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Database: the Journal of Biological Databases and Curation

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https://www.readbyqxmd.com/read/27630202/establishment-of-kawasaki-disease-database-based-on-metadata-standard
#1
Yu Rang Park, Jae-Jung Kim, Young Jo Yoon, Young-Kwang Yoon, Ha Yeong Koo, Young Mi Hong, Gi Young Jang, Soo-Yong Shin, Jong-Keuk Lee
Kawasaki disease (KD) is a rare disease that occurs predominantly in infants and young children. To identify KD susceptibility genes and to develop a diagnostic test, a specific therapy, or prevention method, collecting KD patients' clinical and genomic data is one of the major issues. For this purpose, Kawasaki Disease Database (KDD) was developed based on the efforts of Korean Kawasaki Disease Genetics Consortium (KKDGC). KDD is a collection of 1292 clinical data and genomic samples of 1283 patients from 13 KKDGC-participating hospitals...
July 2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27630201/sieve-based-coreference-resolution-enhances-semi-supervised-learning-model-for-chemical-induced-disease-relation-extraction
#2
Hoang-Quynh Le, Mai-Vu Tran, Thanh Hai Dang, Quang-Thuy Ha, Nigel Collier
The BioCreative V chemical-disease relation (CDR) track was proposed to accelerate the progress of text mining in facilitating integrative understanding of chemicals, diseases and their relations. In this article, we describe an extension of our system (namely UET-CAM) that participated in the BioCreative V CDR. The original UET-CAM system's performance was ranked fourth among 18 participating systems by the BioCreative CDR track committee. In the Disease Named Entity Recognition and Normalization (DNER) phase, our system employed joint inference (decoding) with a perceptron-based named entity recognizer (NER) and a back-off model with Semantic Supervised Indexing and Skip-gram for named entity normalization...
July 2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27888231/text-mining-resources-for-the-life-sciences
#3
REVIEW
Piotr Przybyła, Matthew Shardlow, Sophie Aubin, Robert Bossy, Richard Eckart de Castilho, Stelios Piperidis, John McNaught, Sophia Ananiadou
Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27888230/toxreporter-viewing-the-genome-through-the-eyes-of-a-toxicologist
#4
Mark Gosink
One of the many roles of a toxicologist is to determine if an observed adverse event (AE) is related to a previously unrecognized function of a given gene/protein. Towards that end, he or she will search a variety of public and propriety databases for information linking that protein to the observed AE. However, these databases tend to present all available information about a protein, which can be overwhelming, limiting the ability to find information about the specific toxicity being investigated. ToxReporter compiles information from a broad selection of resources and limits display of the information to user-selected areas of interest...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27777244/disease-named-entity-recognition-by-combining-conditional-random-fields-and-bidirectional-recurrent-neural-networks
#5
Qikang Wei, Tao Chen, Ruifeng Xu, Yulan He, Lin Gui
The recognition of disease and chemical named entities in scientific articles is a very important subtask in information extraction in the biomedical domain. Due to the diversity and complexity of disease names, the recognition of named entities of diseases is rather tougher than those of chemical names. Although there are some remarkable chemical named entity recognition systems available online such as ChemSpot and tmChem, the publicly available recognition systems of disease named entities are rare. This article presents a system for disease named entity recognition (DNER) and normalization...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27694210/the-bel-information-extraction-workflow-belief-evaluation-in-the-biocreative-v-bel-and-iat-track
#6
Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel Peitsch, Juliane Fluck
Network-based approaches have become extremely important in systems biology to achieve a better understanding of biological mechanisms. For network representation, the Biological Expression Language (BEL) is well designed to collate findings from the scientific literature into biological network models. To facilitate encoding and biocuration of such findings in BEL, a BEL Information Extraction Workflow (BELIEF) was developed. BELIEF provides a web-based curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27694209/asap-a-machine-learning-framework-for-local-protein-properties
#7
Nadav Brandes, Dan Ofer, Michal Linial
Determining residue-level protein properties, such as sites of post-translational modifications (PTMs), is vital to understanding protein function. Experimental methods are costly and time-consuming, while traditional rule-based computational methods fail to annotate sites lacking substantial similarity. Machine Learning (ML) methods are becoming fundamental in annotating unknown proteins and their heterogeneous properties. We present ASAP (Amino-acid Sequence Annotation Prediction), a universal ML framework for predicting residue-level properties...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27694208/ordb-horde-odoractor-and-other-on-line-knowledge-resources-of-olfactory-receptor-odorant-interactions
#8
Luis Marenco, Rixin Wang, Robert McDougal, Tsviya Olender, Michal Twik, Elspeth Bruford, Xinyi Liu, Jian Zhang, Doron Lancet, Gordon Shepherd, Chiquito Crasto
We present here an exploration of the evolution of three well-established, web-based resources dedicated to the dissemination of information related to olfactory receptors (ORs) and their functional ligands, odorants. These resources are: the Olfactory Receptor Database (ORDB), the Human Olfactory Data Explorer (HORDE) and ODORactor. ORDB is a repository of genomic and proteomic information related to ORs and other chemosensory receptors, such as taste and pheromone receptors. Three companion databases closely integrated with ORDB are OdorDB, ORModelDB and OdorMapDB; these resources are part of the SenseLab suite of databases (http://senselab...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27694207/3dflu-database-of-sequence-and-structural-variability-of-the-influenza-hemagglutinin-at-population-scale
#9
Giovanni Mazzocco, Michal Lazniewski, Piotr Migdał, Teresa Szczepińska, Jan P Radomski, Dariusz Plewczynski
The influenza virus type A (IVA) is an important pathogen which is able to cause annual epidemics and even pandemics. This fact is the consequence of the antigenic shifts and drifts capabilities of IVA, caused by the high mutation rate and the reassortment capabilities of the virus. The hemagglutinin (HA) protein constitutes the main IVA antigen and has a crucial role in the infection mechanism, being responsible for the recognition of host-specific sialic acid derivatives. Despite the relative abundance of HA sequence and serological studies, comparative structure-based analysis of HA are less investigated...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27694206/the-global-genome-biodiversity-network-ggbn-data-standard-specification
#10
G Droege, K Barker, O Seberg, J Coddington, E Benson, W G Berendsohn, B Bunk, C Butler, E M Cawsey, J Deck, M Döring, P Flemons, B Gemeinholzer, A Güntsch, T Hollowell, P Kelbert, I Kostadinov, R Kottmann, R T Lawlor, C Lyal, J Mackenzie-Dodds, C Meyer, D Mulcahy, S Y Nussbeck, É O'Tuama, T Orrell, G Petersen, T Robertson, C Söhngen, J Whitacre, J Wieczorek, P Yilmaz, H Zetzsche, Y Zhang, X Zhou
Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27616775/pgd-a-pangolin-genome-hub-for-the-research-community
#11
Tze King Tan, Ka Yun Tan, Ranjeev Hari, Aini Mohamed Yusoff, Guat Jah Wong, Cheuk Chuen Siow, Naresh V R Mutha, Mike Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Ian C Paterson, Wesley C Warren, Warren E Johnson, Stephen J O'Brien, Siew Woh Choo
Pangolins (order Pholidota) are the only mammals covered by scales. We have recently sequenced and analyzed the genomes of two critically endangered Asian pangolin species, namely the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla). These complete genome sequences will serve as reference sequences for future research to address issues of species conservation and to advance knowledge in mammalian biology and evolution. To further facilitate the global research effort in pangolin biology, we developed the Pangolin Genome Database (PGD), as a future hub for hosting pangolin genomic and transcriptomic data and annotations, and with useful analysis tools for the research community...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27599750/mining-biomedical-images-towards-valuable-information-retrieval-in-biomedical-and-life-sciences
#12
Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
No abstract text is available yet for this article.
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27589965/peptickddb-peptide-and-protein-centric-database-for-the-investigation-of-genesis-and-progression-of-chronic-kidney-disease
#13
Magdalena Krochmal, Marco Fernandes, Szymon Filip, Claudia Pontillo, Holger Husi, Jerome Zoidakis, Harald Mischak, Antonia Vlahou, Joachim Jankowski
The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27589964/modeling-biochemical-pathways-in-the-gene-ontology
#14
David P Hill, Peter D'Eustachio, Tanya Z Berardini, Christopher J Mungall, Nikolai Renedo, Judith A Blake
The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27589963/discrepancies-between-human-dna-mrna-and-protein-reference-sequences-and-their-relation-to-single-nucleotide-variants-in-the-human-population
#15
Matsuyuki Shirota, Kengo Kinoshita
The protein coding sequences of the human reference genome GRCh38, RefSeq mRNA and UniProt protein databases are sometimes inconsistent with each other, due to polymorphisms in the human population, but the overall landscape of the discordant sequences has not been clarified. In this study, we comprehensively listed the discordant bases and regions between the GRCh38, RefSeq and UniProt reference sequences, based on the genomic coordinates of GRCh38. We observed that the RefSeq sequences are more likely to represent the major alleles than GRCh38 and UniProt, by assigning the alternative allele frequencies of the discordant bases...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27589962/biocreative-v-bioc-track-overview-collaborative-biocurator-assistant-task-for-biogrid
#16
Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cathy H Wu, K Vijay-Shanker, Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W John Wilbur, Donald C Comeau
BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein-protein/genetic interaction passage identification and annotation visualization...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27589961/overview-of-the-interactive-task-in-biocreative-v
#17
Qinghua Wang, Shabbir S Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K Irin, Lars J Jensen, Silvia Jimenez, Toni R Jue, Ingrid Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel M Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D Tadepally, Loukia Tsaprouni, Nicole Vasilevsky, Xiaodong Wang, Andrew Chatr-Aryamontri, Stanley J F Laulederkind, Sherri Matis-Mitchell, Johanna McEntyre, Sandra Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary Schaeffer, Cathy H Wu, Lynette Hirschman, Cecilia N Arighi
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27580923/skeleton-genetics-a-comprehensive-database-for-genes-and-mutations-related-to-genetic-skeletal-disorders
#18
Chong Chen, Yi Jiang, Chenyang Xu, Xinting Liu, Lin Hu, Yanbao Xiang, Qingshuang Chen, Denghui Chen, Huanzheng Li, Xueqin Xu, Shaohua Tang
Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27580922/automated-detection-of-discourse-segment-and-experimental-types-from-the-text-of-cancer-pathway-results-sections
#19
Gully A P C Burns, Pradeep Dasigi, Anita de Waard, Eduard H Hovy
Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27577567/ddrprot-a-database-of-dna-damage-response-related-proteins
#20
Eduardo Andrés-León, Ildefonso Cases, Aida Arcas, Ana M Rojas
The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins...
2016: Database: the Journal of Biological Databases and Curation
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