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The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
2009
Nature Precedings
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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
2016
International Journal of Data Mining and Bioinformatics
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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
2015
2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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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
2011
Standards in Genomic Sciences
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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
2016
Journal of Biomedical Semantics
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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
2010
Journal of Biomedical Semantics
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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
2007
Nature Biotechnology
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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
2011
RNA: A publication of the RNA Society
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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
2015
2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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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
2007
Computer applications in the biosciences : CABIOS
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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
2011
International Journal of Computer Applications
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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
2016
Journal of Biomedical Semantics
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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
2012
Briefings in Bioinformatics
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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
2019
Zenodo
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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
2009
Evolutionary Bioinformatics
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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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