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Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
2014
Journal of Biomedical Semantics
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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
2012
PLoS ONE
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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
2013
F1000Research
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.: 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
2014
F1000Research
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
.: 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]
2021
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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
2013
ACM Computing Classification System
unpublished
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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
2018
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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
2018
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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