Integrating phenotype ontologies across multiple species

By C. Mungall, Georgios Vasileios Gkoutos, Cynthia L. Smith, Melissa A. Haendel, Suzanna Lewis, Michael Ashburner. Genome Biology, 2010

306 citations recorded by the source corpus.

Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a4dbc88e082d35dff726fea494a9c50e9da792c4

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Citations in the corpus

Uberon, an integrative multi-species anatomy ontology (2012, methodology): “In a previous study we described a methodology for enhancing and connecting animal phenotype ontologies [57].”
Standardized description of scientific evidence using the Evidence Ontology (ECO) (2014, background): “These include ontologies for phenotype (3), cell type (4), anatomy (5) and many more (6).”
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species (2016, background): “Prior efforts to map or integrate species-specific anatomical ontologies (24,48), for example, have been utilized in the construction of these species-neutral ontologies.”
Improved exome prioritization of disease genes through cross-species phenotype comparison (2014, background): “2005) to identify similarities between human disease manifestations and observations made in genetically modified model organisms (Washington et al. 2009; Mungall et al. 2010; Doelken et al. 2013; Köhler et al. 2013).”
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation (2009, methodology): “To integrate these valuable data, we first created an equivalence mapping of MP terms to EQ descriptions [17].”