The BioMart community portal: an innovative alternative to large, centralized data repositories
Open accessAbstract
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.
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Only one-to-one ortholog associations were used to obtain a conservative measure of agreement between human and mouse H3K27me3 cluster gene assignments.
“Finally, we considered only one-to-one associations in order to obtain a conservative measure of agreement between cross-species H3K27me3 cluster gene assignment.”
From H3.3K27M Cooperates with Trp53 Loss and PDGFRA Gain in Mouse Embryonic Neural Progenitor Cells to Induce Invasive High-Grade Gliomas (2017) · cites this paper as Smedley et al., 2015
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- Authors
- Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, A. J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J. W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, R. J., Dassi, E., Genova, A. D., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R. C., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, J. M., Goodstein, D., Gray, K., Guerra-Assunção, J. A., Haggarty, B., Han, D.-J., Han, B. W., Harris, T., Harshbarger, J., Hastings, R. K., Hayes, R. D., Hoede, C., Hu, S., Hu, Z.-L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J.-H., Letellier, T., Li, C.-Y., Lio, P., Liu, C.-J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A. M., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, A. A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, D. M., Steinbach, D., Stone, K., Stupka, E., Teague, J. W., Dayem Ullah, A. Z., Wang, J., Ware, D., Wong-Erasmus, M., Youens-Clark, K., Zadissa, A., Zhang, S.-J., & Kasprzyk, A.
- Affiliations
- Wellcome Sanger Institute (GB)
- University of Oxford (GB)
- Genentech (US)
- University of Turin (IT)
- European Bioinformatics Institute (GB)
- Université Paris-Sud (FR)
- King Abdulaziz University (SA)
- Western General Hospital (GB)
- Institut National de la Recherche Agronomique (FR)
- University of Leicester (GB)
- Mary Lyon Centre at MRC Harwell (GB)
- International Potato Center (PE)
- Joint Genome Institute (US)
- Queen Mary University of London (GB)
- Institut national de recherche en sciences et technologies du numérique (FR)
- University of Trento (IT)
- Center for Mathematical Modeling (CL)
- Genotoul coordination (FR)
- Pfizer (United States) (US)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Kazusa DNA Research Institute (JP)
- Seoul National University (KR)
- Ontario Institute for Cancer Research (CA)
- RIKEN (JP)
- University of California, Los Angeles (US)
- Iowa State University (US)
- Jackson Laboratory (US)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Peking University (CN)
- Karolinska Institutet (SE)
- Universitat Pompeu Fabra (ES)
- Inserm (FR)
- Cold Spring Harbor Laboratory (US)
- Corresponding author
- Kasprzyk, Arek
- ORCID
- Smedley, Damian
- Haider, Syed
- Provero, Paolo
- Allen, James
- Arnaiz, Olivier
- Awedh, Mohammad Hamza
- Baldock, Richard
- Bardou, Philippe
- Beck, Tim
- Blake, Andrew
- Bonierbale, Merideth
- Brookes, Anthony J.
- Bucci, Gabriele
- Burge, Sarah
- Cabau, Cédric
- Carlson, Joseph W.
- Chelala, Claude
- Chrysostomou, Charalambos
- Cittaro, Davide
- Collin, Olivier
- Cutts, Rosalind J.
- Dassi, Erik
- Genova, Alex Di
- Djari, Anis
- Eyras, Eduardo
- Fernandez-Banet, Julio
- Free, Robert C.
- Fujisawa, Takatomo
- Gadaleta, Emanuela
- Goodstein, David
- Gray, Kristian
- Haggarty, Bernard
- Han, Byung Woo
- Harris, Todd
- Harshbarger, Jayson
- Hastings, Robert K.
- Hayes, Richard D.
- Hoede, Claire
- Hu, Shen
- Kan, Zhengyan
- Kawaji, Hideya
- Kerhornou, Arnaud
- Klopp, Christophe
- Kong, Lei
- Lawson, Daniel
- Lee, Ji-Hyun
- Luo, Jie
- Maass, Alejandro
- Maurel, Thomas
- Merella, Stefania
- Mohamed, Azza Mostafa
- Ndegwa, Nelson
- Noirot, Céline
- Primig, Michael
- Quattrone, Alessandro
- Quesneville, Hadi
- Reecy, James
- Riba, Michela
- Rosanoff, Steven
- Saddiq, Amna Ali
- Salas, Elisa
- Sallou, Olivier
- Shepherd, Rebecca
- Simon, Reinhard
- Sperling, Linda
- Staines, Daniel M.
- Steinbach, Delphine
- Stupka, Elia
- Teague, Jon W.
- Ware, Doreen
- Zadissa, Amonida
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-04-20
- Volume
- 43
- Issue
- W1
- Pages
- W589-W598
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4489294
- OpenAlex
- W2109488005
- Cited by
- 755
- References
- 54
- Citations by year
- 2026: 22 · 2025: 27 · 2024: 47 · 2023: 46 · 2022: 97 · 2021: 87 · 2020: 91 · 2019: 99 · 2018: 70 · 2017: 74 · 2016: 64 · 2015: 28 · 2013: 1
- FWCI
- 35.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion, cc-by)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
- Iowa State University Digital Repository (Iowa State University) (submittedVersion, other-oa)
- Americanae (AECID Library) (submittedVersion, cc-by-nc-nd)
- Americanae (AECID Library) (submittedVersion, other-oa)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, other-oa)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-nd)
- Leicester Research Archive (University of Leicester) (submittedVersion, cc-by)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Wellcome Trust (095908, WT095908, 077012/Z/05/Z, WT 098051, 077012)
- European Molecular Biology Laboratory
- Universitat Pompeu Fabra
- Breast Cancer Campaign
- National Research Foundation
- Agence Nationale de la Recherche (ANR-12-BSV6-0017, ANR-14-CE10-0005, ANR-10-BLAN-1122, DE-AC02-05CH11231, ANR-12, ANR-10)
- Ministry of Education, Culture, Sports, Science and Technology (DE-AC02-05CH11231)
- Ministry of Science, ICT and Future Planning (2013M3A6A4043695)
- National Research Foundation of Korea (DE‐AC02‐05‐CH11231)
- King Abdulaziz University
- Centre National de la Recherche Scientifique (DE-AC02-05CH11231)
- Fundación Sandra Ibarra de Solidaridad Frente al Cáncer (FSI2013, CSD2009-00080, BIO2011-23920)
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
- RIKEN
- National Human Genome Research Institute (U41HG003345)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- BioMart, enrichment analysis, web services, data visualization tools, genomic data, proteomics data, cancer data, scalable data storage
- MeSH terms
- Database Management Systems, Humans, Neoplasms, Internet, Genomics, Proteomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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