Positions

Selected Publications

Academic Article

Year Title Altmetric
2022 Development and Validation of an Emergency Department Electronic Medical Record Gout Flare Alert.Arthritis Care and Research2022
2022 The precision medicine process for treating rare disease using the artificial intelligence tool mediKanrenFrontiers in Artificial Intelligence.  5. 2022
2022 Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational scienceClinical and Translational Science.  15:1848-1855. 2022
2022 Progress toward a universal biomedical data translatorClinical and Translational Science.  15:1838-1847. 2022
2018 CUILESS2016: A clinical corpus applying compositional normalization of text mentionsJournal of Biomedical Semantics.  9. 2018
2018 Phenotype Detection Registry System (PheDRS) - Implementation of a Generalizable Single Institution Clinical Registry ArchitectureProceedings / AMIA ... Annual Symposium. AMIA Symposium.  2018:847-856. 2018
2016 Efficient identification of nationally mandated reportable cancer cases using natural language processing and machine learningJournal of the American Medical Informatics Association.  23:1077-1084. 2016
2015 Comparative genome analysis of Mycoplasma pneumoniaeBMC Genomics.  16. 2015
2014 Reduction of hydrogen peroxide accumulation and toxicity by a catalase from Mycoplasma iowaePLoS One.  9. 2014
2014 Draft genome sequence of Hymenobacter sp. strain IS2118, isolated from a freshwater lake in Schirmacher Oasis, Antarctica, reveals diverse genes for adaptation to cold ecosystemsMicrobiology Resource Announcements.  2. 2014
2013 Type 1 and type 2 strains of Mycoplasma pneumoniae form different biofilmsMicrobiology.  159:737-747. 2013
2009 Annotating the human genome with Disease OntologyBMC Genomics.  10. 2009
2007 Genomic differences of Vaccinia virus clones from Dryvax smallpox vaccine: The Dryvax-like ACAM2000 and the mouse neurovirulent Clone-3Vaccine.  25:8807-8832. 2007
2007 OBO-Edit - An ontology editor for biologistsBioinformatics.  23:2198-2200. 2007
2007 Other riffs on cooperation are already showing how well a wiki could work [1]Nature.  446:856. 2007
2007 Interpreting microarray results with gene ontology and MeSHMethods in Molecular Biology.  377:223-241. 2007
2007 GeneChip resequencing of the smallpox virus genome can identify novel strains: A biodefense applicationJournal of Clinical Microbiology.  45:358-363. 2007
2007 Interpreting microarray results with gene ontology and MeSH.Methods in Molecular Biology.  377:223-242. 2007
2007 Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).Methods in Molecular Biology.  408:153-169. 2007
2006 Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complicationVirology Journal.  3. 2006
2006 Genome sequence diversity and clues to the evolution of variola (smallpox) virusScience.  313:807-812. 2006
2002 Poxvirus Orthologous Clusters (POCs)Bioinformatics.  18:1544-1545. 2002

Education And Training

  • Doctor of Philosophy in Computer and Information Sciences, University of Alabama at Birmingham 2016
  • Master's Level Degree in Genetics, University of Alberta 1998
  • Bachelor's Level Degree in Computer Science, University of Alberta 1994
  • Full Name

  • John Osborne