phenio

Homepage Link:

Description: Phenio is a tool created, supported, and maintained by the Monarch Initiative. An ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.

• Technical Guide to Phenio: Please see the contributing guide for more information on contributing to Phenio. https://github.com/monarch-initiative/phenio/blob/main/CONTRIBUTING.md

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Knowledge Sources Accessed:

• 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).

Example edge:

Additional Links: Source Code: https://github.com/monarch-initiative/phenio/tree/main See Documentation Requirements for Translator Tools from 2021 Program Milestones from 2021 Program Milestones for more information.