21,874 research outputs found
A pattern-based approach to a cell tracking ontology
Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations
Guidelines to Study Differences in Expressiveness between Ontology Specification Languages: A Case Of Study
We focus on our experiences on translating ontologies between two ontology languages, FLogic and Ontolingua, in the framework of Methontology and ODE. Rather than building "ad hoc" translators between languages or using KIF, our option consists of translating through ODE intermediate representations. So, we have built direct translators from ODE intermediate representations to Ontolingua and FLogic, and we have also built reverse translators from these two languages to ODE intermediate representations. Expressiveness of the target languages is the main feature to analyse when automatically generating ontologies from ODE intermediate representations. Therefore, we analyse the expressiveness of Ontolingua and FLogic for creating classes, instances, relations, functions and axioms, which are the essential components in ontologies. The motivation for this analysis can be found in the (KA)² initiative and can be easily extended to any other domains and languages
A Double Classification of Common Pitfalls in Ontologies
The application of methodologies for building ontologies has improved the ontology quality. However, such a quality is not totally guaranteed because of the difficulties involved in ontology modelling. These difficulties are related to the inclusion of anomalies or worst practices in the modelling. In this context, our aim in this paper is twofold: (1) to provide a catalogue of common worst practices, which we call pitfalls, and (2) to present a double classification of such pitfalls. These two products will serve in the ontology development in two ways: (a) to avoid the appearance of pitfalls in the ontology modelling, and (b) to evaluate and correct ontologies to improve their quality
Knowledge Representation with Ontologies: The Present and Future
Recently, we have seen an explosion of interest in ontologies as
artifacts to represent human knowledge and as critical components in
knowledge management, the semantic Web, business-to-business
applications, and several other application areas. Various research
communities commonly assume that ontologies are the appropriate modeling
structure for representing knowledge. However, little discussion has
occurred regarding the actual range of knowledge an ontology can
successfully represent
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
Magpie: towards a semantic web browser
Web browsing involves two tasks: finding the right web page and then making sense of its content. So far, research has focused on supporting the task of finding web resources through ‘standard’ information retrieval mechanisms, or semantics-enhanced search. Much less attention has been paid to the second problem. In this paper we describe Magpie, a tool which supports the
interpretation of web pages. Magpie offers complementary knowledge sources, which a reader can call upon to quickly gain access to any background knowledge relevant to a web resource. Magpie automatically associates an ontologybased
semantic layer to web resources, allowing relevant services to be invoked within a standard web browser. Hence, Magpie may be seen as a step towards a semantic web browser. The functionality of Magpie is illustrated using examples of how it has been integrated with our lab’s web resources
Ontologies and Information Extraction
This report argues that, even in the simplest cases, IE is an ontology-driven
process. It is not a mere text filtering method based on simple pattern
matching and keywords, because the extracted pieces of texts are interpreted
with respect to a predefined partial domain model. This report shows that
depending on the nature and the depth of the interpretation to be done for
extracting the information, more or less knowledge must be involved. This
report is mainly illustrated in biology, a domain in which there are critical
needs for content-based exploration of the scientific literature and which
becomes a major application domain for IE
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