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The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Colin Batchelor, Thomas Bittner, Karen Eilbeck, Chris Mungall, Jane Richardson, Rob Knight, Jesse Stombaugh, Craig Zirbel, Eric Westhof, Neocles Leontis
2009 Nature Precedings  
We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data.  ...  Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments.  ...  SO is supported by the NHGRI, via the Gene Ontology Consortium, HG004341.  ... 
doi:10.1038/npre.2009.3561.1 fatcat:2ufub5f3sjf6xfwsf6ihl57pca

The development of non-coding RNA ontology

Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin (+11 others)
2016 International Journal of Data Mining and Bioinformatics  
On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field.  ...  We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a Huang et al.  ...  ) and in part by the Abraham A.  ... 
doi:10.1504/ijdmb.2016.077072 pmid:27990175 pmcid:PMC5156483 fatcat:i62jsm2cdze23pdoevo3gtxnjq

A domain ontology for the Non-Coding RNA field

Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He (+5 others)
2015 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
Keywords-non-coding RNA, biological and biomedical ontologies, domain ontology, ontology development, semantic data annotation and integration.  ...  On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities.  ...  The goal of the RNAO project is to enable integration and analysis of diverse RNA datasets.  ... 
doi:10.1109/bibm.2015.7359755 dblp:conf/bibm/HuangEBDNRSZJLW15 fatcat:5mkv5emvybbvvf6l7654myijri

Meeting report of the RNA Ontology Consortium January 8-9, 2011

Amanda Birmingham, Jose C. Clemente, Narayan Desai, Jack Gilbert, Antonio Gonzalez, Nikos Kyrpides, Folker Meyer, Eric Nawrocki, Peter Sterk, Jesse Stombaugh, Zasha Weinberg, Doug Wendel (+4 others)
2011 Standards in Genomic Sciences  
This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011.  ...  The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the  ...  Acknowledgements The organizers gratefully acknowledge support from National Science Foundation grant no. 0443508, as well as the valuable contributions of all the workshop participants.  ... 
doi:10.4056/sigs.1724282 pmid:21677862 pmcid:PMC3111981 fatcat:rwizei7ftjgujcouzyk5q4bfhi

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin (+8 others)
2016 Journal of Biomedical Semantics  
To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the  ...  In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs).  ...  EPSCoR program) and in part by the Abraham A.  ... 
doi:10.1186/s13326-016-0066-0 pmid:27152146 pmcid:PMC4857245 fatcat:i4jghl5vfncdjhbt5rxvmnnlfe

RKB: a Semantic Web knowledge base for RNA

Jose Cruz-Toledo, Michel Dumontier, Marc Parisien, François Major
2010 Journal of Biomedical Semantics  
Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independentlygenerated information arising from  ...  such efforts as genome sequencing projects, microarray analyses, structure determination and RNA SELEX experiments.  ...  Acknowledgements This paper was written with the support of NSERC Discovery Grant for MD. The authors would like to thank Alison Callahan for her assistance with MC-Annotate RDFization.  ... 
doi:10.1186/2041-1480-1-s1-s2 pmid:20626922 pmcid:PMC2903721 fatcat:wdg6ce5kefcynieulxnejqp5ii

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, Neocles Leontis, Philippe Rocca-Serra (+6 others)
2007 Nature Biotechnology  
Smith, Chris Mungall RNA Ontology (RnaO) RNA three-dimensional structures, sequence alignments, and interactions http://roc.bgsu.edu/ RNA Ontology Consortium P E R S P E C T I V E Ontology Scope URL  ...  NCBI, US National Center for Biotechnology Information; CL, Cell Ontology; SO, Sequence Ontology; RnaO, RNA Ontology; PRO, Protein Ontology.  ...  ACKNOWLEDGMENTS The Foundry is receiving ad hoc funding under the BISC Gen e Ontology Consortium, MGED, NCBO and RNA Ontology grants.  ... 
doi:10.1038/nbt1346 pmid:17989687 pmcid:PMC2814061 fatcat:oosohj3ngba6hkpulnljk3hgqa

Sharing and archiving nucleic acid structure mapping data

P. Rocca-Serra, S. Bellaousov, A. Birmingham, C. Chen, P. Cordero, R. Das, L. Davis-Neulander, C. D. S. Duncan, M. Halvorsen, R. Knight, N. B. Leontis, D. H. Mathews (+5 others)
2011 RNA: A publication of the RNA Society  
Supplemental http://rnajournal.cshlp.org/content/suppl/2011/05/13/rna.2753211.DC1.html References http://rnajournal.cshlp.org/content/17/7/1204.full.html#related-urls Article cited in: http://rnajournal.cshlp.org  ...  The RNA Ontology (RNAO) annotates crucial structural features of RNA molecules extracted from atomic-resolution 3D structures, including all non-Watson-Crick base pairs (Leontis et al. 2006; Brown et  ...  (Degtyarenko et al. 2008 (Degtyarenko et al. , 2009 , the Protein Ontology (PRO) (Natale et al. 2007 (Natale et al. , 2011 , and the RNA Ontology (RNAO) (Leontis et al. 2006; Brown et al. 2009; Hoehndorf  ... 
doi:10.1261/rna.2753211 pmid:21610212 pmcid:PMC3138558 fatcat:fbs2tdppyvgornwjwwqx7rd2jy

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, Alan Ruttenberg
2015 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
In our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards  ...  This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions.  ...  The views contained in this paper are solely the responsibility of the authors and do not represent the official views, either expressed or implied, of the NIH or the U.S. Government.  ... 
doi:10.1109/bibm.2015.7359816 dblp:conf/bibm/HuangGDBENSLWLT15 fatcat:4d2mqkvdnvem7ngii34blvvrf4

The qualitative and time-dependent character of spatial relations in biomedical ontologies

Thomas Bittner, Louis J. Goldberg
2007 Computer applications in the biosciences : CABIOS  
Westhof and N. Leontis, 2009, The RNA Ontology (RNAO): An Ontology for integrating RNA sequence and structure data. In B.  ...  Presented at the meeting of the International Neuroinformatics Coordinating Facility (INCF) Program on Ontologies for Neural Structures Representation and Deployment, Pilsen, Czech Republic, September  ...  Annals of Mathematics and Artificial Intelligence  ... 
doi:10.1093/bioinformatics/btm155 pmid:17463018 fatcat:icf3agcr25hp3hdncjcyer6eze

Semantic Grid for Biomedical Ontologies

Farhan Shafiq, Sheikh Kashif Raffat, Muhammad Shahab Siddiqui
2011 International Journal of Computer Applications  
The biomedical ontologies contain the complex distributed heterogeneous data, to analyze and process this data is the big challenge for biomedical communities.  ...  Semantic Grid is the integration of Grid with the Semantic web, which will play the vital role in future web. The semantic grid architecture provides semantic and knowledge support.  ...  Many biomedical ontologies exist in different domains of biology like Gene Ontology (GO), Sequence Ontology (SO), Chemical Entity of Biological Interest (ChEBI), RNA Ontology (RNAO) and Biological Viruses  ... 
doi:10.5120/2887-3765 fatcat:pgvrxbpxg5gg7g2ni33d5irete

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva (+5 others)
2016 Journal of Biomedical Semantics  
We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic  ...  in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development.  ...  Acknowledgements Funding for Huang, J was provided in part by the National Cancer Institute  ... 
doi:10.1186/s13326-016-0064-2 pmid:27175225 pmcid:PMC4863347 fatcat:wgowilvzsjcj7kvabm3wcrk6te

Evaluation of research in biomedical ontologies

R. Hoehndorf, M. Dumontier, G. V. Gkoutos
2012 Briefings in Bioinformatics  
To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated.  ...  the objective evaluation and comparison of research results in applied ontology.  ...  Increased coherence, increased clarity The RNA ontology (RNAO) [51] is a biomedical ontology used to describe RNA structure. The core of RNAO is formalized in first-and second-order logic.  ... 
doi:10.1093/bib/bbs053 pmid:22962340 pmcid:PMC3888109 fatcat:lyepy5en5vfpzgbq6uaaxr7aiu

IMIA LaMB WG related event: Proceedings of 3rd International Conference on Biomedical Ontology, 2012, Graz

Ronald Cornet, Robert Stevens, Melanie Courtot, Trish Whetzel, Janna Hastings, Stefan Schulz, Ludger Jansen
2019 Zenodo  
This conference carried on the tradition of discussing medical ontologies, increasingly used in biology and medicine, and their use in annotation of both clinical and experimental data is now a common  ...  It brings together representatives of all major communities involved in the development and application of ontologies in biomedical research ...  ...  The structured vocabulary-based annotations assist in robust and accurate data mining when posing such complex questions in both computational and individual formats at MGI.  ... 
doi:10.5281/zenodo.3381830 fatcat:pnndilxgzzbujnoqz7pytggtdi

Initial Implementation of a Comparative Data Analysis Ontology

Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli, Julie D. Thompson, Arlin Stoltzfus
2009 Evolutionary Bioinformatics  
A key step in developing such an infrastructure is the definition of a formal ontology.  ...  Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO).  ...  Zmasek and Rutger Vos) for sharing expert knowledge and contributing to the concept glossary.  ... 
doi:10.4137/ebo.s2320 pmid:19812726 pmcid:PMC2747124 fatcat:zhi5eidg4bcs5njalpho7gfg7u
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