6 found
Order:
  1. Towards an Ontological Representation of Resistance: The Case of MRSA.Albert Goldfain, Barry Smith & Lindsay G. Cowell - 2011 - Journal of Biomedical Informatics 44 (1):35-41.
    This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  2. Vital Sign Ontology.Albert Goldfain, Barry Smith, Sivaram Arabandi, Mathias Brochhausen & William R. Hogan - 2011 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Vienna, June 2011. Vienna: pp. 71-74.
    We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...)
    Download  
     
    Export citation  
     
    Bookmark  
  3.  33
    Constructing a Lattice of Infectious Disease Ontologies From a Staphylococcus Aureus Isolate Repository.Albert Goldfain, Lindsay G. Cowell & Barry Smith - 2012 - In Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897).
    A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  4.  53
    Clonal Complexes in Biomedical Ontologies.Albert Goldfain, Lindsay Cowell & Barry Smith - 2009 - In ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. pp. 168.
    An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.
    Download  
     
    Export citation  
     
    Bookmark  
  5.  38
    Dispositions and the Infectious Disease Ontology.Albert Goldfain, Barry Smith & Lindsay Cowell - 2010 - In Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS). IOS Press. pp. 400-413.
    This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  6.  37
    Ontological Representation of CDC Active Bacterial Core Surveillance Case Reports.Albert Goldfain, Barry Smith & Lindsay G. Cowell - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:74-77.
    The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.
    Download  
     
    Export citation  
     
    Bookmark