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Composition of PHENIO

  • BFO: Basic Formal Ontology (https://basic-formal-ontology.org/) - an ontology that provides a set of upper-level categories for organizing knowledge and facilitating interoperability between other ontologies and domain-specific applications.

  • CARO: Common Anatomy Reference Ontology (https://www.obofoundry.org/ontology/caro.html) - an ontology that standardizes the annotation and representation of anatomical structures across different species.

  • CHEBI: Chemical Entities of Biological Interest (https://www.ebi.ac.uk/chebi/) - a dictionary of molecular entities.

  • ECO: Evidence and Conclusion Ontology (https://evidenceontology.org/) - an ontology that categorizes and organizes different types of evidence used in scientific research and draws conclusions based on that evidence.

  • EMAPA: Mouse Developmental Anatomy Ontology (https://obofoundry.org/ontology/emapa.html)- an ontology that provides a standardized framework for describing spatial and temporal gene expression patterns during mouse development.

  • FAO: Fungal Anatomy Ontology (https://obofoundry.org/ontology/fao.html) - a structured controlled vocabulary for the anatomy of fungi.

  • FBBT: FlyBase Drosophila Gross Anatomy Ontology (https://obofoundry.org/ontology/fbbt) - an ontology that describes the gross anatomy of the fruit fly Drosophila melanogaster.

  • GO: Gene Ontology (http://geneontology.org/) - a widely-used ontology that categorizes gene products' functions in various biological processes, cellular components, and molecular functions.

  • HSAPDV: Human Developmental Stage Ontology (https://obofoundry.org/ontology/hsapdv) - an ontology of human developmental stages, covering both embryonic (Carnegie) stages and adult stages.

  • MONDO: Monarch Disease Ontology (https://mondo.monarchinitiative.org/) - an ontology that integrates disease-related information from various sources to facilitate the understanding of human diseases.

  • MPATH: Mouse Pathology Ontology (http://www.pathbase.net/Pathology_Ontology/index.php) - an ontology that standardizes and classifies phenotypic abnormalities observed in various mutant mouse strains.

  • NBO: Neuro Behavior Ontology (http://www.obofoundry.org/ontology/nbo.html) - an ontology that defines behavioral and neurological phenotypes to support research in neuroscience and behavior genetics.

  • NCBITaxon (Slim): NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/taxonomy) - a taxonomy database that classifies and names living organisms; this is a simplified subset (available from http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl).

  • OBA: Ontology of Biological Attributes (https://obofoundry.org/ontology/oba.html) - an ontology that describes biological attributes such as size, shape, color, and behavior across different species.

  • PATO: Phenotypic Quality Ontology (http://www.obofoundry.org/ontology/pato.html) - an ontology that provides a standardized vocabulary to describe phenotypic qualities, such as height, weight, and shape.

  • RO: Relations Ontology (http://www.obofoundry.org/ontology/ro.html) - an ontology that defines relationships between entities in other ontologies and provides a foundation for relating information across different domains.

  • STATO: Statistical Methods Ontology (https://stato-ontology.org/) - an ontology that represents statistical methods and concepts used in the analysis of biological and clinical data.

  • UBERON: Integrated Cross-Species Anatomy Ontology (http://www.obofoundry.org/ontology/uberon.html) - an ontology that integrates anatomical information from different species, facilitating cross-species comparisons.

  • UPHENO: Uberon Phenotype Ontology (https://github.com/obophenotype/upheno) - an ontology that links phenotypic abnormalities to the anatomical entities that are affected, enabling the study of genotype-phenotype relationships.

  • WBBT: WormBase Gross Anatomy Ontology (http://www.obofoundry.org/ontology/wbphenotype.html) - an ontology that describes the gross anatomy of the nematode worm Caenorhabditis elegans.

  • ZFA: Zebrafish Anatomy and Development Ontology (http://www.obofoundry.org/ontology/zfa.html) - an ontology that describes the anatomy and developmental stages of the zebrafish (Danio rerio).