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

Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Andrew; Bonierbale, Merideth; Brookes, Anthony J.; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cédric; Carlson, Joseph W.; Chelala, Claude; Chrysostomou, Charalambos; Cittaro, Davide; Collin, Olivier; Cordova, Raul; Cutts, Rosalind J.; Dassi, Erik; Genova, Alex Di; Djari, Anis; Esposito, Anthony; Estrella, Heather; Eyras, Eduardo; Fernandez-Banet, Julio; Forbes, Simon; Free, Robert C.; Fujisawa, Takatomo; Gadaleta, Emanuela; Garcia-Manteiga, Jose M.; Goodstein, David; Gray, Kristian; Guerra-Assunção, José Afonso; Haggarty, Bernard; Han, Dong-Jin; Han, Byung Woo; Harris, Todd; Harshbarger, Jayson; Hastings, Robert K.; Hayes, Richard D.; Hoede, Claire; Hu, Shen; Hu, Zhi-Liang; Hutchins, Lucie; Kan, Zhengyan; Kawaji, Hideya; Keliet, Aminah; Kerhornou, Arnaud; Kim, Sunghoon; Kinsella, Rhoda; Klopp, Christophe; Kong, Lei; Lawson, Daniel; Lazarevic, Dejan; Lee, Ji-Hyun; Letellier, Thomas; Li, Chuan-Yun; Lio, Pietro; Liu, Chu-Jun; Luo, Jie; Maass, Alejandro; Mariette, Jerome; Maurel, Thomas; Merella, Stefania; Mohamed, Azza Mostafa; Moreews, Francois; Nabihoudine, Ibounyamine; Ndegwa, Nelson; Noirot, Céline; Perez-Llamas, Cristian; Primig, Michael; Quattrone, Alessandro; Quesneville, Hadi; Rambaldi, Davide; Reecy, James; Riba, Michela; Rosanoff, Steven; Saddiq, Amna Ali; Salas, Elisa; Sallou, Olivier; Shepherd, Rebecca; Simon, Reinhard; Sperling, Linda; Spooner, William; Staines, Daniel M.; Steinbach, Delphine; Stone, Kevin; Stupka, Elia; Teague, Jon W.; Dayem Ullah, Abu Z.; Wang, Jun; Ware, Doreen; Wong-Erasmus, Marie; Youens-Clark, Ken; Zadissa, Amonida; Zhang, Shi-Jian; Kasprzyk, Arek

doi:10.1093/nar/gkv350

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

Journal Article · Mon Apr 20 00:00:00 EDT 2015 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkv350· OSTI ID:1904113

Smedley, Damian ^[1]; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Andrew; Bonierbale, Merideth; Brookes, Anthony J.; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cédric; Carlson, Joseph W. more »

Wellcome Trust Sanger Institute, Hinxton (United Kingdom). et al.; OSTI

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 portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. 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 maintained by specialized organizations.

View Accepted Manuscript (DOE)

Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Contributing Organization:: Collaboration

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1904113

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: W1 Vol. 43; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Differences in Whole Blood Gene Expression Associated with Infection Time-Course and Extent of Fetal Mortality in a Reproductive Model of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection Wilkinson, Jamie M.; Ladinig, Andrea; Bao, Hua PLOS ONE, Vol. 11, Issue 4 https://doi.org/10.1371/journal.pone.0153615	journal	April 2016
Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics Mazzoni, Gianluca; Salleh, Suraya M.; Freude, Kristine PLOS ONE, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pone.0175464	journal	April 2017
The Differences in Local Translatome across Distinct Neuron Types Is Mediated by Both Baseline Cellular Differences and Post-transcriptional Mechanisms Ouwenga, Rebecca; Lake, Allison M.; Aryal, Shivani eneuro, Vol. 5, Issue 6 https://doi.org/10.1523/eneuro.0320-18.2018	journal	November 2018
Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds Turner-Hissong, Sarah D.; Bird, Kevin A.; Lipka, Alexander E. G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 11 https://doi.org/10.1534/g3.120.401240	journal	November 2020
The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence. Ivanova, Ivayla; Much, Christian; Di Giacomo, Monica Elsevier BV https://doi.org/10.17863/cam.17910	journalarticle	January 2017
Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. Whitworth, James; Smith, Philip S.; Martin, Jose-Ezequiel Elsevier BV https://doi.org/10.17863/cam.26291	journalarticle	January 2018
DAPPER: a data-mining resource for protein-protein interactions Haider, Syed; Lipinszki, Zoltan; Przewloka, Marcin R. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.4762	text	January 2015
Oncogenomic portals for the visualization and analysis of genome-wide cancer data Klonowska, Katarzyna; Czubak, Karol; Wojciechowska, Marzena Oncotarget, Vol. 7, Issue 1 https://doi.org/10.18632/oncotarget.6128	journal	October 2015
Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity Skinkyte-Juskiene, Ruta; Kogelman, Lisette J. A.; Kadarmideen, Haja N. Current Genomics, Vol. 19, Issue 4 https://doi.org/10.2174/1389202918666171005095059	journal	March 2018
A Population Genomics Analysis of the Native Irish Galway Sheep Breed McHugo, Gillian P.; Browett, Sam; Randhawa, Imtiaz A. S. Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00927	journal	October 2019
E2F4 Promotes Neuronal Regeneration and Functional Recovery after Spinal Cord Injury in Zebrafish Sasagawa, Shota; Nishimura, Yuhei; Hayakawa, Yuka Frontiers in Pharmacology, Vol. 7 https://doi.org/10.3389/fphar.2016.00119	journal	May 2016
A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments Vekris, Antonios; Pilalis, Eleftherios; Chatziioannou, Aristotelis Frontiers in Physiology, Vol. 10 https://doi.org/10.3389/fphys.2019.01160	journal	September 2019
Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines Schulten, Hans-Juergen; Bakhashab, Sherin International Journal of Molecular Sciences, Vol. 20, Issue 13 https://doi.org/10.3390/ijms20133173	journal	June 2019
transPLANT Resources for Triticeae Genomic Data Spannagl, Manuel; Alaux, Michael; Lange, Matthias The Plant Genome, Vol. 9, Issue 1 https://doi.org/10.3835/plantgenome2015.06.0038	journal	March 2016
FANTOM5 CAGE profiles of human and mouse samples Noguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro ETH Zurich https://doi.org/10.3929/ethz-b-000227683	text	January 2017
Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data Barron, Martin; Li, Jun arXiv https://doi.org/10.48550/arxiv.1605.04492	preprint	January 2016
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism Angione, Claudio arXiv https://doi.org/10.48550/arxiv.1809.08289	text	January 2018
Recombination, Meiotic Expression And Human Codon Usage Pouyet, Fanny; Mouchiroud, Dominique; Duret, Laurent Zenodo https://doi.org/10.5281/zenodo.835063	text	January 2017
Additional file 10 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251071	dataset	January 2020
Additional file 1 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251074.v1	dataset	January 2020
Additional file 2 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251077.v1	dataset	January 2020
Additional file 3 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251080.v1	dataset	January 2020
Additional file 4 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251083	dataset	January 2020
Additional file 5 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251086	dataset	January 2020
Additional file 6 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251089.v1	dataset	January 2020
Additional file 7 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251092	dataset	January 2020
Additional file 8 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251095	dataset	January 2020
Additional file 9 of FishDB: an integrated functional genomics database for fishes Yang, Liandong; Xu, Zetan; Zeng, Honghui figshare https://doi.org/10.6084/m9.figshare.13251098	dataset	January 2020
Additional file 2 of Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes Tan, Liqiang; Cheng, Weisheng; Liu, Fang figshare https://doi.org/10.6084/m9.figshare.14776528	dataset	January 2021
Additional file 10 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21258933.v1	dataset	January 2022
Additional file 11 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21258939.v1	dataset	January 2022
Additional file 14 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21258948.v1	dataset	January 2022
Additional file 21 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21258975	dataset	January 2022
Additional file 23 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21258981	dataset	January 2022
Additional file 7 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21259014.v1	dataset	January 2022
Additional file 9 of Transcriptomic analysis of paternal behaviors in prairie voles Duclot, Florian; Liu, Yan; Saland, Samantha K. figshare https://doi.org/10.6084/m9.figshare.21259020.v1	dataset	January 2022
Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice Kojima, Mina L.; de Rooij, Dirk G.; Page, David C. eLife, Vol. 8 https://doi.org/10.7554/elife.43738	journal	February 2019
The myogenic electric organ ofSternopygus macrurus: a non-contractile tissue with a skeletal muscle transcriptome Pinch, Matthew; Güth, Robert; Samanta, Manoj P. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.1828	journal	April 2016

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