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The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck (+93 others)
2015 Nucleic Acids Research  
Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores  ...  The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide.  ...  much more cost-effective alternative to the large data stores maintained by specialized organizations.  ... 
doi:10.1093/nar/gkv350 pmid:25897122 pmcid:PMC4489294 fatcat:vg2axbtz5rauti5yac74id57k4

BioMart Central Portal: an open database network for the biological community

J. M. Guberman, J. Ai, O. Arnaiz, J. Baran, A. Blake, R. Baldock, C. Chelala, D. Croft, A. Cros, R. J. Cutts, A. Di Genova, S. Forbes (+49 others)
2011 Database: The Journal of Biological Databases and Curation  
For users, Central Portal offers a central repository for a vast array of biological data.  ...  Central Portal is constantly evolving thanks to the efforts of the community that supports it and contributes data.  ... 
doi:10.1093/database/bar041 pmid:21930507 pmcid:PMC3263598 fatcat:sypgedelfncfbflx4d7skx2v6a

BioMart: driving a paradigm change in biological data management

A. Kasprzyk
2011 Database: The Journal of Biological Databases and Curation  
Building on the wealth of information that has become accessible through the BioMart interface, the BioMart Central Portal (15) has introduced an innovative alternative to the large data stores maintained  ...  It is an ambition of the BioMart community that the BioMart project remains at the forefront of innovative solutions for biological data management in the years to come.  ... 
doi:10.1093/database/bar049 pmid:22083790 pmcid:PMC3215098 fatcat:nv2fjtmggvgh3nx75yhszghbze

BioMart: a data federation framework for large collaborative projects

J. Zhang, S. Haider, J. Baran, A. Cros, J. M. Guberman, J. Hsu, Y. Liang, L. Yao, A. Kasprzyk
2011 Database: The Journal of Biological Databases and Curation  
Secure communication between BioMart servers is an essential part of the BioMart data federation.  ...  Moreover, as a centralized, permanent resource, the Central Registry can reliably be used to coordinate the creation of large data portals: changes in independently administered data sources can be tracked  ... 
doi:10.1093/database/bar038 pmid:21930506 pmcid:PMC3175789 fatcat:i3657e4ghjgbpl3j3jj3j6r3ja

D8.4_Mirri_Report On Comparison Of Various Integration Software Operating In Life Sciences

B. Bunk, DP Colobraro, P. Dawyndt, P. De Vos, F.O. Glöckner, A. Kopf, V. Robert, P. Romano, D. Smith, C. Söhngen, F. Van Hauwenhuyse, A. Vasilenko
2015 Zenodo  
The objective of this deliverable is the analysis of some data integration architectures and tools in Life Sciences to determine their respective advantages and disadvantages in meeting the objectives  ...  of the MIRRI infrastructure.  ...  The BioMart Central Portal is a community-driven effort able to provide unified access to many biological databases.  ... 
doi:10.5281/zenodo.49968 fatcat:72fy55qtjfgbrecrkslp25s5he

Cre recombinase resources for conditional mouse mutagenesis

Damian Smedley, Ekaterina Salimova, Nadia Rosenthal
2011 Methods  
This chapter provides an update on the current state of Cre driver mouse lines worldwide, and reviews the available public databases and portals that capture critical details of Cre driver lines such as  ...  , to allow the creation of somatic mutations in defined genes.  ...  Acknowledgments We thank members of the CREATE consortium for their participation and contributions:  ... 
doi:10.1016/j.ymeth.2010.12.027 pmid:21195764 fatcat:itx3zx23czbkrp5237y5jodrue

Integration, Warehousing, and Analysis Strategies of Omics Data [chapter]

Srinubabu Gedela
2011 Msphere  
To explore a genome and downstream molecular processes, we need umpteen result at the various levels of cellul ar o rganization by utilizing different experimental designs , data an alysis strategies an  ...  Otnics" i a current uffix for numerous type of large-calc biological data generation procedures, which naturally demand the development of novel algorithm for data storage and analy i .  ...  (http://obi.sourceforge.net) is a collection of controlled vocabularies freely available to the biomedical community. Web- based ontology portals, such as the BioPortal (http://bioportal.  ... 
doi:10.1007/978-1-61779-027-0_18 pmid:21370094 fatcat:rkajbtgwtzdvpb3zmiuac5repq

The European Bioinformatics Institute's data resources

Catherine Brooksbank, Graham Cameron, Janet Thornton
2009 Nucleic Acids Research  
It has also put the need for unrestricted access to biological data at the centre of biology.  ...  and environmental science, has led to unprecedented growth in the amount of data generated.  ...  of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gkp986 pmid:19934258 pmcid:PMC2808956 fatcat:lha7vmv3fnhipb7kunhmvunveu

transPLANT Resources for Triticeae Genomic Data

Manuel Spannagl, Michael Alaux, Matthias Lange, Daniel M. Bolser, Kai C. Bader, Thomas Letellier, Erik Kimmel, Raphael Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer (+17 others)
2016 The Plant Genome  
Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and  ...  content, large sizes, and polyploidy.  ...  DAL were supported by the Leibniz Association (WGL) in the context of the Pakt für Forschung und Innovation/ WGL and the German Federal Ministry of Education and Research (BMBF) in the frame of the projects  ... 
doi:10.3835/plantgenome2015.06.0038 pmid:27898761 fatcat:qbt3ggpfgvbz3okorau7zvsnca

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang (+27 others)
2017 Nucleic Acids Research  
As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes  ...  , and user-defined omics data in the context of these pathways.  ...  that have helped us to improve the overall quality of Gramene as a community resource.  ... 
doi:10.1093/nar/gkx1111 pmid:29165610 pmcid:PMC5753211 fatcat:bxgarlrs6rab5lwpixua6gotgq

Cyberbiosecurity Challenges of Pathogen Genome Databases

Boris A. Vinatzer, Lenwood S. Heath, Hussain M. J. Almohri, Michael J. Stulberg, Christopher Lowe, Song Li
2019 Frontiers in Bioengineering and Biotechnology  
them hostage, or manipulating the data they contain.  ...  Also, while there is the potential to collect pathogen genomic data from infected individuals or agricultural and food products during disease outbreaks to improve disease modeling and forecast, how to  ...  Department of Agriculture and should not be construed to represent any agency determination or policy.  ... 
doi:10.3389/fbioe.2019.00106 pmid:31157218 pmcid:PMC6529814 fatcat:d2npjjees5cfbn2cdavc6zkuzi

An informatics project and online "Knowledge Centre" supporting modern genotype-to-phenotype research

Adam J. Webb, Gudmundur A. Thorisson, Anthony J. Brookes
2011 Human Mutation  
repository, and comprehensive data access portal.  ...  This employs established technologies such as the BioMart data integration system for large-scale data querying [Smedley et al., 2009] (http://www. biomart.org), and the DAS protocol for exchanging record  ... 
doi:10.1002/humu.21469 pmid:21438073 fatcat:ktr4z662qbbcri2etel6ooz73i

Data management in systems biology I - Overview and bibliography [article]

Gerhard Mayer
2009 arXiv   pre-print
An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data in large distributed research projects is given, the pros and cons  ...  reader should be enabled to decide which data management approach is the best suited for his special needs.  ...  Acknowledgements This work was supported by the Federal Ministry of Education and Research (BMBF, Berlin, Germany, HepatoSys systems biology funding initiative, grant 0313080F).  ... 
arXiv:0908.0411v3 fatcat:afmn52bffzb3zooqr3ptghvlcy

The bioinformatics tool box for reproductive biology

Michael Primig
2012 Biochimica et Biophysica Acta - Molecular Basis of Disease  
We are currently witnessing yet another quantum leap in our ability to monitor the flow of information from the genome via the transcriptome to the proteome: tiling arrays that cover both strands of a  ...  These technologies have spawned a thriving discipline within the bioinformatics field that employs information technology for managing and interpreting biological highthroughput data.  ...  Acknowledgements This work was supported by an Inserm Avenir grant R07216NS and an ARC grant No. 7985 awarded to M. Primig. I thank O. Collin and A.  ... 
doi:10.1016/j.bbadis.2012.05.018 pmid:22687534 fatcat:rjlfosfypndzladmwg5dcp3444

Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

Pradeep Kumar Sreenivasaiah, Do Han Kim
2010 Frontiers in Physiology  
Several solutions have been proposed to meet the expectations and novel methods have been developed to address the persisting problems of data integration.  ...  Having familiarized with the pros and cons of the existing technologies, researchers can exploit its capabilities to the maximum potential for integrating data.  ...  Here integration expects no data transfer to any one central repository. The design relies on an agreed data exchange protocol between the participating databases.  ... 
doi:10.3389/fphys.2010.00147 pmid:21423387 pmcid:PMC3059952 fatcat:3e72pyby35cidlaa6jr5llemuq
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