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BioMart Central Portal: an open database network for the biological community
2011
Database: The Journal of Biological Databases and Curation
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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
2015
Nucleic Acids Research
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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
2022
Journal of Personalized Medicine
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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
2007
BMC Bioinformatics
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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
2021
Database: The Journal of Biological Databases and Curation
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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
2017
Thorax
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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
2010
Briefings in Bioinformatics
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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
2015
Zenodo
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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
2015
BioData Mining
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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
2011
Database: The Journal of Biological Databases and Curation
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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
2008
Briefings in Bioinformatics
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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
2011
Database: The Journal of Biological Databases and Curation
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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
2012
IMIA Yearbook of Medical Informatics
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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
2009
Nucleic Acids Research
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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
2013
Database: The Journal of Biological Databases and Curation
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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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