Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Summary: Relation extraction (RE) from large text collections is an important tool for database curation, pathway reconstruction, or functional omics data analysis. In practice, RE often is part of a complex data analysis pipeline requiring specific adaptations like restricting the types of relations or the set of proteins to be considered. However, current systems are either non-programmable web sites or research code with fixed functionality. We present PEDL+, a user-friendly tool for extracting protein-protein and protein-chemical associations from PubMed articles. PEDL+ combines state-of-the-art NLP technology with adaptable ranking and filtering options and can easily be integrated into analysis pipelines. We evaluated PEDL+ in two pathway curation projects and found that 59% to 80% of its extractions were helpful.
Availability And Implementation: PEDL+ is freely available at https://github.com/leonweber/pedl.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10660277 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btad603 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Design and Fabrication of Flexible Silk Fibroin/Lanthanide Ion Membranes with Multifunctional Properties of Fluorescence, Humidity Sensitivity, and Conductivity.
ACS Appl Mater Interfaces
September 2025
College of Chemistry and Chemical Engineering, Instrumental Analysis Center of Qingdao University, Qingdao Application Technology Innovation Center of Photoelectric Biosensing for Clinical Diagnosis and Treatment, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qing
Silk fibroin (SF)-based flexible electronic/photonic materials have gained great attention in wearable devices and soft sensors. However, it remains challenging to understand the molecular interaction mechanisms and subsequently fabricate SF-based flexible materials that exhibit fluorescence, humidity sensitivity, and conductivity properties. In this study, by incorporating lanthanide europium ion (Eu), the design and fabrication of a flexible, fluorescent, and conductive SF membrane was proposed.
View Article and Find Full Text PDFMinimally Invasive vs Open Surgery for Thoracolumbar Fractures in Patients With Ankylosing Spinal Diseases: A Meta-Analysis.
J Am Acad Orthop Surg
August 2025
From the Department of Orthopedic Surgery (Daher, Aoun, Sebaaly), Hotel Dieu de France Hospital, Beirut, LEBANON, the Department of Orthopedic Surgery (Daher, Diebo, Daniels), Brown University, Providence, RI, the Department of Orthopedic Surgery (Daher, Cottrill, Passias), Duke University, Durham,
Background: Surgical management of thoracolumbar fractures in patients with ankylosing spinal disorders such as ankylosing spondylitis (AS) and diffuse idiopathic skeletal hyperostosis remains debated. Although several studies have compared minimally invasive surgery to open fixation of thoracolumbar fractures in this patient population, a meta-analysis compiling the literature on this topic is lacking.
Methods: Following the PRISMA guidelines, PubMed, Cochrane, and Google Scholar (pages 1 to 20) were accessed and explored until October 2024.
serojump: A Bayesian tool for inferring infection timing and antibody kinetics from longitudinal serological data.
PLoS Comput Biol
September 2025
Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
Understanding acute infectious disease dynamics at individual and population levels is critical for informing public health preparedness and response. Serological assays, which measure a range of biomarkers relating to humoral immunity, can provide a valuable window into immune responses generated by past infections and vaccinations. However, traditional methods for interpreting serological data, such as binary seropositivity and seroconversion thresholds, often rely on heuristics that fail to account for individual variability in antibody kinetics and timing of infection, potentially leading to biased estimates of infection rates and post-exposure immune responses.
View Article and Find Full Text PDFAutomated segmentation of retinal vessel using HarDNet fully convolutional networks.
PLoS One
September 2025
School of Medical Engineering, Xinxiang Medical University, Xinxiang, China.
Computer-aided diagnostic (CAD) systems for color fundus images play a critical role in the early detection of fundus diseases, including diabetes, hypertension, and cerebrovascular disorders. Although deep learning has substantially advanced automatic segmentation techniques in this field, several challenges persist, such as limited labeled datasets, significant structural variations in blood vessels, and persistent dataset discrepancies, which continue to hinder progress. These challenges lead to inconsistent segmentation performance, particularly for small vessels and branch regions.
View Article and Find Full Text PDFWhat is known from the existing literature about adolescent knowledge and attitudes towards dementia and interventions to enhance this? A scoping review.
PLoS One
September 2025
School of Psychology, Queens University Belfast, Belfast, Northern Ireland, United Kingdom.
Objectives: Individuals with dementia often experience stigmatisation and social exclusion. To develop dementia-friendly communities, it is important to take a life-course approach to enhance the perception of dementia in the general population. Currently, we lack an overall understanding of adolescent perceptions of dementia.
View Article and Find Full Text PDF