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  1.  14
    The Development of Non-Coding RNA Ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. 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 specific and highly needed niche in semantic annotation of (...)
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  2.  35
    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 & Others - 2007 - Nature Biotechnology 25 (11):1251-1255.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...)
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  3.  5
    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 - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015),. pp. 975-982.
    Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...)
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    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 - 2015 - In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. 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. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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  5. The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data.Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris J. Mungall, Jane S. Richardson, Jesse Stombaugh & Eric Westhof - 2011 - Applied Ontology 6 (1):53-89.
     
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  6. Novel Sequence Feature Variant Type Analysis of the HLA Genetic Association in Systemic Sclerosis.David Karp, Marthandan R., Marsh Nishanth, Ahn Steven Ge, Arnett Chul, C. Frank, David DeLuca, Diehl S., D. Alexander, Raymond Dunivin, Karen Eilbeck, Michael Feolo & Others - 2009 - Human Molecular Genetics 19 (4):707--719.
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