Integrating biological data -: the Distributed Annotation System

被引：63

作者：

Jenkinson, Andrew M. ^{[1
]}

Albrecht, Mario ^{[3
]}

Birney, Ewan ^{[1
]}

Blankenburg, Hagen ^{[3
]}

Down, Thomas ^{[6
]}

Finn, Robert D. ^{[2
]}

Hermjakob, Henning ^{[1
]}

Hubbard, Tim J. P. ^{[2
]}

Jimenez, Rafael C. ^{[1
,5
]}

Jones, Philip ^{[1
]}

Kahari, Andreas ^{[1
]}

Kulesha, Eugene ^{[1
]}

Macias, Jose R. ^{[4
]}

Reeves, Gabrielle A. ^{[1
]}

Prlic, Andreas ^{[2
]}

机构：

[1] European Bioinformat Inst, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[3] Max Planck Inst Informat, D-66123 Saarbrucken, Germany

[4] Natl Biotechnol Ctr, Madrid 28049, Spain

[5] Natl Bioinformat Network, ZA-7405 Cape Town, South Africa

[6] Univ Cambridge, Wellcome Trust Canc Res UK Gurdon Inst, Cambridge CB2 1QN, England

来源：

BMC BIOINFORMATICS | 2008年 / 9卷 / Suppl 8期

基金：

英国惠康基金;

关键词：

D O I：

10.1186/1471-2105-9-S8-S3

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics. Results: Here we describe the various infrastructure components of DAS and present a new extended version of the DAS specification. Version 1.53E incorporates several recent developments, including its extension to serve new data types and an ontology for protein features. Conclusion: Our extensions to the DAS protocol have facilitated the integration of new data types, and our improvements to the existing DAS infrastructure have addressed recent challenges. The steadily increasing numbers of available data sources demonstrates further adoption of the DAS protocol.

引用

页数：7

共 16 条

[1] WormBase:: new content and better access [J].

Bieri, Tamberlyn ;

Blasiar, Darin ;

Ozersky, Philip ;

Antoshechkin, Igor ;

Bastiani, Carol ;

Canaran, Payan ;

Chan, Juancarlos ;

Chen, Nansheng ;

Chen, Wen J. ;

Davis, Paul ;

Fiedler, Tristan J. ;

Girard, Lisa ;

Han, Michael ;

Harris, Todd W. ;

Kishore, Ranjana ;

Lee, Raymond ;

McKay, Sheldon ;

Muller, Hans-Michael ;

Nakamura, Cecilia ;

Petcherski, Andrei ;

Rangarajan, Arun ;

Rogers, Anthony ;

Schindelman, Gary ;

Schwarz, Erich M. ;

Spooner, Will ;

Tuli, Mary Ann ;

Van Auken, Kimberly ;

Wang, Daniel ;

Wang, Xiaodong ;

Williams, Gary ;

Durbin, Richard ;

Stein, Lincoln D. ;

Sternberg, Paul W. ;

Spieth, John .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D506-D510

[2] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[3] The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[4] The Sequence Ontology: a tool for the unification of genome annotations [J].

Eilbeck, K ;

Lewis, SE ;

Mungall, CJ ;

Yandell, M ;

Stein, L ;

Durbin, R ;

Ashburner, M .

GENOME BIOLOGY, 2005, 6 (05)

[5]

FINN RD, 2004, P UK E SCI ALL HANDS, P1069

[6] The Pfam protein families database [J].

Finn, Robert D. ;

Tate, John ;

Mistry, Jaina ;

Coggill, Penny C. ;

Sammut, Stephen John ;

Hotz, Hans-Rudolf ;

Ceric, Goran ;

Forslund, Kristoffer ;

Eddy, Sean R. ;

Sonnhammer, Erik L. L. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D281-D288

[7] ProServer: a simple, extensible Perl DAS server [J].

Finn, Robert D. ;

Stalker, James W. ;

Jackson, David K. ;

Kulesha, Eugene ;

Clements, Jody ;

Pettett, Roger .

BIOINFORMATICS, 2007, 23 (12) :1568-1570

[8] Ensembl 2008 [J].

Flicek, P. ;

Aken, B. L. ;

Beal, K. ;

Ballester, B. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cunningham, F. ;

Cutts, T. ;

Down, T. ;

Dyer, S. C. ;

Eyre, T. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. L. ;

Howe, K. ;

Johnson, N. ;

Jenkinson, A. ;

Kahari, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Prlic, A. ;

Rice, S. ;

Rios, D. ;

Schuster, M. ;

Sealy, I. ;

Slater, G. ;

Smedley, D. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. J. ;

Vogel, J. ;

White, S. ;

Wood, M. ;

Birney, E. ;

Cox, T. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D707-D714

[9] Dasty and UniProt DAS: a perfect pair for protein feature visualization [J].

Jones, P ;

Vinod, N ;

Down, T ;

Hackmann, A ;

Kahari, A ;

Kretschmann, E ;

Quinn, A ;

Wieser, D ;

Hermjakob, H ;

Apweiler, R .

BIOINFORMATICS, 2005, 21 (14) :3198-3199

[10] Integrating electron microscopy information into existing distributed annotation systems [J].

Macias, J. R. ;

Jimenez-Lozano, N. ;

Carazo, J. M. .

JOURNAL OF STRUCTURAL BIOLOGY, 2007, 158 (02) :205-213

← 1 2 →