The Sequence Ontology: a tool for the unification of genome annotations
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* Corresponding author: Michael Ashburner ma11@gen.cam.ac.uk
Genome Biology 2005, 6:R44 doi:10.1186/gb-2005-6-5-r44
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BioMed Central: 32 citations
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Research
Paolo Pannarale, Domenico Catalano, Giorgio De Caro, Giorgio Grillo, Pietro Leo, Graziano Pappadà, Francesco Rubino, Gaetano Scioscia, Flavio Licciulli BMC Bioinformatics 2012, 13(Suppl 4):S4 (28 March 2012) |
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Research
A semantic web framework to integrate cancer omics data with biological knowledge Matthew E Holford, James P McCusker, Kei-Hoi Cheung, Michael Krauthammer BMC Bioinformatics 2012, 13(Suppl 1):S10 (25 January 2012) |
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Software
Carson Holt, Mark Yandell BMC Bioinformatics 2011, 12:491 (22 December 2011) |
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Research article
Exact score distribution computation for ontological similarity searches Marcel H Schulz, Sebastian Köhler, Sebastian Bauer, Peter N Robinson BMC Bioinformatics 2011, 12:441 (12 November 2011) |
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Research article
The BioLexicon: a large-scale terminological resource for biomedical text mining Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, CJ Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann, Sophia Ananiadou BMC Bioinformatics 2011, 12:397 (12 October 2011) |
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Database
The representation of protein complexes in the Protein Ontology (PRO) Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu BMC Bioinformatics 2011, 12:371 (19 September 2011) ProComp is a component of the Protein Ontology (PRO) database for implementing a logical and consistent representation of protein complexes, and facilitates robust annotation of variations in composition and function contexts within and between species
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Proceedings
An open annotation ontology for science on web 3.0 Paolo Ciccarese, Marco Ocana, Leyla Garcia Castro, Sudeshna Das, Tim Clark Journal of Biomedical Semantics 2011, 2(Suppl 2):S4 (17 May 2011) |
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Proceedings
Next generation models for storage and representation of microbial biological annotation Daniel J Quest, Miriam L Land, Thomas S Brettin, Robert W Cottingham BMC Bioinformatics 2010, 11(Suppl 6):S15 (7 October 2010) |
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Methodology article
Relations as patterns: bridging the gap between OBO and OWL Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre BMC Bioinformatics 2010, 11:441 (31 August 2010) |
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Method
A standard variation file format for human genome sequences Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010) The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.
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Research
Roberto Pérez-Torrado, Joaquín Panadero, María Hernández-López, José Prieto, Francisca Randez-Gil Microbial Cell Factories 2010, 9:56 (13 July 2010) |
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Research article
Jérôme Lane, Patrice Duroux, Marie-Paule Lefranc BMC Bioinformatics 2010, 11:223 (30 April 2010) |
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Research
Applying the functional abnormality ontology pattern to anatomical functions Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Janet Kelso Journal of Biomedical Semantics 2010, 1:4 (31 March 2010) |
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Methodology article
The ontology of biological sequences Robert Hoehndorf, Janet Kelso, Heinrich Herre BMC Bioinformatics 2009, 10:377 (18 November 2009) |
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Research article
Construction of an annotated corpus to support biomedical information extraction Paul Thompson, Syed A Iqbal, John McNaught, Sophia Ananiadou BMC Bioinformatics 2009, 10:349 (23 October 2009) |
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Proceedings
TGF-beta signaling proteins and the Protein Ontology Cecilia N Arighi, Hongfang Liu, Darren A Natale, Winona C Barker, Harold Drabkin, Judith A Blake, Barry Smith, Cathy H Wu BMC Bioinformatics 2009, 10(Suppl 5):S3 (6 May 2009) |
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Methodology article
Modeling genomic data with type attributes, balancing stability and maintainability Norbert Busch, Gero Wedemann BMC Bioinformatics 2009, 10:97 (27 March 2009) |
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Methodology article
Quantitative measures for the management and comparison of annotated genomes Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell BMC Bioinformatics 2009, 10:67 (23 February 2009) |
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Proceedings
Towards a semi-automatic functional annotation tool based on decision-tree techniques Jérôme Azé, Lucie Gentils, Claire Toffano-Nioche, Valentin Loux, Jean-François Gibrat, Philippe Bessières, Céline Rouveirol, Anne Poupon, Christine Froidevaux BMC Proceedings 2008, 2(Suppl 4):S3 (17 December 2008) |
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Proceedings
Integrating biological data – the Distributed Annotation System Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R Macías, Gabrielle A Reeves, Andreas Prlić BMC Bioinformatics 2008, 9(Suppl 8):S3 (22 July 2008) |
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Software
Calling on a million minds for community annotation in WikiProteins Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert-Jan van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch Genome Biology 2008, 9:R89 (28 May 2008) WikiProteins is a novel tool that allows community annotation in an open access, wiki-based system. |
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Research
Terminologies for text-mining; an experiment in the lipoprotein metabolism domain Dimitra Alexopoulou, Thomas Wächter, Laura Pickersgill, Cecilia Eyre, Michael Schroeder BMC Bioinformatics 2008, 9(Suppl 4):S2 (25 April 2008) |
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Proceedings
Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo, Yixue Li BMC Bioinformatics 2008, 9(Suppl 1):S6 (13 February 2008) |
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Proceedings
Framework for a Protein Ontology Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, Cathy H Wu BMC Bioinformatics 2007, 8(Suppl 9):S1 (27 November 2007) |
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Method
Simplified ontologies allowing comparison of developmental mammalian gene expression Adele Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide Genome Biology 2007, 8:R229 (25 October 2007) The Developmental eVOC ontologies presented are simplified orthogonal ontologies describing the temporal and spatial distribution of developmental human and mouse anatomy. |
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Software
FlyMine: an integrated database for Drosophila and Anopheles genomics Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem Genome Biology 2007, 8:R129 (5 July 2007) This novel web-based database provides unique accessibility and querying of integrated genomic and proteomic data for |
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Commentary
Mikel Aranguren, Sean Bechhofer, Phillip Lord, Ulrike Sattler, Robert Stevens BMC Bioinformatics 2007, 8:57 (20 February 2007) |
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Software
DiscoverySpace: an interactive data analysis application Neil Robertson, Mehrdad Oveisi-Fordorei, Scott D Zuyderduyn, Richard J Varhol, Christopher Fjell, Marco Marra, Steven Jones, Asim Siddiqui Genome Biology 2007, 8:R6 (8 January 2007) DiscoverySpace, a graphical application for bioinformatics data analysis, in particular analysis of SAGE data, is described |
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Proceedings
Curation of viral genomes: challenges, applications and the way forward Urmila Kulkarni-Kale, Shriram G Bhosle, G Sunitha Manjari, Manali Joshi, Sandeep Bansode, Ashok S Kolaskar BMC Bioinformatics 2006, 7(Suppl 5):S12 (18 December 2006) |
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Database
Leandro Hermida, Olivier Schaad, Philippe Demougin, Patrick Descombes, Michael Primig BMC Bioinformatics 2006, 7:190 (5 April 2006) |