The neXtProt knowledgebase on human proteins: current status

被引:72
作者
Gaudet, Pascale [1 ,2 ]
Michel, Pierre-Andre [1 ]
Zahn-Zabal, Monique [1 ]
Cusin, Isabelle [1 ]
Duek, Paula D. [1 ]
Evalet, Olivier [1 ]
Gateau, Alain [1 ]
Gleizes, Anne [1 ]
Pereira, Mario [1 ]
Teixeira, Daniel [1 ]
Zhang, Ying [1 ]
Lane, Lydie [1 ,2 ]
Bairoch, Amos [1 ,2 ]
机构
[1] SIB Swiss Inst Bioinformat, CALIPHO Grp, CH-1211 Geneva, Switzerland
[2] Univ Geneva, Fac Med, Dept Human Prot Sci, CH-1211 Geneva, Switzerland
关键词
HUMAN PROTEOME; PLATFORM; DATABASE; CANCER;
D O I
10.1093/nar/gku1178
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
neXtProt (http://www.nextprot.org) is a human protein-centric knowledgebase developed at the SIB Swiss Institute of Bioinformatics. Focused solely on human proteins, neXtProt aims to provide a state of the art resource for the representation of human biology by capturing a wide range of data, precise annotations, fully traceable data provenance and a web interface which enables researchers to find and view information in a comprehensive manner. Since the introductory neXtProt publication, significant advances have been made on three main aspects: the representation of proteomics data, an extended representation of human variants and the development of an advanced search capability built around semantic technologies. These changes are presented in the current neXtProt update.
引用
收藏
页码:D764 / D770
页数:7
相关论文
共 27 条
[1]   Database resources of the National Center for Biotechnology Information [J].
Acland, Abigail ;
Agarwala, Richa ;
Barrett, Tanya ;
Beck, Jeff ;
Benson, Dennis A. ;
Bollin, Colleen ;
Bolton, Evan ;
Bryant, Stephen H. ;
Canese, Kathi ;
Church, Deanna M. ;
Clark, Karen ;
DiCuccio, Michael ;
Dondoshansky, Ilya ;
Federhen, Scott ;
Feolo, Michael ;
Geer, Lewis Y. ;
Gorelenkov, Viatcheslav ;
Hoeppner, Marilu ;
Johnson, Mark ;
Kelly, Christopher ;
Khotomlianski, Viatcheslav ;
Kimchi, Avi ;
Kimelman, Michael ;
Kitts, Paul ;
Krasnov, Sergey ;
Kuznetsov, Anatoliy ;
Landsman, David ;
Lipman, David J. ;
Lu, Zhiyong ;
Madden, Thomas L. ;
Madej, Tom ;
Maglott, Donna R. ;
Marchler-Bauer, Aron ;
Karsch-Mizrachi, Ilene ;
Murphy, Terence ;
Ostell, James ;
O'Sullivan, Christopher ;
Panchenko, Anna ;
Phan, Lon ;
Pruitt, Don Preussm Kim D. ;
Rubinstein, Wendy ;
Sayers, Eric W. ;
Schneider, Valerie ;
Schuler, Gregory D. ;
Sequeira, Edwin ;
Sherry, Stephen T. ;
Shumway, Martin ;
Sirotkin, Karl ;
Siyan, Karanjit ;
Slotta, Douglas .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D7-D17
[2]  
[Anonymous], 2014, CURRENT PROTOCOLS BI
[3]   Activities at the Universal Protein Resource (UniProt) [J].
Apweiler, Rolf ;
Bateman, Alex ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Alpi, Emanuele ;
Antunes, Ricardo ;
Arganiska, Joanna ;
Casanova, Elisabet Barrera ;
Bely, Benoit ;
Bingley, Mark ;
Bonilla, Carlos ;
Britto, Ramona ;
Bursteinas, Borisas ;
Chan, Wei Mun ;
Chavali, Gayatri ;
Cibrian-Uhalte, Elena ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dogan, Tunca ;
Fazzini, Francesco ;
Gane, Paul ;
Castro, Leyla Garcia ;
Garmiri, Penelope ;
Hatton-Ellis, Emma ;
Hieta, Reija ;
Huntley, Rachael ;
Legge, Duncan ;
Liu, Wudong ;
Luo, Jie ;
MacDougall, Alistair ;
Mutowo, Prudence ;
Nightingale, Andrew ;
Orchard, Sandra ;
Pichler, Klemens ;
Poggioli, Diego ;
Pundir, Sangya ;
Pureza, Luis ;
Qi, Guoying ;
Rosanoff, Steven ;
Saidi, Rabie ;
Sawford, Tony ;
Shypitsyna, Aleksandra ;
Turner, Edward ;
Volynkin, Vladimir ;
Wardell, Tony ;
Watkins, Xavier ;
Zellner, Hermann ;
Corbett, Matt .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D191-D198
[4]  
Bastian F, 2008, LECT N BIOINFORMAT, V5109, P124, DOI 10.1007/978-3-540-69828-9_12
[5]   MINT, the molecular interaction database: 2009 update [J].
Ceol, Arnaud ;
Aryamontri, Andrew Chatr ;
Licata, Luana ;
Peluso, Daniele ;
Briganti, Leonardo ;
Perfetto, Livia ;
Castagnoli, Luisa ;
Cesareni, Gianni .
NUCLEIC ACIDS RESEARCH, 2010, 38 :D532-D539
[6]   A guided tour of the Trans-Proteomic Pipeline [J].
Deutsch, Eric W. ;
Mendoza, Luis ;
Shteynberg, David ;
Farrah, Terry ;
Lam, Henry ;
Tasman, Natalie ;
Sun, Zhi ;
Nilsson, Erik ;
Pratt, Brian ;
Prazen, Bryan ;
Eng, Jimmy K. ;
Martin, Daniel B. ;
Nesvizhskii, Alexey I. ;
Aebersold, Ruedi .
PROTEOMICS, 2010, 10 (06) :1150-1159
[7]   The UniProt-GO Annotation database in 2011 [J].
Dimmer, Emily C. ;
Huntley, Rachael P. ;
Alam-Faruque, Yasmin ;
Sawford, Tony ;
O'Donovan, Claire ;
Martin, Maria J. ;
Bely, Benoit ;
Browne, Paul ;
Chan, Wei Mun ;
Eberhardt, Ruth ;
Gardner, Michael ;
Laiho, Kati ;
Legge, Duncan ;
Magrane, Michele ;
Pichler, Klemens ;
Poggioli, Diego ;
Sehra, Harminder ;
Auchincloss, Andrea ;
Axelsen, Kristian ;
Blatter, Marie-Claude ;
Boutet, Emmanuel ;
Braconi-Quintaje, Silvia ;
Breuza, Lionel ;
Bridge, Alan ;
Coudert, Elizabeth ;
Estreicher, Anne ;
Famiglietti, Livia ;
Ferro-Rojas, Serenella ;
Feuermann, Marc ;
Gos, Arnaud ;
Gruaz-Gumowski, Nadine ;
Hinz, Ursula ;
Hulo, Chantal ;
James, Janet ;
Jimenez, Silvia ;
Jungo, Florence ;
Keller, Guillaume ;
Lemercier, Phillippe ;
Lieberherr, Damien ;
Masson, Patrick ;
Moinat, Madelaine ;
Pedruzzi, Ivo ;
Poux, Sylvain ;
Rivoire, Catherine ;
Roechert, Bernd ;
Schneider, Michael ;
Stutz, Andre ;
Sundaram, Shyamala ;
Tognolli, Michael ;
Bougueleret, Lydie .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D565-D570
[8]   State of the Human Proteome in 2013 as Viewed through PeptideAtlas: Comparing the Kidney, Urine, and Plasma Proteomes for the Biology- and Disease-Driven Human Proteome Project [J].
Farrah, Terry ;
Deutsch, Eric W. ;
Omenn, Gilbert S. ;
Sun, Zhi ;
Watts, Julian D. ;
Yamamoto, Tadashi ;
Shteynberg, David ;
Harris, Micheleen M. ;
Moritz, Robert L. .
JOURNAL OF PROTEOME RESEARCH, 2014, 13 (01) :60-75
[9]   Current status and new features of the Consensus Coding Sequence database [J].
Farrell, Catherine M. ;
O'Leary, Nuala A. ;
Harte, Rachel A. ;
Loveland, Jane E. ;
Wilming, Laurens G. ;
Wallin, Craig ;
Diekhans, Mark ;
Barrell, Daniel ;
Searle, Stephen M. J. ;
Aken, Bronwen ;
Hiatt, Susan M. ;
Frankish, Adam ;
Suner, Marie-Marthe ;
Rajput, Bhanu ;
Steward, Charles A. ;
Brown, Garth R. ;
Bennett, Ruth ;
Murphy, Michael ;
Wu, Wendy ;
Kay, Mike P. ;
Hart, Jennifer ;
Rajan, Jeena ;
Weber, Janet ;
Snow, Catherine ;
Riddick, Lillian D. ;
Hunt, Toby ;
Webb, David ;
Thomas, Mark ;
Tamez, Pamela ;
Rangwala, Sanjida H. ;
McGarvey, Kelly M. ;
Pujar, Shashikant ;
Shkeda, Andrei ;
Mudge, Jonathan M. ;
Gonzalez, Jose M. ;
Gilbert, James G. R. ;
Trevanion, Stephen J. ;
Baertsch, Robert ;
Harrow, Jennifer L. ;
Hubbard, Tim ;
Ostell, James M. ;
Haussler, David ;
Pruitt, Kim D. .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D865-D872
[10]   Ensembl 2014 [J].
Flicek, Paul ;
Amode, M. Ridwan ;
Barrell, Daniel ;
Beal, Kathryn ;
Billis, Konstantinos ;
Brent, Simon ;
Carvalho-Silva, Denise ;
Clapham, Peter ;
Coates, Guy ;
Fitzgerald, Stephen ;
Gil, Laurent ;
Giron, Carlos Garcia ;
Gordon, Leo ;
Hourlier, Thibaut ;
Hunt, Sarah ;
Johnson, Nathan ;
Juettemann, Thomas ;
Kaehaeri, Andreas K. ;
Keenan, Stephen ;
Kulesha, Eugene ;
Martin, Fergal J. ;
Maurel, Thomas ;
McLaren, William M. ;
Murphy, Daniel N. ;
Nag, Rishi ;
Overduin, Bert ;
Pignatelli, Miguel ;
Pritchard, Bethan ;
Pritchard, Emily ;
Riat, Harpreet S. ;
Ruffier, Magali ;
Sheppard, Daniel ;
Taylor, Kieron ;
Thormann, Anja ;
Trevanion, Stephen J. ;
Vullo, Alessandro ;
Wilder, Steven P. ;
Wilson, Mark ;
Zadissa, Amonida ;
Aken, Bronwen L. ;
Birney, Ewan ;
Cunningham, Fiona ;
Harrow, Jennifer ;
Herrero, Javier ;
Hubbard, Tim J. P. ;
Kinsella, Rhoda ;
Muffato, Matthieu ;
Parker, Anne ;
Spudich, Giulietta ;
Yates, Andy .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D749-D755