Revising the UMLS Semantic Network

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration

RelBAC: Relation Based Access Control

TheWeb 2.0, GRID applications and, more recently, semantic desktop applications are bringing the Web to a situation where more and more data and metadata are shared and made available to large user groups. In this context, metadata may be tags or complex graph structures such as file system or web directories, or (lightweight) ontologies. In turn, users can themselves be tagged by certain properties, and can be organized in complex directory structures, very much in the same way as data. Things are further complicated by the highly unpredictable and autonomous dynamics of data, users, permissions and access control rules. In this paper we propose a new access control model and a logic, called RelBAC (for Relation Based Access Control) which allows us to deal with this novel scenario. The key idea, which differentiates RelBAC from the state of the art, e.g., Role Based Access Control (RBAC), is that permissions are modeled as relations between users and data, while access control rules are their instantiations on specific sets of users and objects. As such, access control rules are assigned an arity which allows a fine tuning of which users can access which data, and can evolve independently, according to the desires of the policy manager(s). Furthermore, the formalization of the RelBAC model as an Entity-Relationship (ER) model allows for its direct translation into Description Logics (DL). In turn, this allows us to reason, possibly at run time, about access control policies

Utilising ontology-based modelling for learning content management

Learning content management needs to support a variety of open, multi-format Web-based software applications. We propose multidimensional, model-based semantic annotation as a way to support the management of access to and change of learning content. We introduce an information architecture model as the central contribution that supports multi-layered learning content structures. We discuss interactive query access, but also change management for multi-layered learning content management. An ontology-enhanced traceability approach is the solution

Natural process – Natural selection

Life is supported by a myriad of chemical reactions. To describe the overall process we have formulated entropy for an open system undergoing chemical reactions. The entropy formula allows us to recognize various ways for the system to move towards more probable states. These correspond to the basic processes of life i.e. proliferation, differentiation, expansion, energy intake, adaptation and maturation. We propose that the rate of entropy production by various mechanisms is the fitness criterion of natural selection. The quest for more probable states results in organization of matter in functional hierarchies

Model evolution and system evolution

In this paper we define an evolution mechanism with formal semantics using the metamodeling methodology [Geisler et al.98] based on dynamic logic. A remarkable feature of the metamodeling methodology is the ability to define the relation of intentional and extensional entities within one level, allowing not only for the description of structural relations among the modeling entities, but also for a formal definition of structural\nconstraints and dynamic semantics of the modeled entities. While dynamic semantics on the extensional level means run-time behavior, dynamic semantics on intentional level describes model evolution in the system life cycle

SNOMED CT standard ontology based on the ontology for general medical science

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications

Model evolution and system evolution

In this paper we define an evolution mechanism with formal semantics using the metamodeling methodology [Geisler et al.98] based on dynamic logic. A remarkable feature of the metamodeling methodology is the ability to define the relation of intentional and extensional entities within one level, allowing not only for the description of structural relations among the modeling entities, but also for a formal definition of structural constraints and dynamic semantics of the modeled entities. While dynamic semantics on the extensional level means run-time behavior, dynamic semantics on intentional level describes model evolution in the system life cycle.Eje: Ingeniería de softwareRed de Universidades con Carreras en Informática (RedUNCI