ArticlePloS one2010
Phenex: ontological annotation of phenotypic diversity.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- An ontological morphological phylogenetic framework for living and extinct ray-finned fishes (Actinopterygii).Anatomical record (Hoboken, N.J. : 2007) · 2026Article
- Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae).Biodiversity data journal · 2024Article
- Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.Systematic biology · 2022Article
- Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research.Journal of biomedical semantics · 2022Article
- FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example.Journal of biomedical semantics · 2021Article
- Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes.Database : the journal of biological databases and curation · 2020Article
- Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS computational biology · 2020Review
- A Logical Model of Homology for Comparative Biology.Systematic biology · 2020Article
- Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits.Systematic biology · 2019Article
- Organizing phenotypic data-a semantic data model for anatomy.Journal of biomedical semantics · 2019Article
- ECO, the Evidence & Conclusion Ontology: community standard for evidence information.Nucleic acids research · 2019Article
- Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes.Systematic biology · 2018Article
- Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.Database : the journal of biological databases and curation · 2018Article
- Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.BMC bioinformatics · 2016Article
- Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases.Journal of biomedical semantics · 2016Article
- Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.Molecular biology and evolution · 2016Article
- Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.PloS one · 2016Article
- Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices.PloS one · 2016Article
- Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.Systematic biology · 2015Article
- Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.Database : the journal of biological databases and curation · 2015Article
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9 authors.
Funding
Abstract
backgroundPhenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. METHODOLOGY/PRINCIPAL
findingsHere we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. CONCLUSIONS/SIGNIFICANCE: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.
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