Guidelines for writing definitions in ontologies

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic

Definitions in ontologies

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies

The functions of definitions in ontologies

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies

Optical reading of typeset music

Thesis (M.S.V.S.)--Massachusetts Institute of Technology, Dept. of Architecture, 1991.Includes bibliographical references (leaves 161-162).by Alan Ruttenberg.M.S.V.S

Developing the Quantitative Histopathology Image Ontology : A case study using the hot spot detection problem

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts

Characteristics of Medical Research News Reported on Front Pages of Newspapers

Background: The placement of medical research news on a newspaper's front page is intended to gain the public's attention, so it is important to understand the source of the news in terms of research maturity and evidence level. Methodology/Principal Findings: We searched LexisNexis to identify medical research reported on front pages of major newspapers published from January 1, 2000 to December 31, 2002. We used MEDLINE and Google Scholar to find journal articles corresponding to the research, and determined their evidence level. Of 734 front-page medical research stories identified, 417 (57%) referred to mature research published in peer-reviewed journals. The remaining 317 stories referred to preliminary findings presented at scientific or press meetings; 144 (45%) of those stories mentioned studies that later matured (i.e. were published in journals within 3 years after news coverage). The evidence-level distribution of the 515 journal articles quoted in news stories reporting on mature research (3% level I, 21% level II, 42% level III, 4% level IV, and 31% level V) differed from that of the 170 reports of preliminary research that later matured (1%, 19%, 35%, 12%, and 33%, respectively; chi-square test, P = .0009). No news stories indicated evidence level. Fewer than 1 in 5 news stories reporting preliminary findings acknowledged the preliminary nature of their content. Conclusions/Significance: Only 57% of front-page stories reporting on medical research are based on mature research, which tends to have a higher evidence level than research with preliminary findings. Medical research news should be clearly referenced and state the evidence level and limitations to inform the public of the maturity and quality of the source. © 2009 Lai, Lane.published_or_final_versio

MIREOT: the Minimum Information to Reference an External Ontology Term

While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions

Ontology and the Future of Dental Research Informatics.

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR)

Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework

The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps

An Extended Nomenclature for Mammalian V-ATPase Subunit Genes and Splice Variants

The vacuolar-type H+-ATPase (V-ATPase) is a multisubunit proton pump that is involved in both intra- and extracellular acidification processes throughout the body. Multiple homologs and splice variants of V-ATPase subunits are thought to explain its varied spatial and temporal expression pattern in different cell types. Recently subunit nomenclature was standardized with a total of 22 subunit variants identified. However this standardization did not accommodate the existence of splice variants and is therefore incomplete. Thus, we propose here an extension of subunit nomenclature along with a literature and sequence database scan for additional V-ATPase subunits. An additional 17 variants were pulled from a literature search while 4 uncharacterized potential subunit variants were found in sequence databases. These findings have been integrated with the current V-ATPase knowledge base to create a new V-ATPase subunit catalogue. It is envisioned this catalogue will form a new platform on which future studies into tissue- and organelle-specific V-ATPase expression, localization and function can be based