Human Proteinpedia enables sharing of human protein data

van Eyk, J.; Mathivanan, Suresh; Ahmed, Mukhtar; Bj�rling, Erik; Ahn, Natalie G.; Alexandre, Hainard; Amanchy, Ramars; Andrews, Philip C.; Bader, Joel S.; Nali, Anuradha; Balgley, Brian M.; Bantscheff, Marcus; Bennett, Keiryn L.; Bjorling, Erik; Blagoev, Blagoy; Bose, Ron; Björling, Erik; Brahmachari, Samir K.; Burlingame, Alma S.; Bustelo, Xosé R.; Cagney, Gerard; Cantin, Greg T.; Cardasis, Helene L.; Celis, Julio E.; Bj{̈o}rling, Erik; Chaerkady, Raghothama; Chu, Feixia; Cole, Philip A.; Costello, Catherine E.; Cotter, Robert J.; Crockett, David; DeLany, James P.; De Marzo, Angelo M.; DeSouza, Leroi V.; Deutsch, Eric W.; Dransfield, Eric; Drewes, Gerard; Droit, Arnaud; Dunn, Michael J.; Elenitoba-Johnson, Kojo; Ewing, Rob M.; Eyk, Jennifer Van; Van Eyk, Jennifer; Faca, Vitor; Falkner, Jayson A.; Fang, Xiangming; Fenselau, Catherine; Figeys, Daniel; Gagné, Pierre; Gelfi, Cecilia; Gevaert, Kris; Gimble, Jeffrey M.; Gnad, Florian; Goel, Renu; Gromov, Pavel; Hanash, Samir M.; Hancock, William Stephen; Harsha, Hc C.; Hart, Gerald; Hays, Faith; He, Fuchu; Korner, R.; Hebbar, Prashantha; Helsens, Kenny; Hermeking, Heiko; Hide, Winston; Hjernø, Karin; Hjern?, K.; Hochstrasser, Denis F.; Hofmann, Oliver; Horn, David M.; Hruban, Ralph H.; Ibarrola, Nieves; James, Peter; Jensen, Ole N.; Jensen, Pia Hønnerup; Jung, Peter; K{̈o}rner, Roman; Kandasamy, Kumaran; Kheterpal, Indu; Kikuno, Reiko F.; Korf, Ulrike; Körner, Roman; Kuster, Bernhard; Kwon, Min-Seok; Lobke, C.; Lee, Hyoung-Joo; Lee, Young-Jin; Lefevre, Michael; Siu, K. W. Michael; Lehvaslaiho, Minna; Lescuyer, Pierre; Levander, Fredrik; L{̈o}bke, Christian; Lim, Megan S.; Löbke, Christian; Loo, Joseph A.; Mann, Matthias; Martens, Lennart; Martinez-Heredia, Juan; McComb, Mark; McRedmond, James; Mehrle, Alexander; Menon, Rajasree; Miller, Christine A.; Mischak, Harald; Mohan, S. Sujatha; Mohmood, Riaz; Molina, Henrik; Gagn�, Pierre; Moran, Michael F.; Morgan, James D.; Moritz, Robert L.; Morzel, Martine; Muddiman, David C.; Nalli, Anuradha; Navarro, J. Daniel; Prasad, Ts Keshava; Neubert, Thomas A.; Ohara, Osamu; Oliva, Rafael; Omenn, Gilbert S.; Oyama, Masaaki; Paik, Young-Ki; Pennington, Kyla; Sujatha Mohan, S.; Pepperkok, Rainer; Periaswamy, Balamurugan; Petricoin, Emanuel F.; Poirier, Guy G.; Prasad, T. S. Keshava; Purvine, Samuel O.; Rahiman, B. Abdul; Siu, Kw Michael; Ramachandran, Prasanna; Ramachandra, Yl L.; Rice, Robert H.; Rick, Jens; Ronnholm, Ragna H.; Salonen, Johanna; Sanchez, Jean-Charles; Hjern�, Karin; Sayd, Thierry; Seshi, Beerelli; Shankari, Kripa; Sheng, Shi Jun; Shetty, Vivekananda; Shivakumar, K.; Simpson, Richard J.; Daniel Navarro, J.; Sirdeshmukh, Ravi; Michael Siu, K. W.; Smith, Jeffrey C.; Smith, Richard D.; States, David J.; Sugano, Sumio; Sullivan, Matthew; Marzo, A. M.; Superti-Furga, Giulio; Takatalo, Maarit; Thongboonkerd, Visith; Trinidad, Jonathan C.; Uhlen, Mathias; Vandekerckhove, Joël; Vasilescu, Julian; Keshava Prasad, T. S.; Veenstra, Timothy D.; Vidal-Taboada, José-Manuel; Vihinen, Mauno; Wait, Robin; Wang, Xiaoyue; Wiemann, Stefan; Abdul Rahiman, B.; Wu, Billy; Xu, Tao; Yates, John R.; Zhong, Jun; Zhou, Ming; Zhu, Yunping; K�rner, Roman; Zurbig, Petra; L�bke, Christian; Pandey, Akhilesh Pandey

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Catherine Costello
van Eyk et al., 2008

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Nature Research, Nature Biotechnology, 2(26), p. 164-167, 2008

DOI: 10.1038/nbt0208-164

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@article{van Eyk2008,
  abstract = {Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/ peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories. Even more difficult is the annotation and display of pertinent information in the context of the corresponding proteins. Wikipedia, an online encyclopedia that anyone can edit, has already proven quite successful1 and can be used as a model for sharing biological data. However, the need for experimental evidence, data standardization and ownership of data creates scientific obstacles.},
  author = {van Eyk, J. and Mathivanan, Suresh and Ahmed, Mukhtar and Bj�rling, Erik and Ahn, Natalie G. and Alexandre, Hainard and Amanchy, Ramars and Andrews, Philip C. and Bader, Joel S. and Nali, Anuradha and Balgley, Brian M. and Bantscheff, Marcus and Bennett, Keiryn L. and Bjorling, Erik and Blagoev, Blagoy and Bose, Ron and Björling, Erik and Brahmachari, Samir K. and Burlingame, Alma S. and Bustelo, Xosé R. and Cagney, Gerard and Cantin, Greg T. and Cardasis, Helene L. and Celis, Julio E. and Bj{̈o}rling, Erik and Chaerkady, Raghothama and Chu, Feixia and Cole, Philip A. and Costello, Catherine E. and Cotter, Robert J. and Crockett, David and DeLany, James P. and De Marzo, Angelo M. and DeSouza, Leroi V. and Deutsch, Eric W. and Dransfield, Eric and Drewes, Gerard and Droit, Arnaud and Dunn, Michael J. and Elenitoba-Johnson, Kojo and Ewing, Rob M. and Eyk, Jennifer Van and Van Eyk, Jennifer and Faca, Vitor and Falkner, Jayson A. and Fang, Xiangming and Fenselau, Catherine and Figeys, Daniel and Gagné, Pierre and Gelfi, Cecilia and Gevaert, Kris and Gimble, Jeffrey M. and Gnad, Florian and Goel, Renu and Gromov, Pavel and Hanash, Samir M. and Hancock, William Stephen and Harsha, Hc C. and Hart, Gerald and Hays, Faith and He, Fuchu and Korner, R. and Hebbar, Prashantha and Helsens, Kenny and Hermeking, Heiko and Hide, Winston and Hjernø, Karin and Hjern?, K. and Hochstrasser, Denis F. and Hofmann, Oliver and Horn, David M. and Hruban, Ralph H. and Ibarrola, Nieves and James, Peter and Jensen, Ole N. and Jensen, Pia Hønnerup and Jung, Peter and K{̈o}rner, Roman and Kandasamy, Kumaran and Kheterpal, Indu and Kikuno, Reiko F. and Korf, Ulrike and Körner, Roman and Kuster, Bernhard and Kwon, Min-Seok and Lobke, C. and Lee, Hyoung-Joo and Lee, Young-Jin and Lefevre, Michael and Siu, K. W. Michael and Lehvaslaiho, Minna and Lescuyer, Pierre and Levander, Fredrik and L{̈o}bke, Christian and Lim, Megan S. and Löbke, Christian and Loo, Joseph A. and Mann, Matthias and Martens, Lennart and Martinez-Heredia, Juan and McComb, Mark and McRedmond, James and Mehrle, Alexander and Menon, Rajasree and Miller, Christine A. and Mischak, Harald and Mohan, S. Sujatha and Mohmood, Riaz and Molina, Henrik and Gagn�, Pierre and Moran, Michael F. and Morgan, James D. and Moritz, Robert L. and Morzel, Martine and Muddiman, David C. and Nalli, Anuradha and Navarro, J. Daniel and Prasad, Ts Keshava and Neubert, Thomas A. and Ohara, Osamu and Oliva, Rafael and Omenn, Gilbert S. and Oyama, Masaaki and Paik, Young-Ki and Pennington, Kyla and Sujatha Mohan, S. and Pepperkok, Rainer and Periaswamy, Balamurugan and Petricoin, Emanuel F. and Poirier, Guy G. and Prasad, T. S. Keshava and Purvine, Samuel O. and Rahiman, B. Abdul and Siu, Kw Michael and Ramachandran, Prasanna and Ramachandra, Yl L. and Rice, Robert H. and Rick, Jens and Ronnholm, Ragna H. and Salonen, Johanna and Sanchez, Jean-Charles and Hjern�, Karin and Sayd, Thierry and Seshi, Beerelli and Shankari, Kripa and Sheng, Shi Jun and Shetty, Vivekananda and Shivakumar, K. and Simpson, Richard J. and Daniel Navarro, J. and Sirdeshmukh, Ravi and Michael Siu, K. W. and Smith, Jeffrey C. and Smith, Richard D. and States, David J. and Sugano, Sumio and Sullivan, Matthew and Marzo, A. M. and Superti-Furga, Giulio and Takatalo, Maarit and Thongboonkerd, Visith and Trinidad, Jonathan C. and Uhlen, Mathias and Vandekerckhove, Joël and Vasilescu, Julian and Keshava Prasad, T. S. and Veenstra, Timothy D. and Vidal-Taboada, José-Manuel and Vihinen, Mauno and Wait, Robin and Wang, Xiaoyue and Wiemann, Stefan and Abdul Rahiman, B. and Wu, Billy and Xu, Tao and Yates, John R. and Zhong, Jun and Zhou, Ming and Zhu, Yunping and K�rner, Roman and Zurbig, Petra and L�bke, Christian and Pandey, Akhilesh Pandey},
  doi = {10.1038/nbt0208-164},
  journal = {Nature Biotechnology},
  month = {jan},
  pages = {164-167},
  title = {Human Proteinpedia enables sharing of human protein data},
  url = {http://www.nature.com/articles/nbt0208-164.pdf},
  volume = {26},
  year = {2008}
}

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Human Proteinpedia enables sharing of human protein data

Journal article published in 2008 by J. van Eyk, Suresh Mathivanan, Mukhtar Ahmed, Erik Bj�rling, Natalie G. Ahn, Hainard Alexandre, Ramars Amanchy, Philip C. Andrews, Joel S. Bader, Anuradha Nali, Brian M. Balgley, Marcus Bantscheff, Keiryn L. Bennett, Erik Bjorling, Blagoy Blagoev and other authors. J. van Eyk, Suresh Mathivanan, Mukhtar Ahmed, Erik Bj�rling, Natalie G. Ahn, Hainard Alexandre, Ramars Amanchy, Philip C. Andrews, Joel S. Bader, Anuradha Nali, Brian M. Balgley, Marcus Bantscheff, Keiryn L. Bennett, Erik Bjorling, Blagoy Blagoev, Ron Bose, Erik Björling, Samir K. Brahmachari, Alma S. Burlingame, Xosé R. Bustelo, Gerard Cagney, Greg T. Cantin, Helene L. Cardasis, Julio E. Celis, Erik Bj{̈o}rling, Raghothama Chaerkady, Feixia Chu, Philip A. Cole, Catherine E. Costello

, Robert J. Cotter, David Crockett, James P. DeLany

, Angelo M. De Marzo, Leroi V. DeSouza, Eric W. Deutsch

, Eric Dransfield, Gerard Drewes, Arnaud Droit, Michael J. Dunn, Kojo Elenitoba-Johnson, Rob M. Ewing, Jennifer Van Eyk, Jennifer Van Eyk, Vitor Faca, Jayson A. Falkner, Xiangming Fang, Catherine Fenselau, Daniel Figeys, Pierre Gagné, Cecilia Gelfi, Kris Gevaert

, Jeffrey M. Gimble, Florian Gnad, Renu Goel, Pavel Gromov, Samir M. Hanash, William Stephen Hancock, Hc C. Harsha, Gerald Hart, Faith Hays, Fuchu He, R. Korner, Prashantha Hebbar, Kenny Helsens, Heiko Hermeking, Winston Hide

, Karin Hjernø, K. Hjern?, Denis F. Hochstrasser, Oliver Hofmann, David M. Horn, Ralph H. Hruban, Nieves Ibarrola, Peter James, Ole N. Jensen, Pia Hønnerup Jensen, Peter Jung, Roman K{̈o}rner, Kumaran Kandasamy, Indu Kheterpal, Reiko F. Kikuno, Ulrike Korf, Roman Körner, Bernhard Kuster, Min-Seok Kwon, C. Lobke, Hyoung-Joo Lee, Young-Jin Lee, Michael Lefevre, K. W. Michael Siu, Minna Lehvaslaiho, Pierre Lescuyer, Fredrik Levander, Christian L{̈o}bke, Megan S. Lim

, Christian Löbke, Joseph A. Loo, Matthias Mann, Lennart Martens

, Juan Martinez-Heredia, Mark McComb, James McRedmond, Alexander Mehrle, Rajasree Menon, Christine A. Miller, Harald Mischak, S. Sujatha Mohan, Riaz Mohmood, Henrik Molina, Pierre Gagn�, Michael F. Moran, James D. Morgan, Robert L. Moritz, Martine Morzel, David C. Muddiman, Anuradha Nalli, J. Daniel Navarro, Ts Keshava Prasad, Thomas A. Neubert, Osamu Ohara, Rafael Oliva, Gilbert S. Omenn, Masaaki Oyama, Young-Ki Paik, Kyla Pennington

, S. Sujatha Mohan, Rainer Pepperkok, Balamurugan Periaswamy, Emanuel F. Petricoin, Guy G. Poirier, T. S. Keshava Prasad, Samuel O. Purvine

, B. Abdul Rahiman, Kw Michael Siu, Prasanna Ramachandran, Yl L. Ramachandra, Robert H. Rice, Jens Rick, Ragna H. Ronnholm, Johanna Salonen, Jean-Charles Sanchez, Karin Hjern�, Thierry Sayd, Beerelli Seshi, Kripa Shankari, Shi Jun Sheng, Vivekananda Shetty, K. Shivakumar, Richard J. Simpson, J. Daniel Navarro, Ravi Sirdeshmukh, K. W. Michael Siu, Jeffrey C. Smith, Richard D. Smith

, David J. States, Sumio Sugano, Matthew Sullivan, A. M. Marzo, Giulio Superti-Furga

, Maarit Takatalo, Visith Thongboonkerd, Jonathan C. Trinidad, Mathias Uhlen, Joël Vandekerckhove, Julian Vasilescu, T. S. Keshava Prasad, Timothy D. Veenstra, José-Manuel Vidal-Taboada, Mauno Vihinen, Robin Wait, Xiaoyue Wang, Stefan Wiemann, B. Abdul Rahiman, Billy Wu, Tao Xu, John R. Yates, Jun Zhong, Ming Zhou, Yunping Zhu, Roman K�rner, Petra Zurbig, Christian L�bke, Akhilesh Pandey Pandey

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Abstract

Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/ peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories. Even more difficult is the annotation and display of pertinent information in the context of the corresponding proteins. Wikipedia, an online encyclopedia that anyone can edit, has already proven quite successful1 and can be used as a model for sharing biological data. However, the need for experimental evidence, data standardization and ownership of data creates scientific obstacles.

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Human Proteinpedia enables sharing of human protein data

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