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Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Melissa A Haendel, James P Balhoff, Frederic B Bastian, David C Blackburn, Judith A Blake, Yvonne Bradford, Aurelie Comte, Wasila M Dahdul, Thomas A Dececchi, Robert E Druzinsky, Terry F Hayamizu, Nizar Ibrahim (+6 others)
2014 Journal of Biomedical Semantics  
Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species.  ...  Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups.  ...  We acknowledge the support of the Phenotype Ontology Research Coordination Network (NSF-DEB-0956049) for bringing together the participants to develop key areas of the ontology.  ... 
doi:10.1186/2041-1480-5-21 pmid:25009735 pmcid:PMC4089931 fatcat:wih6yfno7vg5rdwspfwflmmsri

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  
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics.  ...  skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies  ...  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

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Sebastian Köhler, Sandra C Doelken, Barbara J Ruef, Sebastian Bauer, Nicole Washington, Monte Westerfield, George Gkoutos, Paul Schofield, Damian Smedley, Suzanna E Lewis, Peter N Robinson, Christopher J Mungall
2013 F1000Research  
.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1): 25-9. PubMed Abstract | Publisher Full Text | Free Full Text 10.  ...  Rosse C, Mejino JL Jr: A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2003; 36(6): 478-500. PubMed Abstract | Publisher Full Text 34.  ...  Acknowledgements We would like to thank Anika Oellrich for extensive proofreading of the draft version of the manuscript.  ... 
doi:10.12688/f1000research.2-30.v1 pmid:24358873 pmcid:PMC3799545 fatcat:wraclszcvrfbddvhdqdflkj7zq

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research

Sebastian Köhler, Sandra C Doelken, Barbara J Ruef, Sebastian Bauer, Nicole Washington, Monte Westerfield, George Gkoutos, Paul Schofield, Damian Smedley, Suzanna E Lewis, Peter N Robinson, Christopher J Mungall
2014 F1000Research  
.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1): 25-9. PubMed Abstract | Publisher Full Text | Free Full Text 10.  ...  Oellrich A, Hoehndorf R, Gkoutos GV, et al.: Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases.  ...  Acknowledgements We would like to thank Anika Oellrich for extensive proofreading of the draft version of the manuscript.  ... 
doi:10.12688/f1000research.2-30.v2 pmid:24358873 pmcid:PMC3799545 fatcat:267pqfzlvjfmxlz6xpel6qwtgu

Transforming the study of organisms: Phenomic data models and knowledge bases [article]

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel (+1 others)
2021
In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits.  ...  The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their  ...  Acknowledgments The authors would like to acknowledge the organizers and sponsors of the 2019 US2TS Conference held at Duke University who created space for this discussion.  ... 
doi:10.34657/5073 fatcat:qn453aa37vdzpgs6qzyog5ss54

MAPPING AND MERGING OF ANATOMICAL ONTOLOGIES

Peter Petrov, Peter Petrov
2013 ACM Computing Classification System   unpublished
The problem of mapping and merging ontologies in general is an important one in the area of ontology engineering.  ...  The paper's main topic is the problem of mapping and merging of multiple species-specific AOs and the related approaches , methods, and procedures that can be used for solving it.  ...  The main goal of Uberon is the unification (i.e., the merging, the integration) of the many existing species-specific AOs in one (or in a set of just a few) common, general species-neutral AOs.  ... 
fatcat:huhc5pocqrg2repugxlvc7j3pm

Context-specific subcellular localization prediction: Leveraging protein interaction networks and scientific texts

Lu Zhu
2018
For example, glutamine synthetase localizes in mitochondria in liver cells while in the cytoplasm in brain cells.  ...  Tissue is one particularly crucial biological context for human biology. Proteins show their tissue specificity at the subcellular level by localizing to different SCCs in different tissues.  ...  Likewise, Uber-anatomy ontology (Uberon) (https://uberon.github.io/about.html) is an anatomical ontology that represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates  ... 
doi:10.4119/unibi/2931387 fatcat:odwistvlzzfmxctzqoqdsbehze

Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees

Arshad M Khan, Alice H Grant, Anais Martinez, Gully A P C Burns, Brendan S Thatcher, Vishwanath T Anekonda, Benjamin W Thompson, Zachary S Roberts, Daniel H Moralejo, James E Blevins
2018
A key methodology that enables atlas-based mapping of extracted datasets-laser-capture microdissection-is discussed in detail, with a view of how this technology is a bridge between systems biology and  ...  Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially  ...  Sabiha Khan (UTEP) for thoughtful discussion on the organization of the manuscript, and Dr. Harold Gainer (National Institute of Neurological Disorders and Stroke) for his timely feedback.  ... 
doi:10.1007/978-3-319-94593-4_6 pmid:30334222 pmcid:PMC6310046 fatcat:q42zcsbrzzeubpas6dqcyy43ka