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Prioritization of data quality dimensions and skills requirements in genome annotation work

Hong Huang, Besiki Stvilia, Corinne Jörgensen, Hank W. Bass
2011 Journal of the American Society for Information Science and Technology  
data quality and skills for genome annotation.  ...  This study contributes towards better understanding of scientist perception and priorities for data quality and data quality assurance skills needed in genome annotation.  ...  (in press, 2011). Prioritization of data quality dimensions and skills requirements in genome annotation work.  ... 
doi:10.1002/asi.21652 fatcat:nimqhiu6y5fcbhjwkincelqiju

Genomics data curation roles, skills and perception of data quality

Hong Huang, Corinne Jörgensen, Besiki Stvilia
2015 Library & Information Science Research  
This study examines how genomics scientists' perceived priorities for data quality and data quality skills differ when assuming different roles played in genomics data curation work.  ...  Scientists with different curation roles (including that of end user) may focus on different data quality aspects and skills requirements in a community curation environment.  ...  Introduction scientists' perspectives regarding data quality and skills requirements in genome curation work becomes increasingly important.  ... 
doi:10.1016/j.lisr.2014.08.003 fatcat:qnekvrl44zbpnmembzkegdacsu

Domain knowledge and data quality perceptions in genome curation work

Hong Huang
2015 Journal of Documentation  
Domain knowledge and data quality perceptions in genome curation work. Journal of Documentation. 2  ...  The findings may help develop data quality assurance policies and training seminars and maximize the efficiency of genome data management. Cited as: Huang, H. (in press).  ...  Such skills, as well as other annotation and data mining skills, could facilitate the curation activities, data quality assurance, and data provenance services in genome curation work.  ... 
doi:10.1108/jd-08-2013-0104 fatcat:pyy5iwqnhngi7h745t224f5zmi

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Rute Pereira, Jorge Oliveira, Mário Sousa
2020 Journal of Clinical Medicine  
Even with the huge achievements made in NGS technology and bioinformatics, further improvements in bioinformatic algorithms are still required to deal with complex and genetically heterogeneous disorders  ...  overview of the NGS technology and workflow.  ...  Conflicts of Interest: The authors declare no conflict of interest. J. Clin. Med. 2020, 9, 132  ... 
doi:10.3390/jcm9010132 pmid:31947757 pmcid:PMC7019349 fatcat:on74xvbjmzcwdndq4ylnzrxxte

Immediate Dissemination of Student Discoveries to a Model Organism Database Enhances Classroom-Based Research Experiences

Emily A. Wiley, Nicholas A. Stover, Sarah Elgin
2014 CBE - Life Sciences Education  
Working toward these goals, we designed guides for course-based research aimed to fulfill the need for functional annotation of the Tetrahymena thermophila genome, and developed an interactive Web database  ...  Use of inquiry-based research modules in the classroom has soared over recent years, largely in response to national calls for teaching that provides experience with scientific processes and methodologies  ...  ACKNOWLEDGMENTS We gratefully acknowledge Douglas Chalker and Joshua Smith for their critical contributions to building the Ciliate Genomics Consortium and thank J.  ... 
doi:10.1187/cbe.13-07-0140 pmid:24591511 pmcid:PMC3940453 fatcat:ls67e7jl4zgxtl65axqwfmqz54

MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs

R. M. Podowski, E. L. L. Sonnhammer
2001 Bioinformatics  
This thesis explores the hypothesis that computational methods can facilitate the identification and characterization of poorly annotated genes.  ...  The bioinformatics approaches to this problem assist researchers in advancing our understanding of the functional of human protein encoding genes.  ...  The work, which addresses both diverse types of genomics data and a broad set of computational approaches, is united by the hypothesis that computational approaches to genomics data analysis can assist  ... 
doi:10.1093/bioinformatics/17.7.656 pmid:11448885 fatcat:bmepasqiznhvdabpxrnwlzqy2q

Plateforme numérique pour l'antibiorésistance, ABRomics [article]

Claudine Médigue, Philippe Glaser, Consortium ABRomics
2021 Zenodo  
The integration and analysis of omics data with associated metadata requires the development of databases accessible to the community, the automatic use of standard pipelines for genomic and metagenomic  ...  In order to detect and understand emergence phenomena in time and space it is necessary to archive genomic and phenotypic data in a sustainable way.  ...  Interactions with WP2 will be required in order to address metagenomic data processing with standardized pipelines of ABROmics and pangenome annotation for antimicrobial resistance genes, virulence factors  ... 
doi:10.5281/zenodo.5230261 fatcat:lhtpmfwdjnddhi6cdilfpccc7q

Selected abstracts of "Bioinformatics: from Algorithms to Applications 2020" conference

2020 BMC Bioinformatics  
P8 Installing and searching BLAST databases in a data science framework Graham Alvare 1 , Abiel Roche-Lima 2 , Brian Fristensky 3* Acknowledgments This research was supported by the Russian Science  ...  P10 Transcriptomic signatures of seed maturation heterochrony in garden pea (Pisum sativum L) accessions Acknowledgments This work was financially supported by the Russian Science Foundation (Grant No  ...  In the future, the user of our pipeline can submit metagenome assemblies or raw reads to the input and receive annotated viral genomes from the data.  ... 
doi:10.1186/s12859-020-03838-2 pmid:33327929 fatcat:2t65jee32rgsnohhdwd7vbwj74

Biosurveillance enterprise for operational awareness, a genomic-based approach for tracking pathogen virulence

Willy A Valdivia-Granda
2013 Virulence  
The extent to which isolates can be compared depends not only on the quality of the sequence data available, but in the quality of the "data about the data" and the implementation of decentralized analysis  ...  This effort consists in the integration, annotation, disambiguation, evaluation, and representation of genomic and open source metadata information to conduct assessment including available and projected  ... 
doi:10.4161/viru.26893 pmid:24152965 pmcid:PMC3925708 fatcat:wo62eik5ljdrrnuv4madfmz6iq

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

Gholson J Lyon, Kai Wang
2012 Genome Medicine  
Acknowledgements We apologize to those whose work we could not cite due to reference limitations.  ...  We thank Peter Krawitz, Degui Zhi, Shane McCarthy, Jason O'Rawe, Edwin Nyambi, Reid Robison and three anonymous reviewers for helpful comments and suggestions for the manuscript.  ...  Figure 1 . 1 Two approaches for prioritizing disease causal genes from whole-genome or exome sequencing data.  ... 
doi:10.1186/gm359 pmid:22830651 pmcid:PMC3580414 fatcat:c6ui7sn4gfetjbmvuqe4becloi

ExpressionDB: An open source platform for distributing genome-scale datasets

Laura D. Hughes, Scott A. Lewis, Michael E. Hughes, Chun-Hsi Huang
2017 PLoS ONE  
We estimate that a demo database can be created in under one hour with minimal programming experience, and that a new database with user-supplied expression data can be completed and online in less than  ...  ExpressionDB is based on Shiny, a customizable web application which allows data sharing locally and online with customizable code written in R.  ...  Work in the Hughes Lab is supported by an award from NIAMS (1R21AR069266) and start-up funds from the Department of Medicine at Washington University in St. Louis. Author Contributions  ... 
doi:10.1371/journal.pone.0187457 pmid:29095940 pmcid:PMC5667849 fatcat:qt333b2fyrdalonofa7l53kygq

Landscape of Big Medical Data: A Pragmatic Survey on Prioritized Tasks

Zhifei Zhang, Wanling Gao, Fan Zhang, Yunyou Huang, Shaopeng Dai, Fanda Fan, Jianfeng Zhan, Mengjia Du, Silin Yin, Longxin Xiong, Juan Du, Yumei Cheng (+4 others)
2019 IEEE Access  
Second, what are the prioritized tasks in clinician research and practices utilizing big medical data? And do we have enough publicly available data sets for performing those tasks?  ...  Fifth, what are the performance gaps of the state-of-the-practice and state-of-the-art systems handling big medical data currently or in the future?  ...  He has been involved in clinical work of general surgery for more than 20 years and is skilled in the treatments of benign and malignant liver tumors, gastrointestinal benign and malignant tumors, benign  ... 
doi:10.1109/access.2019.2891948 fatcat:d7yabam6zbdpxdojd4vfeth2rq

Directions for research and training in plant omics: Big Questions and Big Data

Cristiana T. Argueso, Sarah M. Assmann, Kenneth D. Birnbaum, Sixue Chen, José R. Dinneny, Colleen J. Doherty, Andrea L. Eveland, Joanna Friesner, Vanessa R. Greenlee, Julie A. Law, Amy Marshall-Colón, Grace Alex Mason (+8 others)
2019 Plant Direct  
The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through  ...  In this white paper, we provide a summary of the discussions and insights arising from the second ART-21 workshop.  ...  and epigenomic approaches, require only high-quality genome sequence information.  ... 
doi:10.1002/pld3.133 pmid:31245771 pmcid:PMC6589541 fatcat:gwcnbgow3jcqlpzth7ufcotazi

Landscape of Big Medical Data: A Pragmatic Survey on Prioritized Tasks [article]

Zhifei Zhang, Wanling Gao, Fan Zhang, Yunyou Huang, Shaopeng Dai, Fanda Fan, Jianfeng Zhan, Mengjia Du, Silin Yin, Longxin Xiong, Juan Du, Yumei Cheng, Xiexuan Zhou, Rui Ren (+2 others)
2019 arXiv   pre-print
Second, what are the prioritized tasks in clinician research and practices utilizing big medical data? And do we have enough publicly available data sets for performing those tasks?  ...  Fifth, what are the performance gaps of state-of-the-practice and state-of-the-art systems handling big medical data currently or in future?  ...  The worst of all, the knowledge and skills in both fields are very professional, which seriously challenges multi-disciplinary collaboration.  ... 
arXiv:1901.00642v1 fatcat:fak46q7bgzesll6y4h7i6mcysi

BRCA Share: A Collection of Clinical BRCA Gene Variants

Christophe Béroud, Stanley I. Letovsky, Corey D. Braastad, Sandrine M. Caputo, Olivia Beaudoux, Yves Jean Bignon, Brigitte Bressac-De Paillerets, Myriam Bronner, Crystal M. Buell, Gwenaëlle Collod-Béroud, Florence Coulet, Nicolas Derive (+25 others)
2016 Human Mutation  
Germline variants in the BRCA1 and BRCA2 genes can confer substantial lifetime risk of breast and ovarian cancer.  ...  BRCA Share TM databases can therefore be considered as models of successful data sharing between private companies and the academic world.  ...  ClinVar has implemented a star rating system to provide an indication of annotation quality.  ... 
doi:10.1002/humu.23113 pmid:27633797 fatcat:7e7zqhdhbfhoppxgmrdjv3i4qi
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