Datasets:
pmid string | section string | text string | annotations sequence |
|---|---|---|---|
37299942 | intro | 1. Introduction Children who experience handwriting learning disabilities may face significant negative effects on their academic success and daily life. Cognitive, visual perceptual and fine motor skills are essential for learning to write. Dysgraphia refers to the motor performance difficulties of handwriting rather ... | [
[
1595,
1605
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[
2027,
2047
],
[
3054,
3064
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[
3800,
3810
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[
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[
4757,
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[
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[
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5539
],
[
6310,
6320
],
[
6887,
6897
],
[
6904,
6914
]
] |
38861157 | results | Results The anterodorsal thalamic nucleus shows early and consistent vulnerability to tau pathology We examined post-mortem brain samples from 26 cases, grouped by the Braak tau stages of disease progression (Table 1). We assessed early (Braak stages 0–II; n = 15), middle (Braak stages III–IV, n = 6), and late (Braak s... | [
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29457,
29460
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[
33306,
33309
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[
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[
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[
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[
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[
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34620
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[
34736,
34739
],
[
34959,
34962
],
[
34976,
34979
],
[
35037,
... |
38447542 | intro | Introduction The World Health Organization (WHO) defines active aging as “the process of optimizing opportunities for health, participation and security in order to enhance quality of life as people age, allowing people to ‘realize their potential for physical, social and mental well-being throughout the life course.’”... | [
[
4468,
4474
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[
4489,
4495
],
[
4709,
4711
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[
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4478
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[
5368,
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[
5063,
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[
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4918
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[
5601,
5607
],
[
5745,
5748
],
[
5760,
5765
],
[
5844,
5847
],
[
58... |
38259745 | results | Results Between October 1st, 2019, and May 30th, 2022, 225 patients benefited from neuropsychological evaluations or cognitive training and were included in the analyzes (103 Female, mean age 71.53 ± 15.36 years). The patient’s population consisted in post-traumatic disorders (8%), post-stroke patients (23%) and dement... | [
[
8563,
8571
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[
8729,
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[
8808,
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],
[
8836,
8844
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[
12213,
12221
],
[
12240,
12250
],
[
12398,
12408
],
[
12533,
12541
]
] |
33101276 | abstract | The R47H variant in the microglial triggering receptor expressed on myeloid cell 2 (TREM2) receptor is a strong risk factor for Alzheimer's disease (AD). To characterize processes affected by R47H, we performed an integrative network analysis of genes expressed in brains of AD patients with R47H, sporadic AD without th... | [
[
115,
119
],
[
195,
200
],
[
239,
258
],
[
260,
262
],
[
303,
307
],
[
386,
388
],
[
389,
397
],
[
403,
407
],
[
418,
420
],
[
446,
454
],
[
460,
536
],
[
538,
543
],
[
... |
38594369 | title | Design and methods of the mobile assessment of cognition, environment, and sleep (MACES) feasibility study in newly diagnosed breast cancer patients | [
[
82,
87
]
] |
39072940 | intro | INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disease affecting the brain with high incidence in the elderly. The typical clinical manifestations include progressive impairment or loss of cognitive function. Senile plaques formed by extracellular β‐amyloid (Aβ) deposition, and neurofibrillary tangles for... | [
[
2927,
2935
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[
3415,
3423
],
[
2835,
2838
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[
4214,
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[
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[
6094,
6102
],
[
7620,
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],
[
8096,
8101
],
[
8252,
8256
],
[
8260,
8264
],
[
6773,
6776
],
[
69... |
39131307 | abstract | Several age-related oral health problems have been associated with neurodegenerative diseases such as Alzheimer’s Disease (AD), yet how oromotor dysfunction in healthy aging differ from those found in pathological aging is still unknown. This is partly because changes in the cortical and biomechanical (“neuromechanical... | [
[
567,
582
],
[
584,
598
]
] |
38590779 | title | Role of autophagy in ischemic stroke: insights from animal models and preliminary evidence in the human disease | [
[
98,
103
]
] |
36348357 | title | ApoE in Alzheimer's disease: pathophysiology and therapeutic strategies. | [
[
0,
4
],
[
8,
27
]
] |
39290562 | methods | Methods The systematic review was undertaken in accordance with the PRISMA criteria to ensure the reliability and comprehensiveness of the data and findings. The English databases searched included PubMed, Embase, the Cochrane Library, and the Web of Science and Scopus. The language used was English, according to the a... | [
[
8639,
8646
],
[
11579,
11590
]
] |
38813371 | intro | Introduction Mild cognitive impairment is a prodromal state of dementia that manifests with subtle balance control and gait deficits which may affect activities of daily living and contribute to the two folded increased risk of falls in this population. Consequences of these falls lead to reduced physical functioning, ... | [
[
6331,
6337
],
[
8105,
8108
]
] |
38079409 | results | Findings The findings present a narrative and charting of the data from the 45 papers that met the review criteria and this data is mapped onto the five objectives outlined in step one of the framework Within this review, interventions were grouped into five broad types: nature (n = 6 papers), memory/cognitive (n = 11 ... | [
[
15490,
15495
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[
15581,
15587
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[
15604,
15610
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[
34944,
34956
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[
35380,
35383
],
[
35972,
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[
36159,
36162
],
[
36064,
36067
],
[
42946,
42954
],
[
44305,
44310
],
[
47253,
... |
38334239 | intro | INTRODUCTION Parkinson's disease (PD) is a multifaceted neurodegenerative condition impacting upon many aspects of an individual's physical and psychological well‐being. PD is the second most common neurodegenerative disease, and the most common neurodegenerative movement disorder worldwide, with prevalence tending to ... | [
[
2970,
2976
]
] |
38077459 | methods | 2 Materials and methods The trial was done in Osaka, Japan, and was based on approval from the Ethics Committee at the Graduate School of Engineering Science, Osaka University (approval code: 31-3-4). All participants agreed to place our robot at their homes, after a detailed description of the trial, and written conse... | [
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[
14384,
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[
14668,
14674
],
[
18695,
18707
],
[
18995,
... |
End of preview. Expand in Data Studio
Alzheimer's Disease Tagged Articles Dataset
This dataset contains a collection of scientific articles related to Alzheimer's disease, annotated with biomedical entities (such as diseases, genes, and species) using NCBI’s PubTator tools.
Data Sources and Annotation Tools
- Entity annotations were generated using NCBI's standard models and API calls to the PubTator3 API:
- TaggerOne and GNORM for
gene_species_tagged_articles.json - TaggerOne alone for
disease_tagged_articles.json - PubTator3 API for 'converted_from_bioc.json'
- TaggerOne and GNORM for
These tools are widely used in biomedical NLP for tagging mentions of diseases, genes, and species within PubMed articles.
Dataset Structure
The dataset is a flattened version of the original JSON files, where each record represents a tagged article section. The structure includes:
pmid: PubMed ID of the articlesection: Type of section (e.g.,title,abstract)text: Lowercased content of the sectionannotations: List of[start, end]character offsets identifying entity mentions
Example:
{
"pmid": "34379990",
"section": "abstract",
"text": "clinical progression of tauopathies may result...",
"annotations": [[0, 26], [45, 53], ...]
}
Preprocessing
The dataset has been simplified:
- Original nested structures were flattened
- Tuples were converted to JSON-compliant lists
- Only
titleandabstractsections are currently included
Future Work
- Extend tagging beyond titles and abstracts to include full-text sections (e.g., introduction, methods, results)
- Add entity labels (e.g.,
Disease,Gene,Species) in a future version
Usage
from datasets import load_dataset
dataset = load_dataset("AbrehamT/tagged_articles")
License
This dataset is released under the MIT License.
Acknowledgments
This dataset relies on NCBI’s PubTator, GNORM, and TaggerOne models. Credit goes to the developers of these tools and the researchers whose articles form the dataset foundation.
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