Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization. Text corpus for this journal annotated with various levels of linguistic information would be a valuable resource as the process of information extraction requires syntactic, semantic, and higher levels of natural language processing. In this study, we publish our new corpus called GNI Corpus version 1.0, extracted and annotated from full texts of Genomics & Informatics, with NLTK (Natural Language ToolKit)-based text mining script. The preliminary version of the corpus could be used as a training and testing set of a system that serves a variety of functions for future biomedical text mining.
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http://dx.doi.org/10.5808/GI.2018.16.3.75 | DOI Listing |
Gigascience
January 2025
Department of Animal Science, Iowa State University, Ames, IA, 50011, US.
The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Here, we identify the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research.
View Article and Find Full Text PDFAnal Chem
January 2025
Department of Cancer Biology and Molecular Medicine, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California 91010, United States.
Extracellular vesicles (EVs), membrane-encapsulated nanoparticles shed from all cells, are tightly involved in critical cellular functions. Moreover, EVs have recently emerged as exciting therapeutic modalities, delivery vectors, and biomarker sources. However, EVs are difficult to characterize, because they are typically small and heterogeneous in size, origin, and molecular content.
View Article and Find Full Text PDFJ Pathol Inform
January 2025
Harvard Medical School, Boston, MA, United States of America.
Objective: Thrombocytopenia is a common complication of hematopoietic stem-cell transplantation (HSCT), though many patients will become immune refractory to platelet transfusions over time. We built and evaluated an electronic health record (EHR)-integrated, standards-based application that enables blood-bank clinicians to match platelet inventory with patients using data previously not available at the point-of-care, like human leukocyte antigen (HLA) data for donors and recipients.
Materials And Methods: The web-based application launches as an EHR-embedded application or as a standalone application.
3 Biotech
February 2025
Key Laboratory of Optical Technology and Instrument for Medicine, Ministry of Education, University of Shanghai for Science and Technology, Shanghai, 200093 China.
Unlabelled: The study aims to investigate the clinicopathological significance of MRPL24 in human cancers, with a particular focus on breast cancer (BC). Comprehensive bioinformatics analyses were conducted using data from The Cancer Genome Atlas (TCGA) and various advanced database, including cBioPortal, UALCAN, TIMER, Prognoscan, TISIDB, KM Plotter, and The Human Protein Atlas, to provide a detailed evaluation of MRPL55's role in cancer. The findings were further validated through experimental studies.
View Article and Find Full Text PDFGenes Brain Behav
February 2025
Laboratory of Addiction Genetics, Department of Pharmaceutical Sciences and Center for Drug Discovery, Northeastern University, Boston, Massachusetts, USA.
Opioid use disorder is heritable, yet its genetic etiology is largely unknown. C57BL/6J and C57BL/6NJ mouse substrains exhibit phenotypic diversity in the context of limited genetic diversity which together can facilitate genetic discovery. Here, we found C57BL/6NJ mice were less sensitive to oxycodone (OXY)-induced locomotor activation versus C57BL/6J mice in a conditioned place preference paradigm.
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