Article
Computer Science, Software Engineering
T. Harbig, M. Witte Paz, K. Nieselt
Summary: Analysis pipelines in genomics, transcriptomics, and proteomics often produce lists of genes that overlap only partially or not at all and are too large for manual comparison. This paper presents GO-Compass, a visual analytics tool that reduces the redundancy and improves interpretability of gene lists by using semantic similarity. GO-Compass offers interactive visualizations, such as hierarchical clustering, treemaps, heatmaps, and bar charts, to facilitate the comparison of GO terms and gene information.
COMPUTER GRAPHICS FORUM
(2023)
Article
Biochemical Research Methods
Alejandro A. Edera, Diego H. Milone, Georgina Stegmayer
Summary: A novel protocol anc2vec based on neural networks is proposed for constructing vector representations of GO terms, preserving ontological features and showing better performance on diverse tasks.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg
Summary: With the rise in genomic data from sequencing technologies, the functions of many gene products remain unknown. High-throughput experiments are being conducted to address this gap, but the resulting annotations are biased towards less informative Gene Ontology terms. GOThresher, a Python tool, is introduced to identify and remove biases in protein function annotation databases, which is crucial for accurate understanding of protein function and training unbiased machine learning methods.
Article
Biochemical Research Methods
Yang Li, Wang Keqi, Guohua Wang
Summary: The article introduces a novel approach to compute disease similarity by integrating disease-related genes and gene ontology hierarchy to learn disease representation based on deep representation learning. In the experiments, the AUC value of this method is 0.8074, improving the most competitive baseline method by 10.1%.
Article
Biochemical Research Methods
Ioan Ieremie, Rob M. Ewing, Mahesan Niranjan
Summary: In this study, a model named TransformerGO is proposed, which captures the semantic similarity between GO sets dynamically using an attention mechanism. By learning dense graph embeddings for GO terms, TransformerGO can accurately distinguish negative and positive interactions, outperforming other methods in PPI prediction.
Article
Biochemical Research Methods
Lingling Zhao, Huiting Sun, Xinyi Cao, Naifeng Wen, Junjie Wang, Chunyu Wang
Summary: This paper proposes a novel representation model for GO terms, named GT2Vec, which considers both the GO graph structure obtained by graph contrastive learning and the semantic description of GO terms based on BERT encoders. Experimental results demonstrate the effectiveness of the model in learning vector representations for GO terms.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Engineering, Chemical
Yujie Bai, Dong Gao, Lanfei Peng
Summary: HAZOP is widely used in safety evaluation in the petrochemical industry. The combination of knowledge ontology and the ACO-GRNN model can improve the accuracy of semantic comparison and solve the problem of semantic matching.
Article
Computer Science, Information Systems
Samia Zouaoui, Khaled Rezeg
Summary: This paper proposes a novel approach called Multi-agents Indexing System to address plagiarism in Arabic documents. The system consists of three phases: natural language processing, indexing, and evaluation. The results show that the proposed system improves the performance of plagiarism detection in Arabic documents with semantic indexing and multi-agents system.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2022)
Article
Biology
Luke T. Slater, Andreas Karwath, John A. Williams, Sophie Russell, Silver Makepeace, Alexander Carberry, Robert Hoehndorf, Georgios Gkoutos
Summary: This study developed a method to extract patient phenotype profiles from clinical narrative text and used semantic similarity to classify primary patient diagnosis. The results showed that uncurated text phenotypes can be a powerful tool for the differential diagnosis of common diseases.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemical Research Methods
Zhen Tian, Haichuan Fang, Yangdong Ye, Zhenfeng Zhu
Summary: In this article, a novel gene functional similarity calculation method is proposed, which focuses on the specificity of terms and edges. Experimental results show that the proposed method outperforms several baseline methods.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Artificial Intelligence
Sengodan Mani, Samukutty Annadurai
Summary: A new modified model of similarity spreading for ontology mapping is proposed in this paper, which aims to address the heterogeneity issue between ontologies for interoperability. By utilizing node clustering based on edge affinity and coefficient similarity propagation, the model achieves graph matching. The evaluation shows that the proposed model outperforms similar systems.
INTERNATIONAL JOURNAL ON SEMANTIC WEB AND INFORMATION SYSTEMS
(2022)
Article
Chemistry, Multidisciplinary
Marcia Barros, Andre Moitinho, Francisco M. Couto
Summary: In this study, a hybrid recommender model is proposed for identifying compounds of interest to scientific researchers, integrating collaborative-filtering algorithms and a new content-based algorithm based on the semantic similarity between chemical compounds. The hybrid model significantly improved the results of collaborative-filtering algorithms by over ten percentage points in most evaluation metrics when evaluated on the implicit dataset CheRM-20 with over 16,000 chemical compounds.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Biochemical Research Methods
Ahmad Pesaranghader, Stan Matwin, Marina Sokolova, Jean-Christophe Grenier, Robert G. Beiko, Julie Hussin
Summary: This article introduces a deep learning method called deepSimDEF for automatically learning functional similarity estimation of gene pairs. This method calculates the functional similarity by learning the embedding vector representations of GO annotations and gene products. The results show that deepSimDEF outperforms other methods on tasks related to protein-protein interactions, gene co-expression, and sequence homology.
Article
Biochemistry & Molecular Biology
David Lagorce, Emeline Lebreton, Leslie Matalonga, Oscar Hongnat, Maroua Chahdil, Davide Piscia, Ida Paramonov, Kornelia Ellwanger, Sebastian Koehler, Peter Robinson, Holm Graessner, Sergi Beltran, Caterina Lucano, Marc Hanauer, Ana Rath
Summary: Rare diseases are difficult to diagnose, especially when the causative gene is unidentified. The Solve-RD project aims to identify the molecular causes of undiagnosed rare diseases through phenotypic similarity analysis and genomic data reanalysis. Promising results were obtained in the tested cases.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Multidisciplinary Sciences
Amna Binte Kamran, Hammad Naveed
Summary: This study introduces a new method called GOntoSim for determining the functional similarity between genes. GOntoSim quantifies the similarity between pairs of GO terms by considering the graph structure and information content of nodes, and it effectively handles noisy annotations.
SCIENTIFIC REPORTS
(2022)
