The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development
Abstract Background Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an incr...
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-03-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-022-04636-8 |
| _version_ | 1818772553998532608 |
|---|---|
| author | Malcolm E. Fisher Erik Segerdell Nicolas Matentzoglu Mardi J. Nenni Joshua D. Fortriede Stanley Chu Troy J. Pells David Osumi-Sutherland Praneet Chaturvedi Christina James-Zorn Nivitha Sundararaj Vaneet S. Lotay Virgilio Ponferrada Dong Zhuo Wang Eugene Kim Sergei Agalakov Bradley I. Arshinoff Kamran Karimi Peter D. Vize Aaron M. Zorn |
| author_facet | Malcolm E. Fisher Erik Segerdell Nicolas Matentzoglu Mardi J. Nenni Joshua D. Fortriede Stanley Chu Troy J. Pells David Osumi-Sutherland Praneet Chaturvedi Christina James-Zorn Nivitha Sundararaj Vaneet S. Lotay Virgilio Ponferrada Dong Zhuo Wang Eugene Kim Sergei Agalakov Bradley I. Arshinoff Kamran Karimi Peter D. Vize Aaron M. Zorn |
| author_sort | Malcolm E. Fisher |
| collection | DOAJ |
| description | Abstract Background Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. Results Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. Conclusions The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources. |
| first_indexed | 2024-12-18T10:11:12Z |
| format | Article |
| id | doaj.art-c7e3060ff60a4f10a234811dc17e1bfc |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T10:11:12Z |
| publishDate | 2022-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-c7e3060ff60a4f10a234811dc17e1bfc2022-12-21T21:11:26ZengBMCBMC Bioinformatics1471-21052022-03-0123111510.1186/s12859-022-04636-8The Xenopus phenotype ontology: bridging model organism phenotype data to human health and developmentMalcolm E. Fisher0Erik Segerdell1Nicolas Matentzoglu2Mardi J. Nenni3Joshua D. Fortriede4Stanley Chu5Troy J. Pells6David Osumi-Sutherland7Praneet Chaturvedi8Christina James-Zorn9Nivitha Sundararaj10Vaneet S. Lotay11Virgilio Ponferrada12Dong Zhuo Wang13Eugene Kim14Sergei Agalakov15Bradley I. Arshinoff16Kamran Karimi17Peter D. Vize18Aaron M. Zorn19Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterMonarch InitiativeDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDepartment of Biological Science, University of CalgaryDepartment of Biological Science, University of CalgaryEuropean Bioinformatics Institute (EMBL-EBI)Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDepartment of Biological Science, University of CalgaryDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterDepartment of Biological Science, University of CalgaryDepartment of Biological Science, University of CalgaryDepartment of Biological Science, University of CalgaryDepartment of Biological Science, University of CalgaryDepartment of Biological Science, University of CalgaryDepartment of Biological Science, University of CalgaryDivision of Developmental Biology, Cincinnati Children’s Hospital Medical CenterAbstract Background Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. Results Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. Conclusions The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources.https://doi.org/10.1186/s12859-022-04636-8XenopusPhenotypesOntologyDisease models |
| spellingShingle | Malcolm E. Fisher Erik Segerdell Nicolas Matentzoglu Mardi J. Nenni Joshua D. Fortriede Stanley Chu Troy J. Pells David Osumi-Sutherland Praneet Chaturvedi Christina James-Zorn Nivitha Sundararaj Vaneet S. Lotay Virgilio Ponferrada Dong Zhuo Wang Eugene Kim Sergei Agalakov Bradley I. Arshinoff Kamran Karimi Peter D. Vize Aaron M. Zorn The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development BMC Bioinformatics Xenopus Phenotypes Ontology Disease models |
| title | The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development |
| title_full | The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development |
| title_fullStr | The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development |
| title_full_unstemmed | The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development |
| title_short | The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development |
| title_sort | xenopus phenotype ontology bridging model organism phenotype data to human health and development |
| topic | Xenopus Phenotypes Ontology Disease models |
| url | https://doi.org/10.1186/s12859-022-04636-8 |
| work_keys_str_mv | AT malcolmefisher thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT eriksegerdell thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT nicolasmatentzoglu thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT mardijnenni thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT joshuadfortriede thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT stanleychu thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT troyjpells thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT davidosumisutherland thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT praneetchaturvedi thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT christinajameszorn thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT nivithasundararaj thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT vaneetslotay thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT virgilioponferrada thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT dongzhuowang thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT eugenekim thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT sergeiagalakov thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT bradleyiarshinoff thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT kamrankarimi thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT peterdvize thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT aaronmzorn thexenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT malcolmefisher xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT eriksegerdell xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT nicolasmatentzoglu xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT mardijnenni xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT joshuadfortriede xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT stanleychu xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT troyjpells xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT davidosumisutherland xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT praneetchaturvedi xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT christinajameszorn xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT nivithasundararaj xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT vaneetslotay xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT virgilioponferrada xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT dongzhuowang xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT eugenekim xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT sergeiagalakov xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT bradleyiarshinoff xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT kamrankarimi xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT peterdvize xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment AT aaronmzorn xenopusphenotypeontologybridgingmodelorganismphenotypedatatohumanhealthanddevelopment |