Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

By Nicole L. Washington, Melissa A. Haendel, C. Mungall, Michael Ashburner, Monte Westerfield, Suzanna Lewis. PLoS Biology, 2009

314 citations recorded by the source corpus.

A novel method for quantifying the similarity between phenotypes by the use of ontologies can be used to search for candidate genes, pathway members, and human disease models on the basis of phenotypes alone.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d0f417801193ac43662c9dea253cdae7b097d1af

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Citations in the corpus

The Human Phenotype Ontology in 2024: phenotypes around the world (2023, methodology): “The same logical patterns, based on the Entity-Quality model ( 39 ), are used to define attributes in OBA as in HPO.”
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).”
The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery (2015, methodology): “Multiple projects have addressed this need by developing platforms that use genotype and phenotype-driven matching algorithms to identify cases with common phenotypes and disrupted genes [Washington et al., 2009; Gonzalez et al., 2012, Swaminathan et al., 2012, Gonzalez et al., 2013, Robinson et al.”
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data (2013, methodology): “…construction, and provides a tool for integrative computational analysis of human and model organism phenotypes against the background of the knowledge incorporated in ontologies such as Gene Ontology, Foundational Model of Anatomy and Chemical entities of biological interest (ChEBI) (12–15).”
Integrating phenotype ontologies across multiple species (2010, unknown): “Now, by using a reasoner-backed database combined with the anatomical associations in Uberon and the mappings between the phenotype ontologies and respective EQ descriptions, we can ask questions and perform analyses in an automated fashion [ 20 ].”
Next-generation diagnostics and disease-gene discovery with the Exomiser (2015, methodology): “Here we describe a protocol for the Exomiser suite that comprises several methods that use clinical data 5 , model organism phenotype data 5,17–19 , as well as random-walk analysis of protein interactome data 20,21 to perform prioritization.”
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species (2016, methodology): “A phenotypic profile is the subject of non-exact matching within and across species us-ing ontology integration and semantic similarity algorithms (10,11) in software applications such as Exomiser (12) and Genomiser (13), and this approach has been shown to assist disease diagnosis (14–16).”
The digital revolution in phenotyping (2015, methodology): “Furthermore, phenotypes have been used to support the understanding of the genetic mechanism of diseases via direct association with genotype data [5, 9, 12], as a mapping bridge across species data [7, 8] and in conjunction with the entire set of OMICS data [75] or to improve variant prioritization”