title: Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.
abstract: Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. Such unwanted side effects often go unnoticed since biomedical ontologies are large and complex knowledge structures. Abstraction networks, which provide compact summaries of an ontology's content and structure, have been used to uncover structural irregularities, inconsistencies and errors in ontologies. In this paper, we introduce Diff Abstraction Networks ("Diff AbNs"), compact networks that summarize and visualize global structural changes due to ontology editing operations that result in a new ontology release. A Diff AbN can be used to support curators in identifying unintended and unwanted ontology changes. The derivation of two Diff AbNs, the Diff Area Taxonomy and the Diff Partial-area Taxonomy, is explained and Diff Partial-area Taxonomies are derived and analyzed for the Ontology of Clinical Research, Sleep Domain Ontology, and eagle-i Research Resource Ontology. Diff Taxonomy usage for identifying unintended erroneous consequences of quality assurance and ontology merging are demonstrated.
authors.affiliation: Computer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA. Electronic address: cro3@njit.edu.
authors.forename: Christopher
authors.initials: C
authors.lastname: Ochs
authors.affiliation: Computer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA.
authors.forename: Yehoshua
authors.initials: Y
authors.lastname: Perl
authors.affiliation: Computer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA.
authors.forename: James
authors.initials: J
authors.lastname: Geller
authors.affiliation: Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Haendel
authors.affiliation: Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Brush
authors.affiliation: ONTOPRO, Houston, TX 77025, USA.
authors.forename: Sivaram
authors.initials: S
authors.lastname: Arabandi
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.
authors.forename: Samson
authors.initials: S
authors.lastname: Tu
mesh_terms: D000465:Algorithms; D064229:Biological Ontologies; D035843:Biomedical Research; D003625:Data Collection; D015195:Drug Design; D011786:Quality Control; D012890:Sleep; D012984:Software; D013672:Technology; D018875:Vocabulary, Controlled
keywords: Abstraction networks; Ontology diff; Ontology quality assurance; Ontology version change; Summarizing ontology change; Summarizing ontology evolution; Visualizing ontology evolution