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The Unified Medical Language System and the Gene Ontology: Some Critical Reflections
, 2003
"... The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them... ..."
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The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them...
Basic Formal Ontology for Bioinformatics
"... Two senses of ‘ontology ’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or dat ..."
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Two senses of ‘ontology ’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is
Clinical guidelines as plans: an ontological theory
- Methods of Information in Medicine
, 2006
"... Clinical guidelines are special types of plans realized by collective agents in health care organizations. We use this idea as the basis for a new understanding of the way in which guideline-based systems can be employed in the management of workflow in health care organizations. The framework we pr ..."
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Clinical guidelines are special types of plans realized by collective agents in health care organizations. We use this idea as the basis for a new understanding of the way in which guideline-based systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how guidelines are realized through the actions of individuals organized into teams. Implementations built in conformity with our framework will accordingly be marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than are standard guideline-based management systems. 2
Granular computing applied to ontologies
- In printing
"... Abstract. Granular Computing is an emerging conceptual and computing paradigm of information processing. A central notion is an information-processing pyramid with different levels of clarifications. Each level is usually represented by ‘chunks ’ of data or granules, also known as information granul ..."
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Abstract. Granular Computing is an emerging conceptual and computing paradigm of information processing. A central notion is an information-processing pyramid with different levels of clarifications. Each level is usually represented by ‘chunks ’ of data or granules, also known as information granules. Rough Set Theory is one of the most widely used methodologies for handling or defining granules. Ontologies are used to represent the knowledge of a domain for specific ap-plications. A challenge is to define semantic knowledge at different levels of human-depending detail. In this paper we prose four operations in order to have several granular perspectives for a specific ontological commitment. Then these operations are used to have various views of an ontology built with a rough-set approach. In particular, a rough methodology is introduced to construct a specific granular view of an ontology.
The Ontology of Blood Pressure: A Case Study in Creating Ontological Partitions in Biomedicine
"... ven intervals of time. They never exist in full in any single instant. Rather, they unfold themselves through time in the way in which the process of blood circulating through the body unfolds itself in time (Bittner & Smith, 2003). To say that an entity is dependent is to assert that it requir ..."
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Cited by 3 (0 self)
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ven intervals of time. They never exist in full in any single instant. Rather, they unfold themselves through time in the way in which the process of blood circulating through the body unfolds itself in time (Bittner & Smith, 2003). To say that an entity is dependent is to assert that it requires a support from other entities in order to be sustained in existence. There is no Cardiac output without a heart and no Cellular motion without some cell which moves. Independent entities, in contrast, require no support of this sort from other entities. They are the substrates for entities in other categories. Dependence relations can obtain also between dependent entities themselves and we can represent the networks of such relations in graph-theoretical terms (Smith, 1992). At some stage, though, dependence relations must bottom out, in entities which are not themselves dependent on anything else. Two important subspecies of dependence relations linking dependent entities can be distingui
Towards a Geographic Ontology Reference Model for Matching Purposes
"... Abstract. Ontologies and geographic ontologies are becoming important research and application fields for the geographic information systems (GIS) community. Although geographic ontologies (also known as spatial-temporal ontologies, geo-ontologies or geospatial ontologies) are becoming popular, a st ..."
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Abstract. Ontologies and geographic ontologies are becoming important research and application fields for the geographic information systems (GIS) community. Although geographic ontologies (also known as spatial-temporal ontologies, geo-ontologies or geospatial ontologies) are becoming popular, a standard and complete model is still missing. The attempts for establishing standards are yet incipient, i.e., do not fulfill the actual needs. In this paper we propose a reference model for developing geographic ontologies, with the specific purpose of matching. The main idea is to extend the model for conventional, non-geographic, ontologies to make it suitable for describing the particularities of the GIS data and the relationships among them. Resumo. Ontologias e, mais especificamente, ontologias geográficas, estão se tornando um importante campo de aplicação e pesquisa relacionado à comunidade
Formal ontologies for space and time
, 2003
"... We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into ..."
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We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account
Scale in object and process ontologies
"... Abstract. Scale is of great importance to the analysis of real world phenomena, be they enduring objects or perduring processes. This paper presents a new perspective on the concept of scale by considering it within two complementary ontological views. The first, called SNAP, recognizes enduring ent ..."
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Abstract. Scale is of great importance to the analysis of real world phenomena, be they enduring objects or perduring processes. This paper presents a new perspective on the concept of scale by considering it within two complementary ontological views. The first, called SNAP, recognizes enduring entities or objects, the other, called SPAN, perduring entities or processes. Within the meta-theory provided by the complementary SNAP and SPAN ontologies, we apply different theories of formal ontology such as mereology and granular partitions, and ideas derived from hierarchy theory. These theories are applied to objects and processes and form the framework within which we present tentative definitions of scale, which are found to differ between the two ontologies.
An Ontological Framework for the Implementation of Clinical
- Studies In Health Technology And Informatics, 2004
"... The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enable ..."
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The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems.
RESEARCH ARTICLE Open Access
"... Research article Spatio-structural granularity of biological material entities ..."
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Research article Spatio-structural granularity of biological material entities
