•  393
    The Ontology for Biomedical Investigations
    with Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, and Jie Zheng
    PLoS ONE 11 (4). 2016.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, …Read more
  •  340
    A domain ontology for the non-coding RNA field
    with Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, and Guoqian Jiang
    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 o…Read more
  •  315
    The development of non-coding RNA ontology
    with Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Bin Wu, Harrison Strachan, Nisansa de Silva, and Mohan Vamsi Kasukurthi
    International Journal of Data Mining and Bioinformatics 15 (3): 214--232. 2016.
    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 semant…Read more
  •  296
    OAE: The Ontology of Adverse Events
    with Yongqun He, Sirarat Sarntivijai, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, and Barry Smith
    Journal of Biomedical Semantics 5 (29): 1-13. 2014.
    A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO…Read more
  •  134
    OBCS: The Ontology of Biological and Clinical Statistics
    with Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Alfred Hero, Barry Smith, and Yongqun He
    Proceedings of the Fifth International Conference on Biomedical Ontology 1327 65. 2014.
    Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to pres…Read more
  •  33
    We define DNA sequence by a bottom-up approach, starting with a real sequence from an actual biological sample. By providing axioms for notions of string, substring and strand, we formally define a DNA sequence, and a DNA molecule as composed of two antiparallel strands. We note that a sequence is a kind of group in which each member stands a certain relation to every other. The spatial aspects of a DNA sequence are also described.