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Genome Warehouse: A Public Repository Housing Genome-scale Data
[article]
2021
bioRxiv
pre-print
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The Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing ...
Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. ...
dot and 102 an incremental number to represent the version (e.g., GWHAAAA00000000.1). 103
Database components 104 GWH is a centralized resource housing genome-scale data, with the purpose to 105 archive ...
doi:10.1101/2021.02.10.430367
fatcat:ywnzqmoan5dulgz42xlmfs5y3y
PhycoMine: A Microalgae Data Warehouse
[article]
2021
bioRxiv
pre-print
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PhycoMine is data warehouse system created to fostering the analysis of complex and integrated data from microalgae species in a single computational environment. ...
These widgets were created to facilitate data visualization of the gene expression levels in different experimental setups, for which RNA-seq experimental data is available in data repositories. ...
Finally, a script developed in house in R language, processed the data by tximport function, generating the resulting file in a table format that contains the levels of genetic expression and can be included ...
doi:10.1101/2021.09.27.462046
fatcat:weto5ctrwbgprdq3ze4nqoqzea
Migrating a research data warehouse to a public cloud: challenges and opportunities
2021
JAMIA Journal of the American Medical Informatics Association
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Objective Clinical research data warehouses (RDWs) linked to genomic pipelines and open data archives are being created to support innovative, complex data-driven discoveries. ...
We describe our experience in migrating a multi-institutional RDW to a public cloud. Materials and Methods This study is descriptive. ...
Compass as a data steward of fully identified patient clinical and genomic data. ...
doi:10.1093/jamia/ocab278
pmid:34919694
pmcid:PMC8922165
fatcat:d4xflguhyvbmze2necxfmzpmsa
Information and Communication Technology
[chapter]
2007
Warehouse Management
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The aim is to provide a representative example of a research institution in the wider field of information and communications technology (ICT), with a specific focus on cognitive interaction and robotics ...
After a brief introduction to the general structure and mission of CITEC, we will discuss the general scope of the case study, as well as how the methods presented in the introduction to this book have ...
In particular, the module enables the management of a local publication repository which is synchronised with the PUB repository. ...
doi:10.1007/978-3-540-35220-4_7
fatcat:dluy52mstbeqxkrynauxq2ejem
TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery
2011
PLoS ONE
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An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation. ...
It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. ...
In the post-genomic era, attempts at function annotation increasingly employ data from different types of repositories. ...
doi:10.1371/journal.pone.0017844
pmid:21408081
pmcid:PMC3050930
fatcat:fvfqc77ymjfmlmviaqhb6wjkha
Six methodological steps to build medical data warehouses for research
2006
International Journal of Medical Informatics
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Medical data repositories Privacy Ontology building Requirement elicitation Long-term care for elderly a b s t r a c t Purpose: We propose a simple methodology for heterogeneous data collection and central ...
We developed this methodology by the lessons learned when we had to build a data repository, containing information about elderly patients flows in the UK's long-term care system (LTC). ...
Acknowledgements We thank Teresa Temple and Peter Crowther from the London Borough of Merton Social Services Department for providing data and feedback during model development, and Peter Millard, visiting ...
doi:10.1016/j.ijmedinf.2006.04.003
pmid:16762589
fatcat:nwogqatcufefhmyy6hswywnnzi
Data integration and genomic medicine
2007
Journal of Biomedical Informatics
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We conclude this paper with challenges still not addressed in genomic medicine and gaps that remain in data integration research to facilitate genomic medicine. ...
These data integration concepts and methodologies are then aligned with informatics challenges in genomic medicine and presented as potential solutions. ...
Data cleansing is difficult in a federation. No data is housed locally so data cleansing must be done on-the fly [37] . ...
doi:10.1016/j.jbi.2006.02.007
pmid:16574494
fatcat:mndnwkzzpzcu5ayqyg2ohyc75u
InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor
2012
Genome Biology
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However, multiple hurdles related to data management stand in the way of their efficient large-scale utilization. The solution proposed is a web-based data storage hub. ...
Having clear focus, flexibility and adaptability, InSilico DB seamlessly connects genomics dataset repositories to state-of-the-art and free GUI and command-line data analysis tools. ...
are also grateful to Michael Reich, Ted Liefeld, and Peter Carr of the GenePattern and GenomeSpace development teams for their help in the implementation of the InSilico DB/GenePattern and GenomeSpace data ...
doi:10.1186/gb-2012-13-11-r104
pmid:23158523
pmcid:PMC3580496
fatcat:riwbfy7t6zbkzoygltew3wrkia
TEMBLOR – Perspectives of EBI Database Services
2002
Comparative and Functional Genomics
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The availability of complete genomic data allows a whole range of new large-scale experiments such as the generation of whole-genome gene expression data, high-throughput protein identification by mass ...
same time allowing easy submission to the public repository after publication. ...
doi:10.1002/cfg.133
pmid:18628871
pmcid:PMC2447230
fatcat:mm66zbhv4rcy5lfi6722twzf54
Applying data warehouse concepts to gene expression data management
2001
Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)
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In this paper we present a method for applying data warehouse and on-line analytical processing concepts to gene expression data management. ...
This method has been employed in developing the data management system that is used to host Gene Logic's GeneExpress® database products. ...
Resources (NCGR) (see http://www.ncgr.org/genex/index.html), with alternative proposals for organizing gene expression data as part of their efforts to establish public gene expression data repositories ...
doi:10.1109/bibe.2001.974413
dblp:conf/bibe/MarkowitzT01
fatcat:ff4ue4dlwrhkbm7sd6av7vyzp4
Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing
2017
Journal of Personalized Medicine
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To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health ...
The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic. ...
Implementation of the Warehouse
Genomic Data Warehouse The Mayo Clinic genomic data warehouse system is built on the Oracle Translational Research Center (Oracle TRC) product, which provides a central ...
doi:10.3390/jpm7030007
pmid:28829408
pmcid:PMC5618153
fatcat:es2rfye7bzha3g5btqaia6dr7q
Perceptions toward establishing a biobank and clinical data warehouse: Voices from the community
2014
Clinical Nursing Studies
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This qualitative pilot project was designed to engage the community in the planning process of establishing a Biobank and Clinical Data Warehouse. ...
This is a pivotal time in health care, especially in lieu of the evolving genomic era. ...
A clinical data warehouse is a facility or repository that houses all electronic health and clinical data. ...
doi:10.5430/cns.v2n3p97
fatcat:6lkqv6i2sjanrf4li3aprqotuy
Database Resources of the National Genomics Data Center in 2020
2019
Nucleic Acids Research
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The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. ...
Newly released resources include three human genome databases (PGG.SNV, PGG.Han and CGVD), eLMSG, EWAS Data Hub, GWAS Atlas, iSheep and PADS Arsenal. ...
ACKNOWLEDGEMENTS We thank a number of users for submitting data, sending suggestions, reporting bugs and getting involving in community curation. ...
doi:10.1093/nar/gkz913
pmid:31702008
pmcid:PMC7145560
fatcat:rx2p2whldnh5zpg2pyjs3mtaba
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework
2016
Database: The Journal of Biological Databases and Curation
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This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. ...
We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. ...
Comparisons with Similar Resources As a data warehouse, TargetMine is not an alternative to large public databases, rather it is designed to provide an alternative usage to collate and summarize biological ...
doi:10.1093/database/baw009
pmid:26989145
pmcid:PMC4795931
fatcat:g32ewsxnb5gq5chad742fww2ia
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
[article]
2018
bioRxiv
pre-print
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gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. ...
produced by the International Wheat Genome Sequencing Consortium. ...
The IWGSC data repository is thus hosted by URGI to support public and private 53 parties in data management as well as analysis and usage of the sequence data. ...
doi:10.1101/363259
fatcat:n326wu2jqjg4rewisgqneijgta
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