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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/29220479/collaborative-relation-annotation-and-quality-analysis-in-markyt-environment
#2
Martín Pérez-Pérez, Gael Pérez-Rodríguez, Florentino Fdez-Riverola, Anália Lourenço
http://markyt.org.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220478/a-semantic-based-workflow-for-biomedical-literature-annotation
#3
Pedro Sernadela, José Luís Oliveira
Computational annotation of textual information has taken on an important role in knowledge extraction from the biomedical literature, since most of the relevant information from scientific findings is still maintained in text format. In this endeavour, annotation tools can assist in the identification of biomedical concepts and their relationships, providing faster reading and curation processes, with reduced costs. However, the separate usage of distinct annotation systems results in highly heterogeneous data, as it is difficult to efficiently combine and exchange this valuable asset...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220477/update-notifications-for-the-biocyc-collection-of-databases
#4
Suzanne Paley, Peter D Karp
https://BioCyc.org , https://EcoCyc.org , https://MetaCyc.org.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220476/egenpub-a-text-mining-system-for-extending-computationally-mapped-bibliography-for-uniprot-knowledgebase-by-capturing-centrality
#5
Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H Wu, K Vijay-Shanker, Cecilia N Arighi
UniProt Knowledgebase (UniProtKB) is a publicly available database with access to a vast amount of protein sequence and functional information. To widen the scope of the publications associated with a protein entry, UniProt has introduced the computationally mapped additional bibliography section, which includes literature collected from external sources. In this article, we describe a text mining system, eGenPub, which selects articles that are 'about' specific proteins and allows automatic identification of additional bibliography for given UniProt protein entries...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220475/improving-average-ranking-precision-in-user-searches-for-biomedical-research-datasets
#6
Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch
https://biocaddie.org/benchmark-data.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220474/database-of-resistance-related-metabolites-in-wheat-fusarium-head-blight-disease-mwfd
#7
Anuradha Surendra, Miroslava Cuperlovic-Culf
https://bioinfo.nrc.ca/mwfd/index.php.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220473/ygmd-a-repository-for-yeast-cooperative-transcription-factor-sets-and-their-target-gene-modules
#8
Wei-Sheng Wu, Pin-Han Chen, Tsung-Te Chen, Yan-Yuan Tseng
http://cosbi4.ee.ncku.edu.tw/YGMD/ , http://cosbi5.ee.ncku.edu.tw/YGMD/ or http://cosbi.ee.ncku.edu.tw/YGMD/.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220472/proficiency-of-data-interpretation-identification-of-signaling-snps-specific-loci-for-coronary-artery-disease
#9
Asma N Cheema, Samantha L Rosenthal, M Ilyas Kamboh
http://www.regulomedb.org/;https://www.broadinstitute.org/mpg/snap/.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220471/fishtrace-a-genetic-catalogue-of-european-fishes
#10
Antonella Zanzi, Jann Th Martinsohn
https://fishtrace.jrc.ec.europa.eu.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220470/dlrefd-a-database-providing-associations-of-long-non-coding-rnas-environmental-factors-and-phenotypes
#11
Ya-Zhou Sun, De-Hong Zhang, Zhong Ming, Jian-Qiang Li, Xing Chen
http://chengroup.cumt.edu.cn/DLREFD.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220469/edaphostat-interactive-ecological-analysis-of-soil-organism-occurrences-and-preferences-from-the-edaphobase-data-warehouse
#12
Jonas Hausen, Björn Scholz-Starke, Ulrich Burkhardt, Stephan Lesch, Sebastian Rick, David Russell, Martina Roß-Nickoll, Richard Ottermanns
Edaphostat is part of the Edaphobase Web Application available at https://portal.edaphobase.org.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220468/eucanext-an-integrated-database-for-the-exploration-of-genomic-and-transcriptomic-data-from-eucalyptus-species
#13
Leandro Costa Nascimento, Marcela Mendes Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas Salera Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
http://www.lge.ibi.unicamp.br/eucalyptusdb.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220467/query-expansion-using-mesh-terms-for-dataset-retrieval-ohsu-at-the-biocaddie-2016-dataset-retrieval-challenge
#14
Theodore B Wright, David Ball, William Hersh
https://biocaddie.org/benchmark-data.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220466/improving-taxonomic-accuracy-for-fungi-in-public-sequence-databases-applying-one-name-one-species-in-well-defined-genera-with-trichoderma-hypocrea-as-a-test-case
#15
Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch
http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220465/in-cardiome-integrated-knowledgebase-for-coronary-artery-disease-enabling-translational-research
#16
Ankit Sharma, Vrushali Deshpande, Madankumar Ghatge, Rajani Kanth Vangala
www.tri-incardiome.org.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220464/kipho-malaria-parasite-kinome-and-phosphatome-portal
#17
Rajan Pandey, Pawan Kumar, Dinesh Gupta
The Plasmodium kinases and phosphatases play an essential role in the regulation of substrate reversible-phosphorylation and overall cellular homeostasis. Reversible phosphorylation is one of the key post-translational modifications (PTMs) essential for parasite survival. Thus, a complete and comprehensive information of malarial kinases and phosphatases as a single web resource will not only aid in systematic and better understanding of the PTMs, but also facilitate efforts to look for novel drug targets for malaria...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220463/an-online-analytical-processing-multi-dimensional-data-warehouse-for-malaria-data
#18
S M Niaz Arifin, Gregory R Madey, Alexander Vyushkov, Benoit Raybaud, Thomas R Burkot, Frank H Collins
https://dw.vecnet.org/datawarehouse/.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220462/first-steps-in-automatic-summarization-of-transcription-factor-properties-for-regulondb-classification-of-sentences-about-structural-domains-and-regulated-processes
#19
Carlos-Francisco Méndez-Cruz, Socorro Gama-Castro, Citlalli Mejía-Almonte, Marco-Polo Castillo-Villalba, Luis-José Muñiz-Rascado, Julio Collado-Vides
RegulonDB, http://regulondb.ccg.unam.mx.
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29220461/sfmetadb-a-comprehensive-annotation-of-mouse-rna-splicing-factor-rna-seq-datasets
#20
Jin Li, Ching-San Tseng, Antonio Federico, Franjo Ivankovic, Yi-Shuian Huang, Alfredo Ciccodicola, Maurice S Swanson, Peng Yu
http://sfmetadb.ece.tamu.edu/.
January 1, 2017: Database: the Journal of Biological Databases and Curation
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