ArticleBioinformatics (Oxford, England)2010
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 20 citations in OpenAlex.
- A Logical Model of Homology for Comparative Biology.Systematic biology · 2020Article
- BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.F1000Research · 2016Article
- What to compare and how: Comparative transcriptomics for Evo-Devo.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2015Review
- Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.Journal of biomedical semantics · 2014Article
- Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.Nucleic acids research · 2012Article
- vHOG, a multispecies vertebrate ontology of homologous organs groups.Bioinformatics (Oxford, England) · 2012Article
- Comparative modular analysis of gene expression in vertebrate organs.BMC genomics · 2012Article
- Uberon, an integrative multi-species anatomy ontology.Genome biology · 2012Article
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Authors and funding
3 authors at 2 institutions in 1 country.
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Abstract
motivationThe anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species.
resultsWe present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee. AVAILABILITY: download section of the Bgee website http://bgee.unil.ch/
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