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Database: the Journal of Biological Databases and Curation

Ruifeng Hu, Yulin Dai, Peilin Jia, Zhongming Zhao
Studies have shown that genetic factors play an important role in the risk to substance addiction and abuse. So far, various genetic and genomic studies have reported the related evidence. These rich, but highly heterogeneous, data provide us an unprecedented opportunity to systematically collect, curate and assess the genetic and genomic signals from published studies and to perform a comprehensive analysis of their features, functional roles and druggability. Such genetic data resources have been made available for other disease or phenotypes but not for major substance dependence yet...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
No abstract text is available yet for this article.
January 1, 2018: Database: the Journal of Biological Databases and Curation
Cheng-Dong Zhang, Yuan Yang, Huan-Huan Chen, Ting Zhang, Qiang Wang, Yuan Liang, Liang Zhang, Yan Zhou
In recent years, lots of studies have reported the relationship between genetic variation or expression and cancer prognosis with radiotherapy-based treatment. However, due to limitation in available journals or literature database, inconsistent nomenclature system of genetic variation and cancer and time-consuming investigation on literature searching and reading, considerable researches could hardly get found and cited. In this study, we constructed the Radiotherapy Prognosis Database (RTPDB), which contains a comprehensive resource about genes and related cancer prognosis...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Chia-Jung Yang, Jung-Hsien Chiang
OBJECTIVE: A major challenge in precision medicine is the development of patient-specific genetic biomarkers or drug targets. The firsthand information of the genes associated with the pathologic pathways of interest is buried in the ocean of biomedical literature. Gene ontology concept recognition (GOCR) is a biomedical natural language processing task used to extract and normalize the mentions of gene ontology (GO), the controlled vocabulary for gene functions across many species, from biomedical text...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Yu Wei, Jinlong Li, Baiqing Li, Chunfeng Ma, Xuanming Xu, Xu Wang, Aqin Liu, Tengfei Du, Zhonghua Wang, Zhangyong Hong, Jianping Lin
Glaucoma is a group of neurodegenerative diseases that can cause irreversible blindness. The current medications, which mainly reduce intraocular pressure to slow the progression of disease, may have local and systemic side effects. Recently, medications with possible neuroprotective effects have attracted much attention. To assist in the identification of new glaucoma drugs, we created a glaucomatous chemogenomics database (GCDB; in which various glaucoma-related chemogenomics data records are assembled, including 275 genes, 105 proteins, 83 approved or clinical trial drugs, 90 206 chemicals associated with 213 093 records of reported bioactivities from 22 324 corresponding bioassays and 5630 references...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Wei-Sheng Wu, Hao-Ping Tu, Yu-Han Chu, Torbjörn E M Nordling, Yan-Yuan Tseng, Hung-Jiun Liaw
Post-translational modifications of histones (e.g. acetylation, methylation, phosphorylation and ubiquitination) play crucial roles in regulating gene expression by altering chromatin structures and creating docking sites for histone/chromatin regulators. However, the combination patterns of histone modifications, regulatory proteins and their corresponding target genes remain incompletely understood. Therefore, it is advantageous to have a tool for the enrichment/depletion analysis of histone modifications and histone/chromatin regulators from a gene list...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Alejandro Llanes, Carlos Mario Restrepo, Ricardo Lleonart
Leishmania is a protozoan parasite causing several disease presentations collectively known as leishmaniasis. Pathogenic species of Leishmania are divided into two subgenera, L. (Leishmania) and L. (Viannia). Species belonging to the Viannia subgenus have only been reported in Central and South America. These species predominantly cause cutaneous leishmaniasis, but in some cases, parasites can migrate to the nasopharyngeal area and cause a highly disfiguring mucocutaneous presentation. Despite intensive efforts, no effective antileishmanial vaccine is available for use in humans, although a few candidates mainly designed for L...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu
Identifying the interactions between chemical compounds and genes from biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this paper, we describe Linguistic Pattern-Aware Dependency Tree Kernel, a linguistic interaction pattern learning method developed for CHEMPROT task-BioCreative VI, to capture chemical-protein interaction (CPI) patterns within biomedical literatures. We also introduce a framework to integrate these linguistic patterns with smooth partial tree kernel to extract the CPIs...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Hao Wang, Hanwei Yan, Huanlong Liu, Rui Liu, Jun Chen, Yan Xiang
A gene family is formed by duplication of a single original gene. Poplar trees (genus Populus) are important, principally because of their ecological and economic benefits, and are one of the most widely distributed and adaptable trees in the world. Systematic identification and annotation of gene family members are primary steps in studying the function and evolution of poplar genomes. Here, we describe the construction of the Gene Family Database in Poplar (GFDP), which contains information that systematically describes 6551 genes distributed in 145 gene families...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Junhao Chen, Jiawei Zhang, Meigui Lin, Wei Dong, Xinyue Guo, Yang Dong, Zhengjia Wang, Liangsheng Zhang, Fei Chen
Maca (Lepidium meyenii), a Brassicaceae herb plant originated from Andean mountains, has attracted wide interests due to its unique health benefits in reproduction and fertility. Because of its adaptation to the 4000 m high-altitude harsh environment, maca is attracting more and more attention from both crop breeders and basic biologists. After our previous release of the maca genome sequence, there's a growing need to store, query, analyze and integrate various maca resources efficiently. Here, we created Maca Genome Hub (MGH), a genomics and genetics database of maca...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Changhong Yang, Jiarui Li, Qixi Wu, Xiaoxu Yang, August Yue Huang, Jie Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Wei-Zhen Zhou, Lei Kong, Meng Wang, Chen Ai, Dechang Yang, Liping Wei
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with strong genetic contributions. To provide a comprehensive resource for the genetic evidence of ASD, we have updated the Autism KnowledgeBase (AutismKB) to version 2.0. AutismKB 2.0 integrates multiscale genetic data on 1379 genes, 5420 copy number variations and structural variations, 11 669 single-nucleotide variations or small insertions/deletions (SNVs/indels) and 172 linkage regions. In particular, AutismKB 2.0 highlights 5669 de novo SNVs/indels due to their significant contribution to ASD genetics and includes 789 mosaic variants due to their recently discovered contributions to ASD pathogenesis...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Xiang Hu, Wen Chen, Jing Li, Shulan Huang, Xuling Xu, Xuan Zhang, Shuanglin Xiang, Changning Liu
There is emerging evidence showing that lncRNAs can be involved in various critical biological processes. Zebrafish is a fully developed model system being used in a variety of basic research and biomedical studies. Hence, it is an ideal model organism to study the functions and mechanisms of lncRNAs. Here, we constructed ZFLNC-a comprehensive database of zebrafish lncRNA that is dedicated to providing a zebrafish-based platform for deep exploration of zebrafish lncRNAs and their mammalian counterparts to the relevant academic communities...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Tin-Hang Wong, Grace Wing-Chiu But, Hoi-Yan Wu, Stacey Shun-Kei Tsang, David Tai-Wai Lau, Pang-Chui Shaw
Authentication of medicinal materials by deoxyribonucleic acid (DNA) technology is gaining popularity. In 2010, our team has created Medicinal Materials DNA Barcode Database (MMDBD) version 1.0 to provide an interactive database for documenting DNA barcode sequences of medicinal materials. This database now contains DNA barcode sequences of medicinal materials listed in the Chinese Pharmacopoeia, Dietary Supplements Compendium and Herbal Medicine Compendium of the US Pharmacopoeia and selected adulterants. The data archive is regularly updated and currently it stores 62 011 DNA sequences of 2111 medicinal materials...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch
The text-mining services for kinome curation track, part of BioCreative VI, proposed a competition to assess the effectiveness of text mining to perform literature triage. The track has exploited an unpublished curated data set from the neXtProt database. This data set contained comprehensive annotations for 300 human protein kinases. For a given protein and a given curation axis [diseases or gene ontology (GO) biological processes], participants' systems had to identify and rank relevant articles in a collection of 5...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Jongyeun Park, Seung Hyun Ahn, Kwang Moon Cho, Dowoon Gu, Eun-Sook Jang, Sung Wook Chi
Small interfering RNA (siRNA) is widely used to specifically silence target gene expression, but its microRNA (miRNA)-like function inevitably suppresses hundreds of off-targets. Recently, complete elimination of the off-target repression has been achieved by introducing an abasic nucleotide to the pivot (position 6; siRNA-6Ø), of which impaired base pairing destabilizes transitional nucleation (positions 2-6). However, siRNA-6Ø varied in its conservation of on-target activity (∼80-100%), demanding bioinformatics to discover the principles underlying its on-target efficiency...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Nikita Gupta, Shafaque Zahra, Ajeet Singh, Shailesh Kumar
Ribonucleic acids (RNA) interference mechanism has been proved to be an important regulator of both transcriptional and post-transcription controls of gene expression during biotic and abiotic stresses in plants. Virus-derived small interfering RNAs (vsiRNAs) are established components of the RNA silencing mechanism for incurring anti-viral resistance in plants. Some databases like siRNAdb, HIVsirDB and VIRsiRNAdb are available online pertaining to siRNAs as well as vsiRNAs generated during viral infection in humans; however, currently there is a lack of repository for plant exclusive vsiRNAs...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Agnes Kirchhoff, Ulrich Bügel, Eduard Santamaria, Fabian Reimeier, Dominik Röpert, Alexander Tebbje, Anton Güntsch, Fernando Chaves, Karl-Heinz Steinke, Walter Berendsohn
Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Mojarad, Vipin Chaudhary, Hongfang Liu
Relation extraction is an important task in the field of natural language processing. In this paper, we describe our approach for the BioCreative VI Task 5: text mining chemical-protein interactions. We investigate multiple deep neural network (DNN) models, including convolutional neural networks, recurrent neural networks (RNNs) and attention-based (ATT-) RNNs (ATT-RNNs) to extract chemical-protein relations. Our experimental results indicate that ATT-RNN models outperform the same models without using attention and the ATT-gated recurrent unit (ATT-GRU) achieves the best performing micro average F1 score of 0...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Waqar Mahmood, Hafiza Mahnoor Abbasi
Ontologies have gained a lot of popularity and recognition in the semantic web because of their extensive use in Internet-based applications. Ontologies are often considered a fine source of semantics and interoperability in all artificially smart systems. Exponential increase in unstructured data on the web has made automated acquisition of ontology from unstructured text a most prominent research area. Several methodologies exploiting numerous techniques of various fields (machine learning, text mining, knowledge representation and reasoning, information retrieval and natural language processing) are being proposed to bring some level of automation in the process of ontology acquisition from unstructured text...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Bradford Condon, Abdullah Almsaeed, Ming Chen, Joe West, Margaret Staton
Tripal community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable and standardized. As funding for community-level genomics databases declines, Tripal's open-source codebase provides a means for sites to be built and maintained with a minimal investment in staff and new development. Tripal is ultimately as strong as the community of sites and developers that use it. We present a set of developer tools that will make building and maintaining Tripal 3 sites easier for new and returning users...
January 1, 2018: Database: the Journal of Biological Databases and Curation
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