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Database: the Journal of Biological Databases and Curation

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https://www.readbyqxmd.com/read/28334741/benchmarks-for-measurement-of-duplicate-detection-methods-in-nucleotide-databases
#1
Qingyu Chen, Justin Zobel, Karin Verspoor
Duplication of information in databases is a major data quality challenge. The presence of duplicates, implying either redundancy or inconsistency, can have a range of impacts on the quality of analyses that use the data. To provide a sound basis for research on this issue in databases of nucleotide sequences, we have developed new, large-scale validated collections of duplicates, which can be used to test the effectiveness of duplicate detection methods. Previous collections were either designed primarily to test efficiency, or contained only a limited number of duplicates of limited kinds...
January 8, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605776/exploring-convolutional-neural-networks-for-drug-drug-interaction-extraction
#2
Víctor Suárez-Paniagua, Isabel Segura-Bedmar, Paloma Martínez
Drug-drug interaction (DDI), which is a specific type of adverse drug reaction, occurs when a drug influences the level or activity of another drug. Natural language processing techniques can provide health-care professionals with a novel way of reducing the time spent reviewing the literature for potential DDIs. The current state-of-the-art for the extraction of DDIs is based on feature-engineering algorithms (such as support vector machines), which usually require considerable time and effort. One possible alternative to these approaches includes deep learning...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605775/biocuration-in-the-structure-function-linkage-database-the-anatomy-of-a-superfamily
#3
Gemma L Holliday, Shoshana D Brown, Eyal Akiva, David Mischel, Michael A Hicks, John H Morris, Conrad C Huang, Elaine C Meng, Scott C-H Pegg, Thomas E Ferrin, Patricia C Babbitt
No abstract text is available yet for this article.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605774/genomehubs-simple-containerized-setup-of-a-custom-ensembl-database-and-web-server-for-any-species
#4
Richard J Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter
Database URL: http://GenomeHubs.org. As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive application programming interface. Here we introduce GenomeHubs, which provide a containerized environment to facilitate the setup and hosting of custom Ensembl genome browsers...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605773/biom2metdisease-a-manually-curated-database-for-associations-between-micrornas-metabolites-small-molecules-and-metabolic-diseases
#5
Yanjun Xu, Haixiu Yang, Tan Wu, Qun Dong, Zeguo Sun, Desi Shang, Feng Li, Yingqi Xu, Fei Su, Siyao Liu, Yunpeng Zhang, Xia Li
BioM2MetDisease is a manually curated database that aims to provide a comprehensive and experimentally supported resource of associations between metabolic diseases and various biomolecules. Recently, metabolic diseases such as diabetes have become one of the leading threats to people’s health. Metabolic disease associated with alterations of multiple types of biomolecules such as miRNAs and metabolites. An integrated and high-quality data source that collection of metabolic disease associated biomolecules is essential for exploring the underlying molecular mechanisms and discovering novel therapeutics...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605772/annosys-implementation-of-a-generic-annotation-system-for-schema-based-data-using-the-example-of-biodiversity-collection-data
#6
L Suhrbier, W-H Kusber, O Tschöpe, A Güntsch, W G Berendsohn
No abstract text is available yet for this article.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605771/chomine-an-integrated-data-warehouse-for-cho-systems-biology-and-modeling
#7
Matthias P Gerstl, Michael Hanscho, David E Ruckerbauer, Jürgen Zanghellini, Nicole Borth
The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605770/improving-biocuration-of-micrornas-in-diseases-a-case-study-in-idiopathic-pulmonary-fibrosis
#8
Yalbi Itzel Balderas-Martínez, Fabio Rinaldi, Gabriela Contreras, Hilda Solano-Lira, Mishael Sánchez-Pérez, Julio Collado-Vides, Moisés Selman, Annie Pardo
MicroRNAs (miRNAs) are small and non-coding RNA molecules that inhibit gene expression posttranscriptionally. They play important roles in several biological processes, and in recent years there has been an interest in studying how they are related to the pathogenesis of diseases. Although there are already some databases that contain information for miRNAs and their relation with illnesses, their curation represents a significant challenge due to the amount of information that is being generated every day...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605769/triatokey-a-web-and-mobile-tool-for-biodiversity-identification-of-brazilian-triatomine-species
#9
Luciana Márcia de Oliveira, Raissa Nogueira de Brito, Paul Anderson Souza Guimarães, Rômulo Vitor Mastrângelo Amaro Dos Santos, Liléia Gonçalves Diotaiuti, Rita de Cássia Moreira de Souza, Jeronimo Conceição Ruiz
Triatomines are blood-sucking insects that transmit the causative agent of Chagas disease, Trypanosoma cruzi. Despite being recognized as a difficult task, the correct taxonomic identification of triatomine species is crucial for vector control in Latin America, where the disease is endemic. In this context, we have developed a web and mobile tool based on PostgreSQL database to help healthcare technicians to overcome the difficulties to identify triatomine vectors when the technical expertise is missing. The web and mobile version makes use of real triatomine species pictures and dichotomous key method to support the identification of potential vectors that occur in Brazil...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605768/surveying-the-maize-community-for-their-diversity-and-pedigree-visualization-needs-to-prioritize-tool-development-and-curation
#10
Taner Z Sen, Bremen L Braun, David A Schott, John L Portwood Ii, Mary L Schaeffer, Lisa C Harper, Jack M Gardiner, Ethalinda K Cannon, Carson M Andorf
The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in Summer 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered their top priorities for visualization as: (i) displaying single nucleotide polymorphisms in a given region for a given list of lines, (ii) showing haplotypes for a given list of lines and (iii) presenting pedigree relationships visually...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605767/strategies-towards-digital-and-semi-automated-curation-in-regulondb
#11
Fabio Rinaldi, Oscar Lithgow, Socorro Gama-Castro, Hilda Solano, Alejandra López-Fuentes, Luis José Muñiz Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides
No abstract text is available yet for this article.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605766/genehancer-genome-wide-integration-of-enhancers-and-target-genes-in-genecards
#12
Simon Fishilevich, Ron Nudel, Noa Rappaport, Rotem Hadar, Inbar Plaschkes, Tsippi Iny Stein, Naomi Rosen, Asher Kohn, Michal Twik, Marilyn Safran, Doron Lancet, Dana Cohen
A major challenge in understanding gene regulation is the unequivocal identification of enhancer elements and uncovering their connections to genes. We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards. First, we integrated a total of 434 000 reported enhancers from four different genome-wide databases: the Encyclopedia of DNA Elements (ENCODE), the Ensembl regulatory build, the functional annotation of the mammalian genome (FANTOM) project and the VISTA Enhancer Browser...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28605765/workflow-and-web-application-for-annotating-ncbi-bioproject-transcriptome-data
#13
Roberto Vera Alvarez, Newton Medeiros Vidal, Gina A Garzón-Martínez, Luz S Barrero, David Landsman, Leonardo Mariño-Ramírez
Abstract: The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28415075/hopbase-a-unified-resource-for-humulus-genomics
#14
Steven T Hill, Ramcharan Sudarsanam, John Henning, David Hendrix
Hop (Humulus lupulus L. var lupulus) is a dioecious plant of worldwide significance, used primarily for bittering and flavoring in brewing beer. Studies on the medicinal properties of several unique compounds produced by hop have led to additional interest from pharmacy and healthcare industries as well as livestock production as a natural antibiotic. Genomic research in hop has resulted a published draft genome and transcriptome assemblies. As research into the genomics of hop has gained interest, there is a critical need for centralized online genomic resources...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28415074/navicom-a-web-application-to-create-interactive-molecular-network-portraits-using-multi-level-omics-data
#15
Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
Human diseases such as cancer are routinely characterized by high-throughput molecular technologies, and multi-level omics data are accumulated in public databases at increasing rate. Retrieval and visualization of these data in the context of molecular network maps can provide insights into the pattern of regulation of molecular functions reflected by an omics profile. In order to make this task easy, we developed NaviCom, a Python package and web platform for visualization of multi-level omics data on top of biological network maps...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28415073/chemical-induced-disease-relation-extraction-via-convolutional-neural-network
#16
Jinghang Gu, Fuqing Sun, Longhua Qian, Guodong Zhou
This article describes our work on the BioCreative-V chemical-disease relation (CDR) extraction task, which employed a maximum entropy (ME) model and a convolutional neural network model for relation extraction at inter- and intra-sentence level, respectively. In our work, relation extraction between entity concepts in documents was simplified to relation extraction between entity mentions. We first constructed pairs of chemical and disease mentions as relation instances for training and testing stages, then we trained and applied the ME model and the convolutional neural network model for inter- and intra-sentence level, respectively...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28365743/automated-pdf-highlighting-to-support-faster-curation-of-literature-for-parkinson-s-and-alzheimer-s-disease
#17
Honghan Wu, Anika Oellrich, Christine Girges, Bernard de Bono, Tim J P Hubbard, Richard J B Dobson
Neurodegenerative disorders such as Parkinson's and Alzheimer's disease are devastating and costly illnesses, a source of major global burden. In order to provide successful interventions for patients and reduce costs, both causes and pathological processes need to be understood. The ApiNATOMY project aims to contribute to our understanding of neurodegenerative disorders by manually curating and abstracting data from the vast body of literature amassed on these illnesses. As curation is labour-intensive, we aimed to speed up the process by automatically highlighting those parts of the PDF document of primary importance to the curator...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28365742/wikigenomes-an-open-web-application-for-community-consumption-and-curation-of-gene-annotation-data-in-wikidata
#18
Tim E Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory S Stupp, Chunlei Wu, Andrew I Su, Benjamin M Good
With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don't exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28365741/tmpl-a-database-of-experimental-and-theoretical-transmembrane-protein-models-positioned-in-the-lipid-bilayer
#19
Guillaume Postic, Yassine Ghouzam, Catherine Etchebest, Jean-Christophe Gelly
Knowing the position of protein structures within the membrane is crucial for fundamental and applied research in the field of molecular biology. Only few web resources propose coordinate files of oriented transmembrane proteins, and these exclude predicted structures, although they represent the largest part of the available models. In this article, we present TMPL (http://www.dsimb.inserm.fr/TMPL/), a database of transmembrane protein structures (α-helical and β-sheet) positioned in the lipid bilayer. It is the first database to include theoretical models of transmembrane protein structures, making it a large repository with more than 11 000 entries...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28365740/effective-biomedical-document-classification-for-identifying-publications-relevant-to-the-mouse-gene-expression-database-gxd
#20
Xiangying Jiang, Martin Ringwald, Judith Blake, Hagit Shatkay
The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow...
January 1, 2017: Database: the Journal of Biological Databases and Curation
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