Calibrated Typed Decisions for Entity, Relation, and Event Extraction
Paper • 2610.17113 • Published • 9
input stringlengths 8 1.2k | output unknown | schema unknown |
|---|---|---|
Bradycardia-induced coronary angiogenesis is dependent on vascular endothelial growth factor.
A marked coronary angiogenesis is known to occur with chronic bradycardia. We tested the hypothesis that vascular endothelial growth factor (VEGF), an endothelial cell mitogen and a major regulator of angiogenesis, is upregul... | {
"events": {
"positive regulation": [
{
"trigger": {
"text": "upregulated",
"start": 313,
"end": 324
},
"arguments": [
{
"role": "theme",
"text": "vascular endothelial growth factor",
"start": 200,
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
after 3 weeks of treatment. VEGF protein was higher in alinidine-treated rats than in controls after 2 weeks and increased further after 3 weeks of treatment. Injection of VEGF-neutralizing antibodies over a 2-week period completely blocked alinidine-stimulated angiogenesis. In contrast, bFGF mRNA was not altered by al... | {
"events": {
"positive regulation": [
{
"trigger": {
"text": "increased",
"start": 113,
"end": 122
},
"arguments": [
{
"role": "theme",
"text": "VEGF",
"start": 28,
"end": 32
}
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
External beam radiotherapy for subretinal neovascularization in age-related macular degeneration: is this treatment efficient?
PURPOSE: Control of the natural course of subretinal neovascularization (SRNV) in age-related macular degeneration (AMD) is difficult. Only a subset of patients is suitable for laser coagulati... | {
"events": {
"breakdown": [
{
"trigger": {
"text": "degeneration",
"start": 84,
"end": 96
},
"arguments": [
{
"role": "theme",
"text": "macular",
"start": 76,
"end": 83
}
]
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
SRNV refusing radiotherapy served as a control group and were matched with 18 irradiated patients. After 7 months median visual acuity (VA) was 20/160 for the irradiated and 20/400 for the untreated patients. One year after radiotherapy final median VA was 20/400 in both groups. CONCLUSION: These results suggest that 1... | {
"events": {
"planned process": [
{
"trigger": {
"text": "irradiated",
"start": 159,
"end": 169
},
"arguments": [
{
"role": "theme",
"text": "patients",
"start": 199,
"end": 207
}
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
Increased serum levels of vascular endothelial growth factor in patients with renal cell carcinoma.
Neovascularization, an essential event for the growth of solid tumors, is regulated by a number of angiogenic factors. One such factor, vascular endothelial growth factor (VEGF), is considered to exert a potent angiogen... | {
"events": {
"growth": [
{
"trigger": {
"text": "growth",
"start": 148,
"end": 154
},
"arguments": [
{
"role": "theme",
"text": "solid tumors",
"start": 158,
"end": 170
}
]
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
(P less than 0.001) and existence of metastasis (P less than 0.001). s-VEGF significantly correlated with the tumor volume obtained by a three-dimensional measurement (r=0.802, P less than 0.0001). The sensitivity and specificity of s-VEGF at the cut-off level of 100 pg/ml, as determined by the receiver-operating-chara... | {
"events": {
"localization": [
{
"trigger": {
"text": "liberates",
"start": 420,
"end": 429
},
"arguments": [
{
"role": "theme",
"text": "VEGF",
"start": 430,
"end": 434
},
{
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
Insulin-induced vascular endothelial growth factor expression in retina.
PURPOSE: Clinical studies have demonstrated that intensive insulin therapy causes a transient worsening of retinopathy. The mechanisms underlying the initial insulin-induced deterioration of retinal status in patients with diabetes remain unknown... | {
"events": {
"gene expression": [
{
"trigger": {
"text": "expression",
"start": 51,
"end": 61
},
"arguments": [
{
"role": "theme",
"text": "vascular endothelial growth factor",
"start": 16,
"end"... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
increased VEGF mRNA levels in the ganglion, inner nuclear, and RPE cell layers. In vitro, insulin increased VEGF mRNA levels in human RPE cells and enhanced VEGF promoter activity without affecting transcript stability. Insulin treatment also increased VEGF protein levels in conditioned RPE cell media in a dose-depende... | {
"events": {
"gene expression": [
{
"trigger": {
"text": "expression",
"start": 809,
"end": 819
},
"arguments": [
{
"role": "theme",
"text": "VEGF",
"start": 799,
"end": 803
}
]... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
The antiangiogenic agent linomide inhibits the growth rate of von Hippel-Lindau paraganglioma xenografts to mice.
The aim of this study was to ascertain the potential usefulness of the antiangiogenic compound linomide for treatment of von Hippel-Lindau (VHL)-related tumors. Paraganglioma tissue fragments obtained at s... | {
"events": {
"negative regulation": [
{
"trigger": {
"text": "diminution",
"start": 758,
"end": 768
},
"arguments": [
{
"role": "theme",
"text": "tumor",
"start": 772,
"end": 777
}
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
avascularity. Treated animals also displayed a 2.4-fold reduction of tumor vascular endothelial growth factor mRNA levels. Taken together, our data indicate that in VHL disease, therapy directed at inhibition of constitutively expressed VEGF induction of angiogenesis by VHL tumors may constitute an effective medical tr... | {
"events": {
"negative regulation": [
{
"trigger": {
"text": "reduction",
"start": 56,
"end": 65
},
"arguments": [
{
"role": "theme",
"text": "vascular endothelial growth factor",
"start": 75,
"e... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
Vascular proliferation and enhanced expression of endothelial nitric oxide synthase in human peritoneum exposed to long-term peritoneal dialysis.
Long-term peritoneal dialysis (PD) is associated with alterations in peritoneal permeability and loss of ultrafiltration. These changes originate from increased peritoneal s... | {
"events": {
"development": [
{
"trigger": {
"text": "proliferation",
"start": 9,
"end": 22
},
"arguments": [
{
"role": "theme",
"text": "Vascular",
"start": 0,
"end": 8
}
]
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
endothelial NOS. The biologic relevance of increased NOS in long-term PD was demonstrated by enhanced nitrotyrosine immunoreactivity and a significant increase in vascular density and endothelial area in the peritoneum. Immunoblotting and immunostaining studies demonstrated an upregulation of vascular endothelial growt... | {
"events": {
"positive regulation": [
{
"trigger": {
"text": "increased",
"start": 43,
"end": 52
},
"arguments": [
{
"role": "theme",
"text": "NOS",
"start": 53,
"end": 56
}
]
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
Active hair growth (anagen) is associated with angiogenesis.
After the completion of skin development, angiogenesis, i.e., the growth of new capillaries from pre-existing blood vessels, is held to occur in the skin only under pathologic conditions. It has long been noted, however, that hair follicle cycling is associa... | {
"events": {
"growth": [
{
"trigger": {
"text": "growth",
"start": 12,
"end": 18
},
"arguments": [
{
"role": "theme",
"text": "hair",
"start": 7,
"end": 11
}
]
},
{
... | {
"events": [
{
"label": "cell proliferation",
"description": "Multiplication or accumulation of cells (GO cell proliferation), e.g. 'proliferating ECs', 'MCs accumulated'.",
"description_source": "mneb",
"roles": [
{
"label": "theme",
"description": "The entity... |
End of preview. Expand in Data Studio
MLEE
MLEE (event extraction), rebuilt for MNEB from the original release with character-level offsets.
Source: http://nactem.ac.uk/MLEE/MLEE-1.0.2-rev1.tar.gz
| config | split | records |
|---|---|---|
| default | train | 237 |
| default | validation | 80 |
| default | test | 161 |
Labels
events: cell proliferation, development, blood vessel development, growth, death, breakdown, remodeling, synthesis, gene expression, transcription, catabolism, phosphorylation, dephosphorylation, localization, binding, regulation, positive regulation, negative regulation, planned process, acetylation, cell division, dissociation, DNA methylation, metabolism, pathway, protein processing, reproduction, translation, ubiquitination
Format
Each record has input (the text), output (gold annotations grouped by label) and schema (the label set with descriptions). Offsets are character offsets into input, half-open [start, end).
"output": {
"entities": {"<label>": [{"text", "start", "end"}]},
"relations": {"<label>": [{"head": {"text", "start", "end"},
"tail": {"text", "start", "end"}}]},
"events": {"<label>": [{"trigger": {"text", "start", "end"},
"arguments": [{"role", "text", "start", "end"}]}]}
}
Each schema item has a description and a description_source: official when adapted from the dataset's paper or guideline, mneb when written for MNEB. Relation datasets also give setting (end_to_end or gold_entity) and negative_label; relation items give symmetric. Event items list the roles valid for that event type.
Within a record, identical annotations are kept once and outer whitespace is trimmed from spans; source annotations are otherwise kept as annotated.
Notes
- A nested-event argument is represented by the nested event's trigger span; numbered roles are merged into the base role.
- Documents longer than 1,200 characters are cut at whitespace outside every annotated span (CalOn, arXiv:2610.17113); annotations whose parts fall in different pieces are dropped and counted.
Build
Built by scripts/datasets/mlee.py in the MNEB repository.
Citation
Pyysalo et al. (2012), Event extraction across multiple levels of biological organization. Bioinformatics.
License: cc-by-nc-sa-3.0
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