CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

被引：29

作者：

Bleda, Marta ^{[1
,2
]}

Tarraga, Joaquin ^{[1
,3
]}

de Maria, Alejandro ^{[1
]}

Salavert, Francisco ^{[1
,2
]}

Garcia-Alonso, Luz ^{[1
]}

Celma, Matilde ^{[4
]}

Martin, Ainoha ^{[4
]}

Dopazo, Joaquin ^{[1
,2
,3
]}

Medina, Ignacio ^{[1
,3
]}

机构：

[1] CIPF, Dept Bioinformat & Genom, Valencia 46012, Spain

[2] CIBER Enfermedades Raras CIBERER, Valencia 46010, Spain

[3] CIPF, Funct Genom Node INB, Valencia 46012, Spain

[4] Univ Politecn Valencia, DSIC, Res Ctr Software Prod Methods ProS, Valencia 46007, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / W1期

关键词：

DATABASE; RESOURCE; TARGETS; CATALOG;

D O I：

10.1093/nar/gks575

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

引用

页码：W609 / W614

页数：6

共 23 条

[1]

A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[2]

Integrating common and rare genetic variation in diverse human populations [J].

Altshuler, David M. ;

Gibbs, Richard A. ;

Peltonen, Leena ;

Dermitzakis, Emmanouil ;

Schaffner, Stephen F. ;

Yu, Fuli ;

Bonnen, Penelope E. ;

de Bakker, Paul I. W. ;

Deloukas, Panos ;

Gabriel, Stacey B. ;

Gwilliam, Rhian ;

Hunt, Sarah ;

Inouye, Michael ;

Jia, Xiaoming ;

Palotie, Aarno ;

Parkin, Melissa ;

Whittaker, Pamela ;

Chang, Kyle ;

Hawes, Alicia ;

Lewis, Lora R. ;

Ren, Yanru ;

Wheeler, David ;

Muzny, Donna Marie ;

Barnes, Chris ;

Darvishi, Katayoon ;

Hurles, Matthew ;

Korn, Joshua M. ;

Kristiansson, Kati ;

Lee, Charles ;

McCarroll, Steven A. ;

Nemesh, James ;

Keinan, Alon ;

Montgomery, Stephen B. ;

Pollack, Samuela ;

Price, Alkes L. ;

Soranzo, Nicole ;

Gonzaga-Jauregui, Claudia ;

Anttila, Verneri ;

Brodeur, Wendy ;

Daly, Mark J. ;

Leslie, Stephen ;

McVean, Gil ;

Moutsianas, Loukas ;

Nguyen, Huy ;

Zhang, Qingrun ;

Ghori, Mohammed J. R. ;

McGinnis, Ralph ;

McLaren, William ;

Takeuchi, Fumihiko ;

Grossman, Sharon R. .

NATURE, 2010, 467 (7311) :52-58

[3]

Reorganizing the protein space at the Universal Protein Resource (UniProt) [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Casanova, Elisabet Barrera ;

Bely, Benoit ;

Bingley, Mark ;

Bower, Lawrence ;

Bursteinas, Borisas ;

Chan, Wei Mun ;

Chavali, Gayatri ;

Da Silva, Alan ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fazzini, Francesco ;

Fedotov, Alexander ;

Garavelli, John ;

Castro, Leyla Garcia ;

Gardner, Michael ;

Hieta, Reija ;

Huntley, Rachael ;

Jacobsen, Julius ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Pichler, Klemens ;

Poggioli, Diego ;

Pontikos, Nikolas ;

Pundir, Sangya ;

Rosanoff, Steven ;

Sawford, Tony ;

Sehra, Harminder ;

Turner, Edward ;

Wardell, Tony ;

Watkins, Xavier ;

Corbett, Matt ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Goujon, Mickael ;

McWilliam, Hamish ;

Lopez, Rodrigo ;

Xenarios, Ioannis ;

Bougueleret, Lydie ;

Bridge, Alan ;

Poux, Sylvain ;

Redaschi, Nicole .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D71-D75

[4]

The microRNA.org resource: targets and expression [J].

Betel, Doron ;

Wilson, Manda ;

Gabow, Aaron ;

Marks, Debora S. ;

Sander, Chris .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D149-D153

[5]

BioCatalogue: a universal catalogue of web services for the life sciences [J].

Bhagat, Jiten ;

Tanoh, Franck ;

Nzuobontane, Eric ;

Laurent, Thomas ;

Orlowski, Jerzy ;

Roos, Marco ;

Wolstencroft, Katy ;

Aleksejevs, Sergejs ;

Stevens, Robert ;

Pettifer, Steve ;

Lopez, Rodrigo ;

Goble, Carole A. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :W689-W694

[6]

Reactome: a database of reactions, pathways and biological processes [J].

Croft, David ;

O'Kelly, Gavin ;

Wu, Guanming ;

Haw, Robin ;

Gillespie, Marc ;

Matthews, Lisa ;

Caudy, Michael ;

Garapati, Phani ;

Gopinath, Gopal ;

Jassal, Bijay ;

Jupe, Steven ;

Kalatskaya, Irina ;

Mahajan, Shahana ;

May, Bruce ;

Ndegwa, Nelson ;

Schmidt, Esther ;

Shamovsky, Veronica ;

Yung, Christina ;

Birney, Ewan ;

Hermjakob, Henning ;

D'Eustachio, Peter ;

Stein, Lincoln .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D691-D697

[7]

The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

[8]

The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[9]

The UCSC Genome Browser database: extensions and updates 2011 [J].

Dreszer, Timothy R. ;

Karolchik, Donna ;

Zweig, Ann S. ;

Hinrichs, Angie S. ;

Raney, Brian J. ;

Kuhn, Robert M. ;

Meyer, Laurence R. ;

Wong, Mathew ;

Sloan, Cricket A. ;

Rosenbloom, Kate R. ;

Roe, Greg ;

Rhead, Brooke ;

Pohl, Andy ;

Malladi, Venkat S. ;

Li, Chin H. ;

Learned, Katrina ;

Kirkup, Vanessa ;

Hsu, Fan ;

Harte, Rachel A. ;

Guruvadoo, Luvina ;

Goldman, Mary ;

Giardine, Belinda M. ;

Fujita, Pauline A. ;

Diekhans, Mark ;

Cline, Melissa S. ;

Clawson, Hiram ;

Barber, Galt P. ;

Haussler, David ;

Kent, W. James .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D918-D923

[10]

Ensembl 2012 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Gordon, Leo ;

Hendrix, Maurice ;

Hourlier, Thibaut ;

Johnson, Nathan ;

Kaehaeri, Andreas K. ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Komorowska, Monika ;

Koscielny, Gautier ;

Kulesha, Eugene ;

Larsson, Pontus ;

Longden, Ian ;

McLaren, William ;

Muffato, Matthieu ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sobral, Daniel ;

Tang, Y. Amy ;

Taylor, Kieron ;

Trevanion, Stephen ;

Vandrovcova, Jana ;

White, Simon ;

Wilson, Mark ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard ;

Fernandez-Suarez, Xose M. ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D84-D90

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