scholarly journals A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Carlota Cardoso ◽  
Rita T Sousa ◽  
Sebastian Köhler ◽  
Catia Pesquita
Keyword(s):  
Semantic Similarity ◽  
Protein Interactions ◽  
Knowledge Graph ◽  
Data Sets ◽  
Biomedical Domain ◽  
Protein Protein Interactions ◽  
Data Set ◽  
Human Phenotype ◽  
Benchmark Data ◽  
Gene Similarity

Abstract The ability to compare entities within a knowledge graph is a cornerstone technique for several applications, ranging from the integration of heterogeneous data to machine learning. It is of particular importance in the biomedical domain, where semantic similarity can be applied to the prediction of protein–protein interactions, associations between diseases and genes, cellular localization of proteins, among others. In recent years, several knowledge graph-based semantic similarity measures have been developed, but building a gold standard data set to support their evaluation is non-trivial. We present a collection of 21 benchmark data sets that aim at circumventing the difficulties in building benchmarks for large biomedical knowledge graphs by exploiting proxies for biomedical entity similarity. These data sets include data from two successful biomedical ontologies, Gene Ontology and Human Phenotype Ontology, and explore proxy similarities calculated based on protein sequence similarity, protein family similarity, protein–protein interactions and phenotype-based gene similarity. Data sets have varying sizes and cover four different species at different levels of annotation completion. For each data set, we also provide semantic similarity computations with state-of-the-art representative measures. Database URL: https://github.com/liseda-lab/kgsim-benchmark.

scholarly journals Exploring the Human-Nipah Virus Protein-Protein Interactome

2017 ◽  
Vol 91 (23) ◽  
Author(s):  
Luis Martinez-Gil ◽  
Natalia M. Vera-Velasco ◽  
Ismael Mingarro
Keyword(s):  
Protein Interactions ◽  
Affinity Purification ◽  
Nipah Virus ◽  
Productive Infection ◽  
Virus Protein ◽  
Protein Protein Interactions ◽  
Data Set ◽  
Wide Range ◽  
Host Virus Interactions ◽  
Virus Interactions

ABSTRACT Nipah virus is an emerging, highly pathogenic, zoonotic virus of the Paramyxoviridae family. Human transmission occurs by close contact with infected animals, the consumption of contaminated food, or, occasionally, via other infected individuals. Currently, we lack therapeutic or prophylactic treatments for Nipah virus. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. This aim led us to perform the present work, in which we identified 101 human-Nipah virus protein-protein interactions (PPIs), most of which (88) are novel. This data set provides a comprehensive view of the host complexes that are manipulated by viral proteins. Host targets include the PRP19 complex and the microRNA (miRNA) processing machinery. Furthermore, we explored the biologic consequences of the interaction with the PRP19 complex and found that the Nipah virus W protein is capable of altering p53 control and gene expression. We anticipate that these data will help in guiding the development of novel interventional strategies to counter this emerging viral threat. IMPORTANCE Nipah virus is a recently discovered virus that infects a wide range of mammals, including humans. Since its discovery there have been yearly outbreaks, and in some of them the mortality rate has reached 100% of the confirmed cases. However, the study of Nipah virus has been largely neglected, and currently we lack treatments for this infection. To develop these agents we must now improve our understanding of the host-virus interactions that underpin a productive infection. In the present work, we identified 101 human-Nipah virus protein-protein interactions using an affinity purification approach coupled with mass spectrometry. Additionally, we explored the cellular consequences of some of these interactions. Globally, this data set offers a comprehensive and detailed view of the host machinery's contribution to the Nipah virus's life cycle. Furthermore, our data present a large number of putative drug targets that could be exploited for the treatment of this infection.

Deep learning based prediction of reversible HAT/HDAC-specific lysine acetylation

2019 ◽  
Vol 21 (5) ◽  
pp. 1798-1805 ◽  
Author(s):  
Kai Yu ◽  
Qingfeng Zhang ◽  
Zekun Liu ◽  
Yimeng Du ◽  
Xinjiao Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Web Server ◽  
Data Sets ◽  
Lysine Acetylation ◽  
Protein Acetylation ◽  
Protein Protein Interactions ◽  
Cellular Processes ◽  
Protein Lysine Acetylation ◽  
Specific Regulation

Abstract Protein lysine acetylation regulation is an important molecular mechanism for regulating cellular processes and plays critical physiological and pathological roles in cancers and diseases. Although massive acetylation sites have been identified through experimental identification and high-throughput proteomics techniques, their enzyme-specific regulation remains largely unknown. Here, we developed the deep learning-based protein lysine acetylation modification prediction (Deep-PLA) software for histone acetyltransferase (HAT)/histone deacetylase (HDAC)-specific acetylation prediction based on deep learning. Experimentally identified substrates and sites of several HATs and HDACs were curated from the literature to generate enzyme-specific data sets. We integrated various protein sequence features with deep neural network and optimized the hyperparameters with particle swarm optimization, which achieved satisfactory performance. Through comparisons based on cross-validations and testing data sets, the model outperformed previous studies. Meanwhile, we found that protein–protein interactions could enrich enzyme-specific acetylation regulatory relations and visualized this information in the Deep-PLA web server. Furthermore, a cross-cancer analysis of acetylation-associated mutations revealed that acetylation regulation was intensively disrupted by mutations in cancers and heavily implicated in the regulation of cancer signaling. These prediction and analysis results might provide helpful information to reveal the regulatory mechanism of protein acetylation in various biological processes to promote the research on prognosis and treatment of cancers. Therefore, the Deep-PLA predictor and protein acetylation interaction networks could provide helpful information for studying the regulation of protein acetylation. The web server of Deep-PLA could be accessed at http://deeppla.cancerbio.info.

scholarly journals An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 460
Author(s):  
Valentina Cipriani ◽  
Nikolas Pontikos ◽  
Gavin Arno ◽  
Panagiotis I. Sergouniotis ◽  
Eva Lenassi ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Protein Interactions ◽  
Model Organisms ◽  
Protein Protein Interactions ◽  
Sequencing Data ◽  
Variant Prioritization ◽  
Real Patient ◽  
Human Phenotype ◽  
Support Tool ◽  
Variant Frequency

Next-generation sequencing has revolutionized rare disease diagnostics, but many patients remain without a molecular diagnosis, particularly because many candidate variants usually survive despite strict filtering. Exomiser was launched in 2014 as a Java tool that performs an integrative analysis of patients’ sequencing data and their phenotypes encoded with Human Phenotype Ontology (HPO) terms. It prioritizes variants by leveraging information on variant frequency, predicted pathogenicity, and gene-phenotype associations derived from human diseases, model organisms, and protein–protein interactions. Early published releases of Exomiser were able to prioritize disease-causative variants as top candidates in up to 97% of simulated whole-exomes. The size of the tested real patient datasets published so far are very limited. Here, we present the latest Exomiser version 12.0.1 with many new features. We assessed the performance using a set of 134 whole-exomes from patients with a range of rare retinal diseases and known molecular diagnosis. Using default settings, Exomiser ranked the correct diagnosed variants as the top candidate in 74% of the dataset and top 5 in 94%; not using the patients’ HPO profiles (i.e., variant-only analysis) decreased the performance to 3% and 27%, respectively. In conclusion, Exomiser is an effective support tool for rare Mendelian phenotype-driven variant prioritization.

A New Approach for Supervised Dimensionality Reduction

2018 ◽  
Vol 14 (4) ◽  
pp. 20-37 ◽  
Author(s):  
Yinglei Song ◽  
Yongzhong Li ◽  
Junfeng Qu
Keyword(s):  
Eigenvalue Problem ◽  
Dimensionality Reduction ◽  
Image Databases ◽  
Data Sets ◽  
Data Set ◽  
New Approach ◽  
Local Structures ◽  
Benchmark Data ◽  
Global And Local

This article develops a new approach for supervised dimensionality reduction. This approach considers both global and local structures of a labelled data set and maximizes a new objective that includes the effects from both of them. The objective can be approximately optimized by solving an eigenvalue problem. The approach is evaluated based on a few benchmark data sets and image databases. Its performance is also compared with a few other existing approaches for dimensionality reduction. Testing results show that, on average, this new approach can achieve more accurate results for dimensionality reduction than existing approaches.

scholarly journals GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Xiaoshi Zhong ◽  
Rama Kaalia ◽  
Jagath C. Rajapakse
Keyword(s):  
Information Content ◽  
Semantic Similarity ◽  
Protein Interactions ◽  
Large Scale ◽  
Functional Similarity ◽  
Experimental Results ◽  
Graph Embeddings ◽  
Protein Protein Interactions ◽  
Vector Representations ◽  
Go Terms

Abstract Background Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research exploited information content to estimate the semantic similarity between GO terms; recently some research exploited word embeddings to learn vector representations for GO terms from a large-scale corpus. In this paper, we proposed a novel method, named GO2Vec, that exploits graph embeddings to learn vector representations for GO terms from GO graph. GO2Vec combines the information from both GO graph and GO annotations, and its learned vectors can be applied to a variety of bioinformatics applications, such as calculating functional similarity between proteins and predicting protein-protein interactions. Results We conducted two kinds of experiments to evaluate the quality of GO2Vec: (1) functional similarity between proteins on the Collaborative Evaluation of GO-based Semantic Similarity Measures (CESSM) dataset and (2) prediction of protein-protein interactions on the Yeast and Human datasets from the STRING database. Experimental results demonstrate the effectiveness of GO2Vec over the information content-based measures and the word embedding-based measures. Conclusion Our experimental results demonstrate the effectiveness of using graph embeddings to learn vector representations from undirected GO and GOA graphs. Our results also demonstrate that GO annotations provide useful information for computing the similarity between GO terms and between proteins.

Artificial bee colony algorithm for feature selection and improved support vector machine for text classification

2019 ◽  
Vol 47 (3) ◽  
pp. 154-170
Author(s):  
Janani Balakumar ◽  
S. Vijayarani Mohan
Keyword(s):  
Support Vector Machine ◽  
Feature Selection ◽  
Text Classification ◽  
Support Vector ◽  
Data Sets ◽  
Selection Algorithm ◽  
Data Set ◽  
Content Type ◽  
Benchmark Data ◽  
Bee Colony

Purpose Owing to the huge volume of documents available on the internet, text classification becomes a necessary task to handle these documents. To achieve optimal text classification results, feature selection, an important stage, is used to curtail the dimensionality of text documents by choosing suitable features. The main purpose of this research work is to classify the personal computer documents based on their content. Design/methodology/approach This paper proposes a new algorithm for feature selection based on artificial bee colony (ABCFS) to enhance the text classification accuracy. The proposed algorithm (ABCFS) is scrutinized with the real and benchmark data sets, which is contrary to the other existing feature selection approaches such as information gain and χ2 statistic. To justify the efficiency of the proposed algorithm, the support vector machine (SVM) and improved SVM classifier are used in this paper. Findings The experiment was conducted on real and benchmark data sets. The real data set was collected in the form of documents that were stored in the personal computer, and the benchmark data set was collected from Reuters and 20 Newsgroups corpus. The results prove the performance of the proposed feature selection algorithm by enhancing the text document classification accuracy. Originality/value This paper proposes a new ABCFS algorithm for feature selection, evaluates the efficiency of the ABCFS algorithm and improves the support vector machine. In this paper, the ABCFS algorithm is used to select the features from text (unstructured) documents. Although, there is no text feature selection algorithm in the existing work, the ABCFS algorithm is used to select the data (structured) features. The proposed algorithm will classify the documents automatically based on their content.

scholarly journals Multi-SimLex: A Large-Scale Evaluation of Multilingual and Cross-Lingual Lexical Semantic Similarity

2020 ◽  
pp. 1-51
Author(s):  
Ivan Vulić ◽  
Simon Baker ◽  
Edoardo Maria Ponti ◽  
Ulla Petti ◽  
Ira Leviant ◽  
...  
Keyword(s):  
Semantic Similarity ◽  
Large Scale ◽  
Representation Learning ◽  
Data Sets ◽  
Word Embeddings ◽  
Data Set ◽  
Lexical Representations ◽  
Language Data ◽  
Weakly Supervised ◽  
Cross Lingual

We introduce Multi-SimLex, a large-scale lexical resource and evaluation benchmark covering data sets for 12 typologically diverse languages, including major languages (e.g., Mandarin Chinese, Spanish, Russian) as well as less-resourced ones (e.g., Welsh, Kiswahili). Each language data set is annotated for the lexical relation of semantic similarity and contains 1,888 semantically aligned concept pairs, providing a representative coverage of word classes (nouns, verbs, adjectives, adverbs), frequency ranks, similarity intervals, lexical fields, and concreteness levels. Additionally, owing to the alignment of concepts across languages, we provide a suite of 66 crosslingual semantic similarity data sets. Because of its extensive size and language coverage, Multi-SimLex provides entirely novel opportunities for experimental evaluation and analysis. On its monolingual and crosslingual benchmarks, we evaluate and analyze a wide array of recent state-of-the-art monolingual and crosslingual representation models, including static and contextualized word embeddings (such as fastText, monolingual and multilingual BERT, XLM), externally informed lexical representations, as well as fully unsupervised and (weakly) supervised crosslingual word embeddings. We also present a step-by-step data set creation protocol for creating consistent, Multi-Simlex -style resources for additional languages.We make these contributions—the public release of Multi-SimLex data sets, their creation protocol, strong baseline results, and in-depth analyses which can be be helpful in guiding future developments in multilingual lexical semantics and representation learning—available via aWeb site that will encourage community effort in further expansion of Multi-Simlex to many more languages. Such a large-scale semantic resource could inspire significant further advances in NLP across languages.

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