The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
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* Corresponding author: Janan T Eppig jte@informatics.jax.org
Genome Biology 2004, 6:R7 doi:10.1186/gb-2004-6-1-r7
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BioMed Central: 24 citations
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Proceedings
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL Simon Jupp, Robert Stevens, Robert Hoehndorf Journal of Biomedical Semantics 2012, 3(Suppl 1):S3 (24 April 2012) |
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Short report
Joseph D Buxbaum, Catalina Betancur, Ozlem Bozdagi, Nate P Dorr, Gregory A Elder, Patrick R Hof Molecular Autism 2012, 3:1 (20 February 2012) |
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Method
Uberon, an integrative multi-species anatomy ontology Christopher J Mungall, Carlo Torniai, Georgios V Gkoutos, Suzanna E Lewis, Melissa A Haendel Genome Biology 2012, 13:R5 (31 January 2012) A description of the Uberon ontology tool that allows comparisons of genomic information across multiple animal phyla
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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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Software
Improving ontologies by automatic reasoning and evaluation of logical definitions Sebastian Köhler, Sebastian Bauer, Chris J Mungall, Gabriele Carletti, Cynthia L Smith, Paul Schofield, Georgios V Gkoutos, Peter N Robinson BMC Bioinformatics 2011, 12:418 (27 October 2011) |
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Research
Toralf Kirsten, Anika Gross, Michael Hartung, Erhard Rahm Journal of Biomedical Semantics 2011, 2:6 (13 September 2011) |
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Technical Note
OntoFox: web-based support for ontology reuse Zuoshuang Xiang, Mélanie Courtot, Ryan R Brinkman, Alan Ruttenberg, Yongqun He BMC Research Notes 2010, 3:175 (22 June 2010) OntoFox facilitates knowledge sharing by supporting extraction and reuse of user-defined subsets of terms from existing ontologies, enabling interoperability between projects through standardization of concepts and definitions.
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Research article
Michael Gruenberger, Rudi Alberts, Damian Smedley, Morris Swertz, Paul Schofield, Klaus Schughart BMC Research Notes 2010, 3:16 (22 January 2010) This article is part of a collection on Databases |
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Method
Integrating phenotype ontologies across multiple species Christopher J Mungall, Georgios V Gkoutos, Cynthia L Smith, Melissa A Haendel, Suzanna E Lewis, Michael Ashburner Genome Biology 2010, 11:R2 (8 January 2010) A phenotypic ontology that can be used for the analysis of phenotype-genotype data across multiple species, paving the way for truly cross species translational research. |
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Review
Linking genes to diseases: it's all in the data Nicki Tiffin, Miguel A Andrade-Navarro, Carolina Perez-Iratxeta Genome Med 2009, 1:77 (7 August 2009) Computational approaches to disease-gene associations, especially those that use phenotype ontologies, can help to prioritize the most likely candidate genes.
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Research
Annotating the human genome with Disease Ontology John D Osborne, Jared Flatow, Michelle Holko, Simon M Lin, Warren A Kibbe, Lihua Zhu, Maria I Danila, Gang Feng, Rex L Chisholm BMC Genomics 2009, 10(Suppl 1):S6 (7 July 2009) |
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Proceedings
Open Biomedical Ontology-based Medline exploration Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson, Fan Meng BMC Bioinformatics 2009, 10(Suppl 5):S6 (6 May 2009) |
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Proceedings
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data Tim Beck, Hugh Morgan, Andrew Blake, Sara Wells, John M Hancock, Ann-Marie Mallon BMC Bioinformatics 2009, 10(Suppl 5):S2 (6 May 2009) |
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Proceedings
PhenoGO: an integrated resource for the multiscale mining of clinical and biological data Lee T Sam, Eneida A Mendonça, Jianrong Li, Judith Blake, Carol Friedman, Yves A Lussier BMC Bioinformatics 2009, 10(Suppl 2):S8 (5 February 2009) |
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Research article
Information-based methods for predicting gene function from systematic gene knock-downs Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne, Joshua M Stuart BMC Bioinformatics 2008, 9:463 (29 October 2008) |
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Research
An en masse phenotype and function prediction system for Mus musculus Murat Taşan, Weidong Tian, David P Hill, Francis D Gibbons, Judith A Blake, Frederick P Roth Genome Biology 2008, 9(Suppl 1):S8 (27 June 2008) |
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Research article
Improved human disease candidate gene prioritization using mouse phenotype Jing Chen, Huan Xu, Bruce J Aronow, Anil G Jegga BMC Bioinformatics 2007, 8:392 (16 October 2007) |
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Methodology article
Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre BMC Bioinformatics 2007, 8:377 (9 October 2007) The problem of interoperability of fixed anatomy ontologies with the more flexible phenotype ontologies can be solved by treating canonical information as the default that can be modified when more information is available.
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Method
Celsius: a community resource for Affymetrix microarray data Allen Day, Marc RJ Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson Genome Biology 2007, 8:R112 (14 June 2007) Celsius is a new system that serves as a warehouse by aggregating Affymetrix files and associated metadata, and containing the largest publicly available source of Affymetrix microarray data. |
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Software
MPHASYS: a mouse phenotype analysis system R Calder, Rudolf B Beems, Harry van Steeg, I Mian, Paul HM Lohman, Jan Vijg BMC Bioinformatics 2007, 8:183 (6 June 2007) |
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Commentary
Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R George, Martin J Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A Javitch, Fabien Campagne, Marta Filizola BMC Bioinformatics 2007, 8:177 (30 May 2007) |
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Research
New genes in the evolution of the neural crest differentiation program Juan-Ramon Martinez-Morales, Thorsten Henrich, Mirana Ramialison, Joachim Wittbrodt Genome Biology 2007, 8:R36 (12 March 2007) The phylogenetic classification of genes that are ontologically associated with neural crest development reveals that neural crest evolution is associated with the emergence of new signalling peptides. |
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Software
The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald Genome Biology 2005, 6:R29 (15 February 2005) This article is part of a collection on Ontologies The Adult Mouse Anatomical Dictionary was developed to provide an ontology for standardized nomenclature for anatomical terms in the postnatal mouse. The ontology will be used to annotate and integrate different types of data pertinent to anatomy. |
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Method
Using ontologies to describe mouse phenotypes Georgios V Gkoutos, Eain CJ Green, Ann-Marie Mallon, John M Hancock, Duncan Davidson Genome Biology 2004, 6:R8 (20 December 2004) This article is part of a collection on Ontologies By combining ontologies from different sources the authors developed a novel approach to describing phenotypes of mutant mice in a standard, structured manner. |