Ontological Reengineering for Reuse

This paper presents the concept of Ontological Reengineering as the process of retrieving and transforming a conceptual model of an existing and implemented ontology into a new, more correct and more complete conceptual model which is reimplemented. Three activities have been identified in this process: reverse engineering, restructuring and forward engineering. The aim of Reverse Engineering is to output a possible conceptual model on the basis of the code in which the ontology is implemented. The goal of Restructuring is to reorganize this initial conceptual model into a new conceptual model, which is built bearing in mind the use of the restructured ontology by the ontology/application that reuses it. Finally, the objective of Forward Engineering is output a new implementation of the ontology. The paper also discusses how the ontological reengineering process has been applied to the Standard-Units ontology [18], which is included in a Chemical-Elements [12] ontology. These two ontologies will be included in a Monatomic-Ions and Environmental-Pollutants ontologies

Rationalized development of a campus-wide cell line dataset for implementation in the biobank LIMS system at Bioresource center Ghent

The Bioresource center Ghent is the central hospital-integrated biobank of Ghent University Hospital. Our mission is to facilitate translational biomedical research by collecting, storing and providing high quality biospecimens to researchers. Several of our biobank partners store large amounts of cell lines. As cell lines are highly important both in basic research and preclinical screening phases, good annotation, authentication, and quality of these cell lines is pivotal in translational biomedical science. A Biobank Information Management System (BIMS) was implemented as sample and data management system for human bodily material. The samples are annotated by the use of defined datasets, based on the BRISQ (Biospecimen Reporting for Improved Study Quality) and Minimum Information About Biobank data Sharing (MIABIS) guidelines completed with SPREC (Standard PREanalytical Coding) information. However, the defined dataset for human bodily material is not ideal to capture the specific cell line data. Therefore, we set out to develop a rationalized cell line dataset. Through comparison of different datasets of online cell banks (human, animal, and stem cell), we established an extended cell line dataset of 156 data fields that was further analyzed until a smaller dataset-the survey dataset of 54 data fields-was obtained. The survey dataset was spread throughout our campus to all cell line users to rationalize the fields of the dataset and their potential use. Analysis of the survey data revealed only small differences in preferences in data fields between human, animal, and stem cell lines. Hence, one essential dataset for human, animal and stem cell lines was compiled consisting of 33 data fields. The essential dataset was prepared for implementation in our BIMS system. Good Clinical Data Management Practices formed the basis of our decisions in the implementation phase. Known standards, reference lists and ontologies (such as ICD-10-CM, animal taxonomy, cell line ontology...) were considered. The semantics of the data fields were clearly defined, enhancing the data quality of the stored cell lines. Therefore, we created an essential cell line dataset with defined data fields, useable for multiple cell line users

Facets, Tiers and Gems: Ontology Patterns for Hypernormalisation

There are many methodologies and techniques for easing the task of ontology building. Here we describe the intersection of two of these: ontology normalisation and fully programmatic ontology development. The first of these describes a standardized organisation for an ontology, with singly inherited self-standing entities, and a number of small taxonomies of refining entities. The former are described and defined in terms of the latter and used to manage the polyhierarchy of the self-standing entities. Fully programmatic development is a technique where an ontology is developed using a domain-specific language within a programming language, meaning that as well defining ontological entities, it is possible to add arbitrary patterns or new syntax within the same environment. We describe how new patterns can be used to enable a new style of ontology development that we call hypernormalisation

A group learning management method for intelligent tutoring systems

In this paper we propose a group management specification and execution method that seeks a compromise between simple course design and complex adaptive group interaction. This is achieved through an authoring method that proposes predefined scenarios to the author. These scenarios already include complex learning interaction protocols in which student and group models use and update are automatically included. The method adopts ontologies to represent domain and student models, and object Petri nets to specify the group interaction protocols. During execution, the method is supported by a multi-agent architecture