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The compositional structure of Gene Ontology terms

P V Ogren, K B Cohen, G K Acquaah-Mensah, J Eberlein, L Hunter
2004 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
An analysis of the term names in the Gene Ontology reveals the prevalence of substring relations between terms: 65.3% of all GO terms contain another GO term as a proper substring.  ...  Further, we note that particular substrings which are not themselves GO terms (e.g. regulation of in the preceding example) recur frequently and in consistent subtrees of the ontology, and that these frequently  ...  This work would not have been possible without the tremendous investment of time and effort by the GO Consortium into the development of the Gene Ontology.  ... 
pmid:14992505 pmcid:PMC2490823 fatcat:qulzmfbqezdzdar5yezgdh4k7y

THE COMPOSITIONAL STRUCTURE OF GENE ONTOLOGY TERMS

P.V. OGREN, K.B. COHEN, G.K. ACQUAAH-MENSAH, J. EBERLEIN, L. HUNTER
2003 Biocomputing 2004  
An analysis of the term names in the Gene Ontology reveals the prevalence of substring relations between terms: 65.3% of all GO terms contain another GO term as a proper substring.  ...  Further, we note that particular substrings which are not themselves GO terms (e.g. regulation of in the preceding example) recur frequently and in consistent subtrees of the ontology, and that these frequently  ...  This work would not have been possible without the tremendous investment of time and effort by the GO Consortium into the development of the Gene Ontology.  ... 
doi:10.1142/9789812704856_0021 fatcat:mkqaecnavjemdjxy2befepkc6a

Ontology Usage at ZFIN [article]

Doug Howe, Christian Pich
2010 arXiv   pre-print
In addition, ontologies are used to help users find and cluster data more quickly without the need of knowing the exact technical name for a term.  ...  Four different ontologies are currently used to annotate data to the most specific term available facilitating a better comparison between inter-species data.  ...  Currently, ZFIN accomplishes this through a technique of post-composition, annotation-time term composition in which a new entity is emulated as the intersection of two existing ontology terms.  ... 
arXiv:1012.1898v1 fatcat:xfs2y63fgfgadhyi3pyupd22ve

A METHODOLOGY TO MIGRATE THE GENE ONTOLOGY TO A DESCRIPTION LOGIC ENVIRONMENT USING DAML+OIL

C. J. WROE, R. STEVENS, C. A. GOBLE, M. ASHBURNER
2002 Biocomputing 2003  
The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal  ...  Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology.  ...  We would like to thank Midori Harris and Jane Lomax of the GO Consortium Editorial Team for their advice and guidance.  ... 
doi:10.1142/9789812776303_0058 fatcat:gjsw2sveebaebbt3fabwy7kz44

Using Multiple Ontologies to Integrate Complex Biological Data

Mary Shimoyama, Victoria Petri, Dean Pasko, Susan Bromberg, Wenhua Wu, Jiali Chen, Nataliya Nenasheva, Anne Kwitek, Simon Twigger, Howard Jacob
2005 Comparative and Functional Genomics  
The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic  ...  Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a  ...  Because of the flexibility of the composite annotation records, data mining tools can be designed to allow researchers to search for data based on any of the ontologies used.  ... 
doi:10.1002/cfg.498 pmid:18629202 pmcid:PMC2447497 fatcat:5e5tzh5aizh4vpqfkabxanl6re

The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
Conclusions: The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain.  ...  Results: We introduce the design considerations and implementation details of the Bone Dysplasia Ontology.  ...  Especial thanks also to Tania Tudorache, Timothy Redmond and Matthew Horridge for the extremely useful feed-back on the logical correctness of the class axioms and of the grounding in BFO.  ... 
doi:10.1186/1471-2105-13-50 pmid:22449239 pmcid:PMC3338382 fatcat:flu5hsohtvahhmd5kwfec4es6u

Composite annotations: Requirements for mapping multiscale data and models to biomedical ontologies

D.L. Cook, J.L.V. Mejino, M.L. Neal, J.H. Gennari
2009 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies.  ...  For such integrative challenges, we describe a "composite annotation" schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation  ...  This work was supported in part by the National Institutes of Health under Grant R01HL087706-01.  ... 
doi:10.1109/iembs.2009.5333830 pmid:19964601 pmcid:PMC2797541 fatcat:qqbnj7acxnebdn2vob7ecau2ky

Implications of compositionality in the gene ontology for its curation and usage

Philip V Ogren, K Bretonnel Cohen, Lawrence Hunter
2005 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
In this paper we argue that a richer underlying representational model for the Gene Ontology that captures the implicit compositional structure of GO terms could have a positive impact on two activities  ...  compositional structure of its terms.  ...  Acknowledgments The authors thank Midori Harris, Jane Lomax, Chris Mungall, Sonia Leach, and Andrew Dolbey.  ... 
pmid:15759624 fatcat:72gxakexhfd7rbicfy76t4jmhu

Cross-Product Extensions of the Gene Ontology

Christopher Mungall, Michael Bada, Tanya Berardini, Jennifer Deegan, Amelia Ireland, Midori Harris, David Hill, Jane Lomax
2009 Nature Precedings  
The Gene Ontology is being normalized and extended to include computable logical definitions.  ...  The results can be used to reason over the ontology, and to make cross-ontology queries.  ...  Acknowledgments This work is supported by the NHGRI, via the Gene Ontology Consortium, HG002273.  ... 
doi:10.1038/npre.2009.3496.1 fatcat:q325uuyb4zfebj6m6pbgjvuevi

Cross-product extensions of the Gene Ontology

Christopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax
2011 Journal of Biomedical Informatics  
The Gene Ontology is being normalized and extended to include computable logical definitions.  ...  The results can be used to reason over the ontology, and to make cross-ontology queries.  ...  Acknowledgments This work is supported by the NHGRI, via the Gene Ontology Consortium, HG002273.  ... 
doi:10.1016/j.jbi.2010.02.002 pmid:20152934 pmcid:PMC2910209 fatcat:prsvqfowtzei5eqf553mzvb5c4

A network-theoretic approach for decompositional translation across Open Biological Ontologies

Chintan O. Patel, James J. Cimino
2010 Journal of Biomedical Informatics  
We use a network-theoretic measure, called the clustering coefficient, to find relevant atomic terms in the neighborhood of a composite term.  ...  Many of these ontologies are hosted under the umbrella of the Open Biological Ontologies Foundry.  ...  Cimino is supported by funds from the intramural research program at the NIH Clinical Center and the National Library of Medicine.  ... 
doi:10.1016/j.jbi.2010.01.007 pmid:20144734 pmcid:PMC3444745 fatcat:2xiszipvtnffnavqhuob57dsoq

Using Ontology Graphs to Understand Annotations and Reason about Them

Mary E. Dolan, Judith A. Blake
2006 Conference on Knowledge Representation in Medicine  
We are exploring the power of ontology visualization to enhance the understanding of annotations by placing annotations in the graph context of the broader biological knowledge the ontology provides.  ...  Biomedical ontologies not only capture a wealth of biological knowledge but also provide a representational system to support the integration and retrieval of biological information.  ...  Currently, the three ontologies of GO contain nearly 20,000 terms [3] .  ... 
dblp:conf/krmed/DolanB06 fatcat:72bfn3wggvh5fokyzjoyxo77sm

RTO, An Specific Crop Ontology for Rice Trait Concepts

Xinzhi Yao, Yun Liu, Qidong Deng, Yusha Liu, Xinchen Ma, Yufei Shen, Qianqian Peng, Zaiwen Feng, Jingbo Xia
2022 Zenodo  
Unfortunately, a standardization of rice trait ontology has been lacking, and make it challenging to normalize the description of lab results.  ...  In this work, a rice trait ontology (RTO) is manually curated by aligning three existed terminology set of rice trait.  ...  ACKNOWLEDGEMENTS The authors expressed their gratitude for many instructive discussions with Dr. Claire Nédellec and Dr. Pierre Larmande.  ... 
doi:10.5281/zenodo.6950749 fatcat:t7wbu4s33zfizdqvixksvgeopi

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  
Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition.  ...  The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community  ...  Acknowledgments Thanks to the Phenoscape team, the many contributors to the project (http://phenoscape.org/wiki/Acknowledgments), curators at Xenbase and ZFIN, and Peter Midford for technical assistance  ... 
doi:10.1371/journal.pone.0051070 pmid:23251424 pmcid:PMC3519498 fatcat:bqn6ahk3v5dxdja63dsslhu3aq

Knowledge representation and data sharing to unlock crop variation for nutritional food security

Liliana Andrés‐Hernández, Abdul Baten, Razlin Azman Halimi, Ramona Walls, Graham J. King
2020 Crop science  
We propose development of a Crop Dietary Nutrition Ontology (CDNO) as a robust structured controlled vocabulary for dietary nutritional composition and function, and provide examples of specific use cases  ...  This development is likely to transform the way in which crops may be compared in terms of optimal dietary nutritional values.  ...  The PO highlights the advantages of ontological representation, where the terms or nodes may be related to more than one parent or ancestor term (e.g., "gynoecium" is a "collective phyllome structure"  ... 
doi:10.1002/csc2.20092 fatcat:6ohb4rq2hnfajbonkelimkd7x4
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