1 3 | document_id stringlengths 11 13 | passages list | entities list | events list | coreferences list | relations list |
|---|---|---|---|---|---|---|
0 | PMID-15193260 | [
{
"id": "PMID-15193260__text",
"type": "abstract",
"text": [
"Dynein light chain 1, a p21-activated kinase 1-interacting substrate, promotes cancerous phenotypes. \nWe identified dynein light chain 1 (DLC1) as a physiologic substrate of p21-activated kinase 1 (Pak1). Pak1-DLC1 interaction plays an... | [
{
"id": "PMID-15193260_T1",
"type": "Gene_or_gene_product",
"text": [
"Dynein light chain 1"
],
"offsets": [
[
0,
20
]
],
"normalized": []
},
{
"id": "PMID-15193260_T2",
"type": "Gene_or_gene_product",
"text": [
"p21-activated kinas... | [
{
"id": "PMID-15193260_E1",
"type": "Binding",
"trigger": {
"text": [
"interacting"
],
"offsets": [
[
47,
58
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-15193260_T2"
},
{
"r... | [
{
"id": "PMID-15193260_1",
"entity_ids": [
"PMID-15193260_T4",
"PMID-15193260_T5"
]
},
{
"id": "PMID-15193260_2",
"entity_ids": [
"PMID-15193260_T6",
"PMID-15193260_T7"
]
}
] | [] |
1 | PMID-10913166 | [
{
"id": "PMID-10913166__text",
"type": "abstract",
"text": [
"TEL, a putative tumor suppressor, modulates cell growth and cell morphology of ras-transformed cells while repressing the transcription of stromelysin-1. \nTEL is a member of the ETS family of transcription factors that interacts with t... | [
{
"id": "PMID-10913166_T1",
"type": "Gene_or_gene_product",
"text": [
"TEL"
],
"offsets": [
[
0,
3
]
],
"normalized": []
},
{
"id": "PMID-10913166_T2",
"type": "Cancer",
"text": [
"tumor"
],
"offsets": [
[
16,
... | [
{
"id": "PMID-10913166_E1",
"type": "Regulation",
"trigger": {
"text": [
"modulates"
],
"offsets": [
[
34,
43
]
]
},
"arguments": [
{
"role": "Cause",
"ref_id": "PMID-10913166_T1"
},
{
"... | [] | [] |
2 | PMID-12484699 | [
{
"id": "PMID-12484699__text",
"type": "abstract",
"text": [
"Regulation of transforming growth factor-beta signaling and vascular diseases.\nPURPOSE: Members of the transforming growth factor (TGF)-beta superfamily play critical roles in regulation of various cellular functions. Dysregulation of ... | [
{
"id": "PMID-12484699_T1",
"type": "Gene_or_gene_product",
"text": [
"transforming growth factor-beta"
],
"offsets": [
[
14,
45
]
],
"normalized": []
},
{
"id": "PMID-12484699_T2",
"type": "Multi-tissue_structure",
"text": [
"vascu... | [
{
"id": "PMID-12484699_E1",
"type": "Regulation",
"trigger": {
"text": [
"Regulation"
],
"offsets": [
[
0,
10
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-12484699_E2"
}
]
},
{
... | [] | [] |
3 | PMID-16268479 | [
{
"id": "PMID-16268479__text",
"type": "abstract",
"text": [
"Domain 5 of cleaved high molecular weight kininogen inhibits endothelial cell migration through Akt.\nDomain 5 (D5) of cleaved high molecular weight kininogen (HKa) inhibits angiogenesis in vivo and endothelial cell migration in vitro, ... | [
{
"id": "PMID-16268479_T1",
"type": "Gene_or_gene_product",
"text": [
"high molecular weight kininogen"
],
"offsets": [
[
20,
51
]
],
"normalized": []
},
{
"id": "PMID-16268479_T2",
"type": "Cell",
"text": [
"endothelial cell"
]... | [
{
"id": "PMID-16268479_E1",
"type": "Protein_processing",
"trigger": {
"text": [
"cleaved"
],
"offsets": [
[
12,
19
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-16268479_T1"
}
]
},
... | [
{
"id": "PMID-16268479_1",
"entity_ids": [
"PMID-16268479_T4",
"PMID-16268479_T5"
]
},
{
"id": "PMID-16268479_2",
"entity_ids": [
"PMID-16268479_T12",
"PMID-16268479_T13"
]
},
{
"id": "PMID-16268479_3",
"entity_ids": [
"PMID-16268479_T14",
... | [] |
4 | PMID-11121230 | [
{
"id": "PMID-11121230__text",
"type": "abstract",
"text": [
"RNA damage and inhibition of neoplastic endothelial cell growth: effects of human and amphibian ribonucleases.\nAngiogenesis defines the many steps involved in the growth and migration of endothelial cell-derived blood vessels. This pro... | [
{
"id": "PMID-11121230_T1",
"type": "Cell",
"text": [
"neoplastic endothelial cell"
],
"offsets": [
[
29,
56
]
],
"normalized": []
},
{
"id": "PMID-11121230_T2",
"type": "Organism",
"text": [
"human"
],
"offsets": [
[
... | [
{
"id": "PMID-11121230_E1",
"type": "Negative_regulation",
"trigger": {
"text": [
"inhibition"
],
"offsets": [
[
15,
25
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11121230_E2"
}
]
... | [
{
"id": "PMID-11121230_1",
"entity_ids": [
"PMID-11121230_T15",
"PMID-11121230_T16"
]
}
] | [] |
5 | PMID-12610665 | [
{
"id": "PMID-12610665__text",
"type": "abstract",
"text": [
"Arteriogenesis: the development and growth of collateral arteries.\nIn patients with atherosclerotic vascular diseases, collateral vessels bypassing major arterial obstructions have frequently been observed. This may explain why some pa... | [
{
"id": "PMID-12610665_T1",
"type": "Multi-tissue_structure",
"text": [
"collateral arteries"
],
"offsets": [
[
46,
65
]
],
"normalized": []
},
{
"id": "PMID-12610665_T2",
"type": "Organism",
"text": [
"patients"
],
"offsets... | [
{
"id": "PMID-12610665_E1",
"type": "Blood_vessel_development",
"trigger": {
"text": [
"Arteriogenesis"
],
"offsets": [
[
0,
14
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-12610665_T1"
}
... | [] | [] |
6 | PMID-20978953 | [
{
"id": "PMID-20978953__text",
"type": "abstract",
"text": [
"Role of stromal myofibroblasts in invasive breast cancer: stromal expression of alpha-smooth muscle actin correlates with worse clinical outcome. \nBACKGROUND: Recently, the desmoplastic reaction has been implicated as having an importa... | [
{
"id": "PMID-20978953_T1",
"type": "Cell",
"text": [
"stromal myofibroblasts"
],
"offsets": [
[
8,
30
]
],
"normalized": []
},
{
"id": "PMID-20978953_T2",
"type": "Cancer",
"text": [
"breast cancer"
],
"offsets": [
[
... | [
{
"id": "PMID-20978953_E1",
"type": "Regulation",
"trigger": {
"text": [
"Role"
],
"offsets": [
[
0,
4
]
]
},
"arguments": [
{
"role": "Cause",
"ref_id": "PMID-20978953_T1"
},
{
"role": ... | [] | [] |
7 | PMID-7474113 | [
{
"id": "PMID-7474113__text",
"type": "abstract",
"text": [
"The inhibition of cultured myoblast differentiation by the simian virus 40 large T antigen occurs after myogenin expression and Rb up-regulation and is not exerted by transformation-competent cytoplasmic mutants. \nWe have investigated t... | [
{
"id": "PMID-7474113_T1",
"type": "Cell",
"text": [
"myoblast"
],
"offsets": [
[
27,
35
]
],
"normalized": []
},
{
"id": "PMID-7474113_T2",
"type": "Organism",
"text": [
"simian virus 40"
],
"offsets": [
[
59,... | [
{
"id": "PMID-7474113_E1",
"type": "Negative_regulation",
"trigger": {
"text": [
"inhibition"
],
"offsets": [
[
4,
14
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-7474113_E2"
},
{
... | [
{
"id": "PMID-7474113_1",
"entity_ids": [
"PMID-7474113_T8",
"PMID-7474113_T9"
]
}
] | [] |
8 | PMID-17462601 | [
{
"id": "PMID-17462601__text",
"type": "abstract",
"text": [
"An antibody directed against PDGF receptor beta enhances the antitumor and the anti-angiogenic activities of an anti-VEGF receptor 2 antibody.\nPlatelet-derived growth factor (PDGF) and its receptors (PDGFR) play important roles in tumo... | [
{
"id": "PMID-17462601_T1",
"type": "Gene_or_gene_product",
"text": [
"antibody directed against PDGF receptor beta"
],
"offsets": [
[
3,
47
]
],
"normalized": []
},
{
"id": "PMID-17462601_T2",
"type": "Cancer",
"text": [
"tumor"
... | [
{
"id": "PMID-17462601_E1",
"type": "Positive_regulation",
"trigger": {
"text": [
"enhances"
],
"offsets": [
[
48,
56
]
]
},
"arguments": [
{
"role": "Cause",
"ref_id": "PMID-17462601_T1"
},
{
... | [
{
"id": "PMID-17462601_1",
"entity_ids": [
"PMID-17462601_T4",
"PMID-17462601_T5"
]
}
] | [] |
9 | PMID-19369582 | [
{
"id": "PMID-19369582__text",
"type": "abstract",
"text": [
"Characterization of the metabolic changes underlying growth factor angiogenic activation: identification of new potential therapeutic targets.\nAngiogenesis is a fundamental process to normal and abnormal tissue growth and repair, which... | [
{
"id": "PMID-19369582_T1",
"type": "Tissue",
"text": [
"tissue"
],
"offsets": [
[
204,
210
]
],
"normalized": []
},
{
"id": "PMID-19369582_T2",
"type": "Cell",
"text": [
"endothelial cells"
],
"offsets": [
[
2... | [
{
"id": "PMID-19369582_E1",
"type": "Blood_vessel_development",
"trigger": {
"text": [
"angiogenic"
],
"offsets": [
[
67,
77
]
]
},
"arguments": []
},
{
"id": "PMID-19369582_E2",
"type": "Positive_regulation",
"t... | [
{
"id": "PMID-19369582_1",
"entity_ids": [
"PMID-19369582_T8",
"PMID-19369582_T9"
]
},
{
"id": "PMID-19369582_2",
"entity_ids": [
"PMID-19369582_T17",
"PMID-19369582_T18"
]
},
{
"id": "PMID-19369582_3",
"entity_ids": [
"PMID-19369582_T19",
... | [] |
10 | PMID-10589785 | [
{
"id": "PMID-10589785__text",
"type": "abstract",
"text": [
"The antiangiogenic agent linomide inhibits the growth rate of von Hippel-Lindau paraganglioma xenografts to mice.\nThe aim of this study was to ascertain the potential usefulness of the antiangiogenic compound linomide for treatment of ... | [
{
"id": "PMID-10589785_T1",
"type": "Simple_chemical",
"text": [
"linomide"
],
"offsets": [
[
25,
33
]
],
"normalized": []
},
{
"id": "PMID-10589785_T2",
"type": "Cancer",
"text": [
"von Hippel-Lindau paraganglioma xenografts"
]... | [
{
"id": "PMID-10589785_E1",
"type": "Blood_vessel_development",
"trigger": {
"text": [
"angiogenic"
],
"offsets": [
[
8,
18
]
]
},
"arguments": []
},
{
"id": "PMID-10589785_E2",
"type": "Negative_regulation",
"tr... | [] | [] |
11 | PMID-12140030 | [
{
"id": "PMID-12140030__text",
"type": "abstract",
"text": [
"Optimizing treatment of choroidal neovascularization feeder vessels associated with age-related macular degeneration.\nPURPOSE: To optimize the method of treating choroidal neovascularization (CNV) associated with age-related macular de... | [
{
"id": "PMID-12140030_T1",
"type": "Multi-tissue_structure",
"text": [
"choroidal"
],
"offsets": [
[
24,
33
]
],
"normalized": []
},
{
"id": "PMID-12140030_T2",
"type": "Multi-tissue_structure",
"text": [
"feeder vessels"
],
... | [
{
"id": "PMID-12140030_E1",
"type": "Planned_process",
"trigger": {
"text": [
"treatment"
],
"offsets": [
[
11,
20
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-12140030_E2"
}
]
},
... | [
{
"id": "PMID-12140030_1",
"entity_ids": [
"PMID-12140030_T8",
"PMID-12140030_T9"
]
},
{
"id": "PMID-12140030_2",
"entity_ids": [
"PMID-12140030_T10",
"PMID-12140030_T11"
]
}
] | [] |
12 | PMID-11238633 | [
{
"id": "PMID-11238633__text",
"type": "abstract",
"text": [
"IL-12 inhibition of endothelial cell functions and angiogenesis depends on lymphocyte-endothelial cell cross-talk.\nIn vivo IL-12-dependent tumor inhibition rests on the ability of IL-12 to activate a CD8-mediated cytotoxicity, inhibit ... | [
{
"id": "PMID-11238633_T1",
"type": "Gene_or_gene_product",
"text": [
"IL-12"
],
"offsets": [
[
0,
5
]
],
"normalized": []
},
{
"id": "PMID-11238633_T2",
"type": "Cell",
"text": [
"endothelial cell"
],
"offsets": [
[
... | [
{
"id": "PMID-11238633_E1",
"type": "Negative_regulation",
"trigger": {
"text": [
"inhibition"
],
"offsets": [
[
6,
16
]
]
},
"arguments": [
{
"role": "Cause",
"ref_id": "PMID-11238633_T1"
},
{
... | [
{
"id": "PMID-11238633_1",
"entity_ids": [
"PMID-11238633_T16",
"PMID-11238633_T15"
]
},
{
"id": "PMID-11238633_2",
"entity_ids": [
"PMID-11238633_T19",
"PMID-11238633_T18"
]
},
{
"id": "PMID-11238633_3",
"entity_ids": [
"PMID-11238633_T20",
... | [] |
13 | PMID-16310808 | [
{
"id": "PMID-16310808__text",
"type": "abstract",
"text": [
"Effect of thalidomide affecting VEGF secretion, cell migration, adhesion and capillary tube formation of human endothelial EA.hy 926 cells.\nAngiogenesis, new blood vessel formation, is a multistep process, precisely regulated by pro-an... | [
{
"id": "PMID-16310808_T1",
"type": "Simple_chemical",
"text": [
"thalidomide"
],
"offsets": [
[
10,
21
]
],
"normalized": []
},
{
"id": "PMID-16310808_T2",
"type": "Gene_or_gene_product",
"text": [
"VEGF"
],
"offsets": [
... | [
{
"id": "PMID-16310808_E1",
"type": "Regulation",
"trigger": {
"text": [
"affecting"
],
"offsets": [
[
22,
31
]
]
},
"arguments": [
{
"role": "Cause",
"ref_id": "PMID-16310808_T1"
},
{
"... | [
{
"id": "PMID-16310808_1",
"entity_ids": [
"PMID-16310808_T13",
"PMID-16310808_T14"
]
}
] | [] |
14 | PMID-16855378 | [
{
"id": "PMID-16855378__text",
"type": "abstract",
"text": [
"Differential mechanisms of radiosensitization by 2-deoxy-D-glucose in the monolayers and multicellular spheroids of a human glioma cell line.\nIn vitro studies using monolayer cultures of human tumor cell lines have shown that 2-DG sele... | [
{
"id": "PMID-16855378_T1",
"type": "Simple_chemical",
"text": [
"2-deoxy-D-glucose"
],
"offsets": [
[
49,
66
]
],
"normalized": []
},
{
"id": "PMID-16855378_T2",
"type": "Cell",
"text": [
"monolayers"
],
"offsets": [
... | [
{
"id": "PMID-16855378_E1",
"type": "Development",
"trigger": {
"text": [
"develop"
],
"offsets": [
[
445,
452
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-16855378_T15"
}
]
},
{
... | [
{
"id": "PMID-16855378_1",
"entity_ids": [
"PMID-16855378_T25",
"PMID-16855378_T26"
]
}
] | [] |
15 | PMID-15725689 | [
{
"id": "PMID-15725689__text",
"type": "abstract",
"text": [
"Role of thrombogenic factors in the development of atherosclerosis.\nHemostatic factors play a crucial role in generating thrombotic plugs at sites of vascular damage (atherothrombosis). However, whether hemostatic factors contribute di... | [
{
"id": "PMID-15725689_T1",
"type": "Gene_or_gene_product",
"text": [
"thrombogenic factors"
],
"offsets": [
[
8,
28
]
],
"normalized": []
},
{
"id": "PMID-15725689_T2",
"type": "Gene_or_gene_product",
"text": [
"Hemostatic factors"... | [
{
"id": "PMID-15725689_E1",
"type": "Positive_regulation",
"trigger": {
"text": [
"play a crucial role"
],
"offsets": [
[
87,
106
]
]
},
"arguments": [
{
"role": "Cause",
"ref_id": "PMID-15725689_T2"
... | [
{
"id": "PMID-15725689_1",
"entity_ids": [
"PMID-15725689_T15",
"PMID-15725689_T16"
]
}
] | [] |
16 | PMID-9206208 | [
{
"id": "PMID-9206208__text",
"type": "abstract",
"text": [
"[Expression of metastasis suppressor gene nm23 in human hepatocellular carcinoma]. \nFor the purpose of investigating the relationship between the metastatic potential of the tumor as well as the expression of nm23-H1 mRNA, and for deter... | [
{
"id": "PMID-9206208_T1",
"type": "Gene_or_gene_product",
"text": [
"nm23"
],
"offsets": [
[
42,
46
]
],
"normalized": []
},
{
"id": "PMID-9206208_T2",
"type": "Organism",
"text": [
"human"
],
"offsets": [
[
5... | [
{
"id": "PMID-9206208_E1",
"type": "Gene_expression",
"trigger": {
"text": [
"Expression"
],
"offsets": [
[
1,
11
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-9206208_T1"
}
]
},
{
... | [] | [] |
End of preview. Expand in Data Studio
Dataset Card for BioNLP 2013 CG
the Cancer Genetics (CG) is a event extraction task and a main task of the BioNLP Shared Task (ST) 2013. The CG task is an information extraction task targeting the recognition of events in text, represented as structured n-ary associations of given physical entities. In addition to addressing the cancer domain, the CG task is differentiated from previous event extraction tasks in the BioNLP ST series in addressing a wide range of pathological processes and multiple levels of biological organization, ranging from the molecular through the cellular and organ levels up to whole organisms. Final test set submissions were accepted from six teams
Citation Information
@inproceedings{pyysalo-etal-2013-overview,
title = "Overview of the Cancer Genetics ({CG}) task of {B}io{NLP} Shared Task 2013",
author = "Pyysalo, Sampo and
Ohta, Tomoko and
Ananiadou, Sophia",
booktitle = "Proceedings of the {B}io{NLP} Shared Task 2013 Workshop",
month = aug,
year = "2013",
address = "Sofia, Bulgaria",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/W13-2008",
pages = "58--66",
}
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