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

Research output: Contribution to journalArticle

264 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)W589-W598
JournalNucleic Acids Research
Volume43
Issue numberW1
DOIs
Publication statusPublished - 2015

Fingerprint

Organizations
Databases
Computer Communication Networks
Information Services
Genomics
Proteomics
Technology
Neoplasms
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., ... Kasprzyk, A. (2015). The BioMart community portal: An innovative alternative to large, centralized data repositories. Nucleic Acids Research, 43(W1), W589-W598. https://doi.org/10.1093/nar/gkv350

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; Di Genova, Alex; 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.

In: Nucleic Acids Research, Vol. 43, No. W1, 2015, p. W589-W598.

Research output: Contribution to journalArticle

Smedley, D, Haider, S, Durinck, S, Pandini, L, Provero, P, Allen, J, Arnaiz, O, Awedh, MH, Baldock, R, Barbiera, G, Bardou, P, Beck, T, Blake, A, Bonierbale, M, Brookes, AJ, Bucci, G, Buetti, I, Burge, S, Cabau, C, Carlson, JW, Chelala, C, Chrysostomou, C, Cittaro, D, Collin, O, Cordova, R, Cutts, RJ, Dassi, E, Di Genova, A, Djari, A, Esposito, A, Estrella, H, Eyras, E, Fernandez-Banet, J, Forbes, S, Free, RC, Fujisawa, T, Gadaleta, E, Garcia-Manteiga, JM, Goodstein, D, Gray, K, Guerra-Assunção, JA, Haggarty, B, Han, DJ, Han, BW, Harris, T, Harshbarger, J, Hastings, RK, Hayes, RD, Hoede, C, Hu, S, Hu, ZL, Hutchins, L, Kan, Z, Kawaji, H, Keliet, A, Kerhornou, A, Kim, S, Kinsella, R, Klopp, C, Kong, L, Lawson, D, Lazarevic, D, Lee, JH, Letellier, T, Li, CY, Lio, P, Liu, CJ, Luo, J, Maass, A, Mariette, J, Maurel, T, Merella, S, Mohamed, AM, 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, AA, Salas, E, Sallou, O, Shepherd, R, Simon, R, Sperling, L, Spooner, W, Staines, DM, Steinbach, D, Stone, K, Stupka, E, Teague, JW, Dayem Ullah, AZ, Wang, J, Ware, D, Wong-Erasmus, M, Youens-Clark, K, Zadissa, A, Zhang, SJ & Kasprzyk, A 2015, 'The BioMart community portal: An innovative alternative to large, centralized data repositories', Nucleic Acids Research, vol. 43, no. W1, pp. W589-W598. https://doi.org/10.1093/nar/gkv350
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 ; Di Genova, Alex ; 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. / The BioMart community portal : An innovative alternative to large, centralized data repositories. In: Nucleic Acids Research. 2015 ; Vol. 43, No. W1. pp. W589-W598.
@article{8e68839fb60540d2868c3c4ca9b2fa59,
title = "The BioMart community portal: An innovative alternative to large, centralized data repositories",
abstract = "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.",
author = "Damian Smedley and Syed Haider and Steffen Durinck and Luca Pandini and Paolo Provero and James Allen and Olivier Arnaiz and Awedh, {Mohammad Hamza} and Richard Baldock and Giulia Barbiera and Philippe Bardou and Tim Beck and Andrew Blake and Merideth Bonierbale and Brookes, {Anthony J.} and Gabriele Bucci and Iwan Buetti and Sarah Burge and C{\'e}dric Cabau and Carlson, {Joseph W.} and Claude Chelala and Charalambos Chrysostomou and Davide Cittaro and Olivier Collin and Raul Cordova and Cutts, {Rosalind J.} and Erik Dassi and {Di Genova}, Alex and Anis Djari and Anthony Esposito and Heather Estrella and Eduardo Eyras and Julio Fernandez-Banet and Simon Forbes and Free, {Robert C.} and Takatomo Fujisawa and Emanuela Gadaleta and Garcia-Manteiga, {Jose M.} and David Goodstein and Kristian Gray and Guerra-Assun{\cc}{\~a}o, {Jos{\'e} Afonso} and Bernard Haggarty and Han, {Dong Jin} and Han, {Byung Woo} and Todd Harris and Jayson Harshbarger and Hastings, {Robert K.} and Hayes, {Richard D.} and Claire Hoede and Shen Hu and Hu, {Zhi Liang} and Lucie Hutchins and Zhengyan Kan and Hideya Kawaji and Aminah Keliet and Arnaud Kerhornou and Sunghoon Kim and Rhoda Kinsella and Christophe Klopp and Lei Kong and Daniel Lawson and Dejan Lazarevic and Lee, {Ji Hyun} and Thomas Letellier and Li, {Chuan Yun} and Pietro Lio and Liu, {Chu Jun} and Jie Luo and Alejandro Maass and Jerome Mariette and Thomas Maurel and Stefania Merella and Mohamed, {Azza Mostafa} and Francois Moreews and Ibounyamine Nabihoudine and Nelson Ndegwa and C{\'e}line Noirot and Cristian Perez-Llamas and Michael Primig and Alessandro Quattrone and Hadi Quesneville and Davide Rambaldi and James Reecy and Michela Riba and Steven Rosanoff and Saddiq, {Amna Ali} and Elisa Salas and Olivier Sallou and Rebecca Shepherd and Reinhard Simon and Linda Sperling and William Spooner and Staines, {Daniel M.} and Delphine Steinbach and Kevin Stone and Elia Stupka and Teague, {Jon W.} and {Dayem Ullah}, {Abu Z.} and Jun Wang and Doreen Ware and Marie Wong-Erasmus and Ken Youens-Clark and Amonida Zadissa and Zhang, {Shi Jian} and Arek Kasprzyk",
year = "2015",
doi = "10.1093/nar/gkv350",
language = "English",
volume = "43",
pages = "W589--W598",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = ". This work is written by (a) US Government employee(s) and is in the public domain in the US",
number = "W1",

}

TY - JOUR

T1 - The BioMart community portal

T2 - An innovative alternative to large, centralized data repositories

AU - Smedley, Damian

AU - Haider, Syed

AU - Durinck, Steffen

AU - Pandini, Luca

AU - Provero, Paolo

AU - Allen, James

AU - Arnaiz, Olivier

AU - Awedh, Mohammad Hamza

AU - Baldock, Richard

AU - Barbiera, Giulia

AU - Bardou, Philippe

AU - Beck, Tim

AU - Blake, Andrew

AU - Bonierbale, Merideth

AU - Brookes, Anthony J.

AU - Bucci, Gabriele

AU - Buetti, Iwan

AU - Burge, Sarah

AU - Cabau, Cédric

AU - Carlson, Joseph W.

AU - Chelala, Claude

AU - Chrysostomou, Charalambos

AU - Cittaro, Davide

AU - Collin, Olivier

AU - Cordova, Raul

AU - Cutts, Rosalind J.

AU - Dassi, Erik

AU - Di Genova, Alex

AU - Djari, Anis

AU - Esposito, Anthony

AU - Estrella, Heather

AU - Eyras, Eduardo

AU - Fernandez-Banet, Julio

AU - Forbes, Simon

AU - Free, Robert C.

AU - Fujisawa, Takatomo

AU - Gadaleta, Emanuela

AU - Garcia-Manteiga, Jose M.

AU - Goodstein, David

AU - Gray, Kristian

AU - Guerra-Assunção, José Afonso

AU - Haggarty, Bernard

AU - Han, Dong Jin

AU - Han, Byung Woo

AU - Harris, Todd

AU - Harshbarger, Jayson

AU - Hastings, Robert K.

AU - Hayes, Richard D.

AU - Hoede, Claire

AU - Hu, Shen

AU - Hu, Zhi Liang

AU - Hutchins, Lucie

AU - Kan, Zhengyan

AU - Kawaji, Hideya

AU - Keliet, Aminah

AU - Kerhornou, Arnaud

AU - Kim, Sunghoon

AU - Kinsella, Rhoda

AU - Klopp, Christophe

AU - Kong, Lei

AU - Lawson, Daniel

AU - Lazarevic, Dejan

AU - Lee, Ji Hyun

AU - Letellier, Thomas

AU - Li, Chuan Yun

AU - Lio, Pietro

AU - Liu, Chu Jun

AU - Luo, Jie

AU - Maass, Alejandro

AU - Mariette, Jerome

AU - Maurel, Thomas

AU - Merella, Stefania

AU - Mohamed, Azza Mostafa

AU - Moreews, Francois

AU - Nabihoudine, Ibounyamine

AU - Ndegwa, Nelson

AU - Noirot, Céline

AU - Perez-Llamas, Cristian

AU - Primig, Michael

AU - Quattrone, Alessandro

AU - Quesneville, Hadi

AU - Rambaldi, Davide

AU - Reecy, James

AU - Riba, Michela

AU - Rosanoff, Steven

AU - Saddiq, Amna Ali

AU - Salas, Elisa

AU - Sallou, Olivier

AU - Shepherd, Rebecca

AU - Simon, Reinhard

AU - Sperling, Linda

AU - Spooner, William

AU - Staines, Daniel M.

AU - Steinbach, Delphine

AU - Stone, Kevin

AU - Stupka, Elia

AU - Teague, Jon W.

AU - Dayem Ullah, Abu Z.

AU - Wang, Jun

AU - Ware, Doreen

AU - Wong-Erasmus, Marie

AU - Youens-Clark, Ken

AU - Zadissa, Amonida

AU - Zhang, Shi Jian

AU - Kasprzyk, Arek

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84979860632&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84979860632&partnerID=8YFLogxK

U2 - 10.1093/nar/gkv350

DO - 10.1093/nar/gkv350

M3 - Article

C2 - 25897122

AN - SCOPUS:84979860632

VL - 43

SP - W589-W598

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -