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The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species

Carissa A Park, Susan M Bello, Cynthia L Smith, Zhi-Liang Hu, Diane H Munzenmaier, Rajni Nigam, Jennifer R Smith, Mary Shimoyama, Janan T Eppig, James M Reecy
2013 Journal of Biomedical Semantics  
The VT provides a common basis for the description of traits in multiple vertebrate species.  ...  The VT is a unified trait vocabulary created to aid in the transfer of data within and between species and to facilitate investigation of the genetic basis of traits.  ...  We wish to thank Molly Bogue for consultation and helpful suggestions to improve the VT and Chris Mungall for advice regarding improvement of the manuscript.  ... 
doi:10.1186/2041-1480-4-13 pmid:23937709 pmcid:PMC3851175 fatcat:zb7vxbpq2rfj7iysuxnbwa2nme

Editorial: biological ontologies and semantic biology

John M. Hancock
2014 Frontiers in Genetics  
The Anatomical Entity Ontology (AEO) (Bard, 2012) provides a typology of anatomical entities across species that is linked to cell types (via links to the cell ontology).  ... February 2014 | Volume 5 | Article 18 | 1 The major purpose of developing biological ontologies (rather than simpler controlled vocabularies) is to make use of the relations implicit  ... 
doi:10.3389/fgene.2014.00018 pmid:24550936 pmcid:PMC3912459 fatcat:jzgsht7ewnfkdewouq7omlotsi

Implementation of Zebrafish Ontologies for Toxicology Screening

Anne E. Thessen, Skylar Marvel, J. C. Achenbach, Stephan Fischer, Melissa A. Haendel, Kimberly Hayward, Nils Klüver, Sarah Könemann, Jessica Legradi, Pamela Lein, Connor Leong, J. Erik Mylroie (+15 others)
2022 Frontiers in Toxicology  
In the second survey, researchers were asked to annotate the images from a list of terms and definitions from the Zebrafish Phenotype Ontology.  ...  Substantial variability has been observed among researchers in phenotypes reported from similar studies, as well as a lack of consistent data annotation, indicating a need for both terminological and data  ...  Here we discuss the use of biological ontologies as data integration infrastructure and present the results of a preliminary annotation exercise to investigate the impact of a hierarchical controlled vocabulary  ... 
doi:10.3389/ftox.2022.817999 pmid:35387429 pmcid:PMC8979167 fatcat:mmrigwbc4nfufi63dlro7ggt2m

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky (+3 others)
2016 Journal of Biomedical Semantics  
For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies.  ...  The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent  ...  In support of these projects, the CL is being used both as a controlled vocabulary of cell types for use as metadata, and as part of an analytical pipeline for analyzing high-dimensional flow cytometry  ... 
doi:10.1186/s13326-016-0088-7 pmid:27377652 pmcid:PMC4932724 fatcat:otjugknudng4vilqqufaxppst4

Phenotype ontologies: the bridge between genomics and evolution

2007 Trends in Ecology & Evolution  
Understanding the developmental and genetic underpinnings of particular evolutionary changes has been hindered by inadequate databases of evolutionary anatomy and by the lack of a computational approach  ...  This would facilitate computing on evolutionary questions pertaining to the genetic basis of evolutionary change, the genetic and developmental bases of correlated characters and independent evolution,  ...  G.V.G. is supported by the National Center for Biomedical Ontology (NIH: 1-U54-HG004028-01). We thank Adam Amsterdam and Nancy Hopkins for use of the image in Figure 2 .  ... 
doi:10.1016/j.tree.2007.03.013 pmid:17416439 fatcat:lub7w3xaxbghhcf7ygb7c2o36a

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

Cynthia L. Smith, Janan T. Eppig
2009 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Use of this ontology allows comparisons of data from diverse sources, can facilitate comparisons across mammalian species, assists in identifying appropriate experimental disease models, and aids in the  ...  Here we describe a tool, the Mammalian Phenotype Ontology (MP), for classifying and organizing phenotypic information related to the mouse and other mammalian species.  ...  Michael Sasner, Molly Bogue and Susan Bello for helpful comments on the manuscript. This work was supported by grant HG000330 from the National Human Genome Research Institute.  ... 
doi:10.1002/wsbm.44 pmid:20052305 pmcid:PMC2801442 fatcat:5q5pxaz4mbem5kygimgookxj64

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies [article]

Diego Sasso Porto, Wasila Dahdul, Hilmar Lapp, James Balhoff, Todd Vision, Paula Mabee, Josef Uyeda
2022 bioRxiv   pre-print
Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa.  ...  Here we assess whether the proximity of ontology-annotated characters within an ontology predicts evolutionary patterns.  ...  Pennell and his lab for the insightful discussions in their lab meeting. DSP is grateful to Fabio A. Machado for helping fixing issues with the code used in ontobayes.  ... 
doi:10.1101/2022.01.06.475250 fatcat:5kqhgwojwrexhdbbsvr6rydzge

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies

Diego S Porto, Wasila M Dahdul, Hilmar Lapp, James P Balhoff, Todd J Vision, Paula M Mabee, Josef Uyeda
2022 Systematic Biology  
Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa.  ...  To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure  ...  Pennell and his lab for the insightful discussions in their lab meeting. D.S.P. is grateful to Fabio A. Machado for helping fixing issues with the code used in ontobayes.  ... 
doi:10.1093/sysbio/syac022 pmid:35285502 fatcat:qgutbn2ugrcm7kxx5sk5pp7ymm

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish

Paula M. Mabee, Gloria Arratia, Miles Coburn, Melissa Haendel, Eric J. Hilton, John G. Lundberg, Richard L. Mayden, Nelson Rios, Monte Westerfield
2007 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
/ GO-Gene Ontology, developed by a consortium of model organism databases for annotating gene products MGI-Model organism database for mouse (Mouse Genome Informatics) http  ...  Ontologies are controlled vocabularies that formally represent hierarchical relationships among defined biological concepts.  ...  ACKNOWLEDGMENTS We thank the NSF National Evolutionary Synthesis Center (EF-0423641), NSF Cypriniformes Tree of Life (DEB-0431290), NIH HG002659 and HG004028 for support.  ... 
doi:10.1002/jez.b.21181 pmid:17599725 fatcat:g3zxqegl2jherodstnvyfo2kwm

A Unified Anatomy Ontology of the Vertebrate Skeletal System

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke (+4 others)
2012 PLoS ONE  
Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.  ...  Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the  ...  We also thank Marc Robinson-Rechavi and the two anonymous reviewers for providing helpful comments.  ... 
doi:10.1371/journal.pone.0051070 pmid:23251424 pmcid:PMC3519498 fatcat:bqn6ahk3v5dxdja63dsslhu3aq

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

Gary Schindelman, Jolene S Fernandes, Carol A Bastiani, Karen Yook, Paul W Sternberg
2011 BMC Bioinformatics  
Results: We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO).  ...  Conclusions: We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community.  ...  suggestions; Norie de la Cruz for his work on the phenotype ontology search tool and fellow curators at WormBase for their valuable input.  ... 
doi:10.1186/1471-2105-12-32 pmid:21261995 pmcid:PMC3039574 fatcat:j7nmqr5wirfxpnxd65zx3lfmay

The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant

K. Ilic, E. A. Kellogg, P. Jaiswal, F. Zapata, P. F. Stevens, L. P. Vincent, S. Avraham, L. Reiser, A. Pujar, M. M. Sachs, N. T. Whitman, S. R. McCouch (+4 others)
2006 Plant Physiology  
To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant.  ...  of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database.  ...  ., for contributing their species-specific ontologies.  ... 
doi:10.1104/pp.106.092825 pmid:17142475 pmcid:PMC1803752 fatcat:7vfy5lqnvraorgzpamizo74vra

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications

Jennifer R Smith, Carissa A Park, Rajni Nigam, Stanley JF Laulederkind, G Hayman, Shur-Jen Wang, Timothy F Lowry, Victoria Petri, Jeff Pons, Marek Tutaj, Weisong Liu, Elizabeth A Worthey (+2 others)
2013 Journal of Biomedical Semantics  
Use of these vocabularies to standardize data representation for quantitative phenotypes and quantitative trait loci across databases for multiple species has demonstrated their utility for integrating  ...  In addition, new applications of these ontologies, such as annotation of Quantitative Trait Loci (QTL), have been added at the sites actively using them, including RGD and the Animal QTL Database.  ...  Acknowledgements This project was supported by grants HL064541 (RGD) and HL094271 (PhenoMiner) from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health.  ... 
doi:10.1186/2041-1480-4-26 pmid:24103152 pmcid:PMC3882879 fatcat:nszdruvaffer5mms66nucddxpe

Phenotype Ontologies and Cross-Species Analysis for Translational Research

Peter N. Robinson, Caleb Webber, Jonathan Flint
2014 PLoS Genetics  
The use of model organisms as tools for the investigation of human genetic variation has significantly and rapidly advanced our understanding of the aetiologies underlying hereditary traits.  ...  , in the model species.  ...  Acknowledgments CW would like to thank Frantisek Honti for his help in the production of  ... 
doi:10.1371/journal.pgen.1004268 pmid:24699242 pmcid:PMC3974665 fatcat:oynuzmmdcnay7g6nhxomeqw4t4

Integrating phenotype ontologies across multiple species

Christopher J Mungall, Georgios V Gkoutos, Cynthia L Smith, Melissa A Haendel, Suzanna E Lewis, Michael Ashburner
2010 Genome Biology  
Multi-species Phenotype ontologies A phenotypic ontology that can be used for the analysis of phenotype-genotype data across multiple species, paving the way for truly cross species translational research  ...  We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.  ...  Many thanks to Nicole Washington for comments on the manuscript. We would also like to thank the two anonymous reviewers who provided helpful comments for improvement.  ... 
doi:10.1186/gb-2010-11-1-r2 pmid:20064205 pmcid:PMC2847714 fatcat:naewkc73jbejlpxog4ztvhkfnu
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