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  1. No Access

    Protocol

    Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS)

    Detailed instruction is described for map** unstructured, free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Trans...

    John D. Osborne, Simon Lin, Lihua Julie Zhu, Warren A. Kibbe in Gene Function Analysis (2007)

  2. No Access

    Protocol

    Interpreting Microarray Results With Gene Ontology and MeSH

    Methods are described to take a list of genes generated from a microarray experiment and interpret these results using various tools and ontologies. A workflow is described that details how to convert gene ide...

    John D. Osborne, Lihua (Julie) Zhu, Simon M. Lin in Microarray Data Analysis (2007)

  3. Article

    Open Access

    Annotating the human genome with Disease Ontology

    The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases.

    John D Osborne, Jared Flatow, Michelle Holko, Simon M Lin, Warren A Kibbe in BMC Genomics (2009)

  4. Article

    Open Access

    Comparative genome analysis of Mycoplasma pneumoniae

    Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40 % of community-acquired pneumonias. ...

    Li **ao, Travis Ptacek, John D. Osborne, Donna M. Crabb, Warren L. Simmons in BMC Genomics (2015)