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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.  ...  directions BioMart 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

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  
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide.  ...  The latest version of the portal comes with many new databases that have been created by our ever-growing community.  ...  Figure 1 . 1 BioMart community databases and their host countries. Figure 2 . 2 The network graphic output of the BioMart enrichment tool.  ... 
doi:10.1093/nar/gkv350 pmid:25897122 pmcid:PMC4489294 fatcat:vg2axbtz5rauti5yac74id57k4

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Houcemeddine Othman, Lyndon Zass, Jorge E. B. da Rocha, Fouzia Radouani, Chaimae Samtal, Ichrak Benamri, Judit Kumuthini, Yasmina J. Fakim, Yosr Hamdi, Nessrine Mezzi, Maroua Boujemaa, Chiamaka Jessica Okeke (+24 others)
2022 Journal of Personalized Medicine  
To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations.  ...  The portal and its corresponding technical documentation, implementation code and content are publicly available.  ...  Second, we aim to increase engagement with the scientific community involved in genomic medicine research in Africa by promoting the portal to the wider community, establishing an extended network of experts  ... 
doi:10.3390/jpm12020265 pmid:35207753 pmcid:PMC8879570 fatcat:s6fu5apwpbgzvmhcpa4i6rtz2m

Biowep: a workflow enactment portal for bioinformatics applications

Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Luciano Milanesi
2007 BMC Bioinformatics  
The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity  ...  Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing.  ...  Acknowledgements This work was partially supported by the Italian Ministry of Education, University and Research (MIUR), projects "Oncology over Internet -O 2 I" and "Laboratory of Interdisciplinary Technologies  ... 
doi:10.1186/1471-2105-8-s1-s19 pmid:17430563 pmcid:PMC1885848 fatcat:qwul45szxjgufievmtcsyqkeiq

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Faisal M Fadlelmola, Kais Ghedira, Yosr Hamdi, Mariem Hanachi, Fouzia Radouani, Imane Allali, Anmol Kiran, Lyndon Zass, Nihad Alsayed, Meriem Fassatoui, Chaimae Samtal, Samah Ahmed (+15 others)
2021 Database: The Journal of Biological Databases and Curation  
The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate  ...  Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal]  ...  The authors would also like to thank the H3ABioNet Central Node at the University of Cape Town for organizing the second hackathon.  ... 
doi:10.1093/database/baab016 pmid:33864455 pmcid:PMC8052916 fatcat:q654gkgvoncthov3ur64cwsyxi

Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development

Yina Du, Joseph A Kitzmiller, Anusha Sridharan, Anne K Perl, James P Bridges, Ravi S Misra, Gloria S Pryhuber, Thomas J Mariani, Soumyaroop Bhattacharya, Minzhe Guo, S Steven Potter, Phillip Dexheimer (+4 others)
2017 Thorax  
Lung Gene Expression Analysis (LGEA) web portal is an extended version of LungGENS useful for the analysis, display and interpretation of gene expression patterns obtained from single cells, sorted cell  ...  LungGENS', our previously developed web tool for mapping single-cell gene expression in the developing lung, has been well received by the pulmonary research community.  ...  Open Access This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build  ... 
doi:10.1136/thoraxjnl-2016-209598 pmid:28070014 pmcid:PMC5520249 fatcat:wqakukq3vrdhrai42ocngptiai

Online resources of cancer data: barriers, benefits and lessons

E. Gadaleta, N. R. Lemoine, C. Chelala
2010 Briefings in Bioinformatics  
With advances in high-throughput techniques, the volume of data generated has resulted in the creation of a plethora of resources for the cancer research community.  ...  cancer databases.  ...  All BioMart-powered resources can be accessed via the BioMart central portal (Table 1 ) [22] .  ... 
doi:10.1093/bib/bbq010 pmid:20348133 fatcat:tinslegov5hyxnx44bm2qvz6ua

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  
of the MIRRI infrastructure.  ...  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  ...  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

DAPPER: a data-mining resource for protein-protein interactions

Syed Haider, Zoltan Lipinszki, Marcin R. Przewloka, Yaseen Ladak, Pier Paolo D'Avino, Yuu Kimata, Pietro Lio', David M. Glover
2015 BioData Mining  
The identification of protein interaction networks can offers insights into the molecular mechanisms that regulate many biological processes.  ...  The identification of interaction networks between proteins and complexes holds the promise of offering novel insights into the molecular mechanisms that regulate many biological processes.  ...  The database is also made available through the BioMart Central Portal [11] .  ... 
doi:10.1186/s13040-015-0063-3 pmid:26405458 pmcid:PMC4581157 fatcat:xovfrzrgkvdifjxpwet76ufpsm

Towards BioDBcore: a community-defined information specification for biological databases

P. Gaudet, A. Bairoch, D. Field, S.-A. Sansone, C. Taylor, T. K. Attwood, A. Bateman, J. A. Blake, C. J. Bult, J. M. Cherry, R. L. Chisholm, G. Cochrane (+26 others)
2011 Database: The Journal of Biological Databases and Curation  
For example, the MIBBI (Minimum Information for Biological and Biomedical Investigations) portal [http://mibbi.org; (8) ] contains over 30 MI checklists.  ...  Having a uniform system for describing biological databases available in a single, centralized location would benefit both users and database providers: it would be much easier for users to find appropriate  ... 
doi:10.1093/database/baq027 pmid:21205783 pmcid:PMC3017395 fatcat:zfghil52nramtih22wxuqe2xqq

Solutions for data integration in functional genomics: a critical assessment and case study

D. Smedley, M. A. Swertz, K. Wolstencroft, G. Proctor, M. Zouberakis, J. Bard, J. M. Hancock, P. Schofield
2008 Briefings in Bioinformatics  
We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval.  ...  with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases.  ...  BioMart query optimized data management system BioMart is an open-source, data management system that can act as a central access point to provide interoperability between databases of interest.  ... 
doi:10.1093/bib/bbn040 pmid:19112082 fatcat:6hoxfuktznhkbcfemik2rb4jqq

SigReannot-mart: a query environment for expression microarray probe re-annotations

F. Moreews, G. Rauffet, P. Dehais, C. Klopp
2011 Database: The Journal of Biological Databases and Curation  
The oligo set is then used for several years. During this time period, the knowledge gathered by the community on the genome and the transcriptome increases and gets more precise.  ...  It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.  ...  Haider,S., Ballester,B., Smedley,D. et al. (2009) BioMart Central Portal-unified access to biological data. Nucleic Acids Res., 37, W23-W27. 12. Bioconductor R packages.  ... 
doi:10.1093/database/bar025 pmid:21930501 pmcid:PMC3263592 fatcat:djqqni2zyvda7douxmifnc6sti

Data Integration in Genomic Medicine: Trends and Applications

J. A. Seoane, V. Aguiar-Pulido, A. Pazos, J. Dorado
2012 IMIA Yearbook of Medical Informatics  
All the genomic data, as well as other 'omics' and clinical data necessary for personalized medicine, are stored in several distributed databases.  ...  In that precise moment, genomic medicine will be fundamental for clinical practice, as an essential key of personalized medicine.  ...  Acknowledgments This work is supported by the following projects: "Ibero-American Network of the Nano-Bio-Info-Cogno Convergent Technologies", Ibero-NBIC Network (209RT-0366) funded by CYTED (Spain), "  ... 
doi:10.1055/s-0038-1639441 fatcat:hz5gpjymdzdwrnmxantc3g4qom

EMMA--mouse mutant resources for the international scientific community

P. Wilkinson, J. Sengerova, R. Matteoni, C.-K. Chen, G. Soulat, A. Ureta-Vidal, S. Fessele, M. Hagn, M. Massimi, K. Pickford, R. H. Butler, S. Marschall (+14 others)
2009 Nucleic Acids Research  
The European Mouse Mutant Archive (EMMA) is a leading international network infrastructure for archiving and worldwide provision of mouse mutant strains.  ...  The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website.  ...  ACKNOWLEDGEMENTS The authors would like to thank the members of the EMMA Technical Working Group, Board of  ... 
doi:10.1093/nar/gkp799 pmid:19783817 pmcid:PMC2808872 fatcat:o66qke2t6vbb7bk6h5za27xpfm

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

Delphine Steinbach, Michael Alaux, Joelle Amselem, Nathalie Choisne, Sophie Durand, Raphaël Flores, Aminah-Olivia Keliet, Erik Kimmel, Nicolas Lapalu, Isabelle Luyten, Célia Michotey, Nacer Mohellibi (+5 others)
2013 Database: The Journal of Biological Databases and Curation  
GnpIS: an information system to integrate genetic and genomic data from plants and fungi.  ...  Acknowledgements We are very grateful to all our INRA and Genoplante colleagues for their submissions of data and for their participation in bioinformatics meetings to help define and enrich the GnpIS  ...  INRA has also accumulated large volumes of data for genetic improvement of wheat. GnpIS stores these data, offering an integrated view to the wheat research community ( Figure 3 ).  ... 
doi:10.1093/database/bat058 pmid:23959375 pmcid:PMC3746681 fatcat:kdk4jjbmavcm5lradzvo42nxjy
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