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Database: the Journal of Biological Databases and Curation

Michael A Farnum, Mathangi Ashok, Daniel Kowalski, Fang Du, Lalit Mohanty, Paul Konstant, Joseph Ciervo, Victor S Lobanov, Dimitris K Agrafiotis
Assembly of complete and error-free clinical trial data sets for statistical analysis and regulatory submission requires extensive effort and communication among investigational sites, central laboratories, pharmaceutical sponsors, contract research organizations and other entities. Traditionally, this data is captured, cleaned and reconciled through multiple disjointed systems and processes, which is resource intensive and error prone. Here, we introduce a new system for clinical data review that helps data managers identify missing, erroneous and inconsistent data and manage queries in a unified, system-agnostic and efficient way...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Ryan Barrett, Cynthia L Neben, Anjali D Zimmer, Gilad Mishne, Wendy McKennon, Alicia Y Zhou, Jeremy Ginsberg
Next generation sequencing multi-gene panels have greatly improved the diagnostic yield and cost effectiveness of genetic testing and are rapidly being integrated into the clinic for hereditary cancer risk. With this technology comes a dramatic increase in the volume, type and complexity of data. This invaluable data though is too often buried or inaccessible to researchers, especially to those without strong analytical or programming skills. To effectively share comprehensive, integrated genotypic-phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Gaole An, Jiaqi Sun, Chao Ren, Zhangyi Ouyang, Lingyun Zhu, Xiaochen Bo, Shaoliang Peng, Wenjie Shu
Advances in studies of long noncoding RNAs (lncRNAs) have provided data regarding the regulatory roles of lncRNAs, which perform functional roles through interactions with other functional elements. To track the underlying relationships among lncRNAs, various databases have been developed as repositories for lncRNA data. However, the ability to comprehensively explore the diverse interactions between lncRNAs and other functional elements is limited. To this end, we developed LIVE (LncRNA Interaction Validated Encyclopaedia), an interactive resource to integrate the diverse interactions of functional elements with lncRNAs...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Si Zhe Xiao, Chris Armit, Scott Edmunds, Laurie Goodman, Peter Li, Mary Ann Tuli, Christopher Ian Hunter
With a large increase in the volume and type of data archived in GigaScience Database (GigaDB) since its launch in 2011, we have studied the metrics and user patterns to assess the important aspects needed to best suit current and future use. This has led to new front-end developments and enhanced interactivity and functionality that greatly improve user experience. In this article, we present an overview of the current practices including the Biocurational role of the GigaDB staff, the broad usage metrics of GigaDB datasets and an update on how the GigaDB platform has been overhauled and enhanced to improve the stability and functionality of the codebase...
January 1, 2019: Database: the Journal of Biological Databases and Curation
V Sureshkumar, Bipratip Dutta, Vishesh Kumar, G Prakash, Dwijesh C Mishra, K K Chaturvedi, Anil Rai, Amitha Mithra Sevanthi, Amolkumar U Solanke
Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Shur-Jen Wang, Stanley J F Laulederkind, Yiqing Zhao, G Thomas Hayman, Jennifer R Smith, Monika Tutaj, Jyothi Thota, Marek A Tutaj, Matthew J Hoffman, Elizabeth R Bolton, Jeffrey De Pons, Melinda R Dwinell, Mary Shimoyama
Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J Khoury, Zhiyong Lu
Tracking scientific research publications on the evaluation, utility and implementation of genomic applications is critical for the translation of basic research to impact clinical and population health. In this work, we utilize state-of-the-art machine learning approaches to identify translational research in genomics beyond bench to bedside from the biomedical literature. We apply the convolutional neural networks (CNNs) and support vector machines (SVMs) to the bench/bedside article classification on the weekly manual annotation data of the Public Health Genomics Knowledge Base database...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Salman Sadullah Usmani, Piyush Agrawal, Manika Sehgal, Pradeep Kumar Patel, Gajendra P S Raghava
Immunosuppression proved as a captivating therapy in several autoimmune disorders, asthma as well as in organ transplantation. Immunosuppressive peptides are specific for reducing efficacy of immune system with wide range of therapeutic implementations. `ImmunoSPdb' is a comprehensive, manually curated database of around 500 experimentally verified immunosuppressive peptides compiled from 79 research article and 32 patents. The current version comprises of 553 entries providing extensive information including peptide name, sequence, chirality, chemical modification, origin, nature of peptide, its target as well as mechanism of action, amino acid frequency and composition, etc...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Anastasia A Nikitina, Alexey A Orlov, Liubov I Kozlovskaya, Vladimir A Palyulin, Dmitry I Osolodkin
The discovery of antiviral drugs is a rapidly developing area of medicinal chemistry research. The emergence of resistant variants and outbreaks of poorly studied viral diseases make this area constantly developing. The amount of antiviral activity data available in ChEMBL consistently grows, but virus taxonomy annotation of these data is not sufficient for thorough studies of antiviral chemical space. We developed a procedure for semi-automatic extraction of antiviral activity data from ChEMBL and mapped them to the virus taxonomy developed by the International Committee for Taxonomy of Viruses (ICTV)...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Hee-Ju Yu, Seunghoon Baek, Young-Joon Lee, Ara Cho, Jeong-Hwan Mun
Radish (Raphanus sativus L.) is an important root vegetable crop in the family Brassicaceae, which provides diverse nutrients for human health and is closely related to the Brassica crop species. Recently, we sequenced and assembled the radish genome into nine chromosome pseudomolecules. In addition, we developed diverse genomic resources, including genetic maps, molecular markers, transcriptome, genome-wide methylation and variome data. In this study, we describe the radish genome database (RadishGD), including details of data sets that we generated and the web interface that allows access to these data...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Sam M Ireland, Andrew C R Martin
Zinc is one of the most important biologically active metals. Ten per cent of the human genome is thought to encode a zinc binding protein and its uses encompass catalysis, structural stability, gene expression and immunity. At present, there is no specific resource devoted to identifying and presenting all currently known zinc binding sites. Here we present ZincBind, a database of zinc binding sites and its web front-end. Using the structural data in the Protein Data Bank, ZincBind identifies every instance of zinc binding to a protein, identifies its binding site and clusters sites based on 90% sequence identity...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Edith D Wong, Marek S Skrzypek, Shuai Weng, Gail Binkley, Birgit H M Meldal, Livia Perfetto, Sandra E Orchard, Stacia R Engel, J Michael Cherry
Proteins seldom function individually. Instead, they interact with other proteins or nucleic acids to form stable macromolecular complexes that play key roles in important cellular processes and pathways. One of the goals of Saccharomyces Genome Database (SGD; is to provide a complete picture of budding yeast biological processes. To this end, we have collaborated with the Molecular Interactions team that provides the Complex Portal database at EMBL-EBI to manually curate the complete yeast complexome...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Xianwen Meng, Dahui Hu, Peijing Zhang, Qi Chen, Ming Chen
Increasing evidence reveals that circular RNAs (circRNAs) are widespread in eukaryotes and play important roles in diverse biological processes. However, a comprehensive functionally annotated circRNA database is still lacking. CircFunBase is a web-accessible database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions. The current version of CircFunBase documents more than 7000 manually curated functional circRNA entries, mainly including Homo sapiens, Mus musculus etc...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Helen Attrill, Pascale Gaudet, Rachael P Huntley, Ruth C Lovering, Stacia R Engel, Sylvain Poux, Kimberly M Van Auken, George Georghiou, Marcus C Chibucos, Tanya Z Berardini, Valerie Wood, Harold Drabkin, Petra Fey, Penelope Garmiri, Midori A Harris, Tony Sawford, Leonore Reiser, Rebecca Tauber, Sabrina Toro
High-throughput studies constitute an essential and valued source of information for researchers. However, high-throughput experimental workflows are often complex, with multiple data sets that may contain large numbers of false positives. The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of a gene's role in biology. To address this, representatives from annotation teams within the GO Consortium reviewed high-throughput data annotation practices...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Diego Alonso-López, Francisco J Campos-Laborie, Miguel A Gutiérrez, Luke Lambourne, Michael A Calderwood, Marc Vidal, Javier De Las Rivas
The collection and integration of all the known protein-protein physical interactions within a proteome framework are critical to allow proper exploration of the protein interaction networks that drive biological processes in cells at molecular level. APID Interactomes is a public resource of biological data ( that provides a comprehensive and curated collection of `protein interactomes' for more than 1100 organisms, including 30 species with more than 500 interactions, derived from the integration of experimentally detected protein-to-protein physical interactions (PPIs)...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Gerhard Rambold, Pelin Yilmaz, Janno Harjes, Sabrina Klaster, Veronica Sanz, Anton Link, Frank Oliver Glöckner, Dagmar Triebel
With the advent of advanced molecular meta-omics techniques and methods, a new era commenced for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine the origin, identity and traits of environmental (biological) objects and organisms. In this context, the need for new data structures is evident and former approaches for data processing need to be expanded according to the new meta-omics techniques and operational standards...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Alberto Grand, Emanuele Geda, Andrea Mignone, Andrea Bertotti, Alessandro Fiori
In the last years, Laboratory Information Management Systems (LIMS) have been growing from mere inventory systems into increasingly comprehensive software platforms, spanning functionalities as diverse as data search, annotation and analysis. Our institution started in 2011 a LIMS project named the Laboratory Assistant Suite with the purpose of assisting researchers throughout all of their laboratory activities, providing graphical tools to support decision-making tasks and building complex analyses on integrated data...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Saber A Akhondi, Hinnerk Rey, Markus Schwörer, Michael Maier, John Toomey, Heike Nau, Gabriele Ilchmann, Mark Sheehan, Matthias Irmer, Claudia Bobach, Marius Doornenbal, Michelle Gregory, Jan A Kors
In commercial research and development projects, public disclosure of new chemical compounds often takes place in patents. Only a small proportion of these compounds are published in journals, usually a few years after the patent. Patent authorities make available the patents but do not provide systematic continuous chemical annotations. Content databases such as Elsevier's Reaxys provide such services mostly based on manual excerptions, which are time-consuming and costly. Automatic text-mining approaches help overcome some of the limitations of the manual process...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-Aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu
The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Ran Kang, Yiming Zhang, Qingqing Huang, Junhua Meng, Ruofan Ding, Yunjian Chang, Lili Xiong, Zhiyun Guo
Enhancers can act as cis-regulatory elements to control transcriptional regulation by recruiting DNA-binding transcription factors (TFs) in a tissue-specific manner. Recent studies show that enhancers regulate not only protein-coding genes but also microRNAs (miRNAs), and mutations within the TF binding sites (TFBSs) located on enhancers will cause a variety of diseases such as cancer. However, a comprehensive resource to integrate these regulation elements for revealing transcriptional regulations in the context of enhancers is not currently available...
January 1, 2019: Database: the Journal of Biological Databases and Curation
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