Building ontologies in a domain oriented software engineering environment

Ontologies can be used in Domain Oriented Software Engineering Environments (DOSEEs) to organize and describe knowledge and to support management, acquisition and sharing of knowledge regarding some domain. However, ontology construction is not a simple task. Thus, it is necessary to provide tools that support ontology development. This paper discusses the use of ontologies to support domain-oriented software development in ODE, an Ontology-based software Development Environment, and presents ODEd, an ontology editor developed to satisfy the requirements for an ontology editor in a DOSEE. These requirements include the definition of concepts and relations using graphic representations, automatic generation of some classes of axioms, derivation of object frameworks from ontologies, and ontology instantiation and browsing.Eje: Ingeniería de Software y Bases de Datos (ISBD)Red de Universidades con Carreras en Informática (RedUNCI

Building ontologies in a domain oriented software engineering environment

Ontologies can be used in Domain Oriented Software Engineering Environments (DOSEEs) to organize and describe knowledge and to support management, acquisition and sharing of knowledge regarding some domain. However, ontology construction is not a simple task. Thus, it is necessary to provide tools that support ontology development. This paper discusses the use of ontologies to support domain-oriented software development in ODE, an Ontology-based software Development Environment, and presents ODEd, an ontology editor developed to satisfy the requirements for an ontology editor in a DOSEE. These requirements include the definition of concepts and relations using graphic representations, automatic generation of some classes of axioms, derivation of object frameworks from ontologies, and ontology instantiation and browsing.Eje: Ingeniería de Software y Bases de Datos (ISBD)Red de Universidades con Carreras en Informática (RedUNCI

ODE: ontology-based software development environment

Software tools processing partially common set of data should share an understanding of what these data mean. Since ontologies have been used to express formally a shared understanding of information, we argue that they can be used to improve integration in Software Engineering Environments (SEE). In this paper we discuss an ontology-based approach to improve tool integration and present ODE, an ontology-based SEE.Eje: Ingeniería de Software y Bases de Datos (ISBD)Red de Universidades con Carreras en Informática (RedUNCI

ODE: ontology-based software development environment

Software tools processing partially common set of data should share an understanding of what these data mean. Since ontologies have been used to express formally a shared understanding of information, we argue that they can be used to improve integration in Software Engineering Environments (SEE). In this paper we discuss an ontology-based approach to improve tool integration and present ODE, an ontology-based SEE.Eje: Ingeniería de Software y Bases de Datos (ISBD)Red de Universidades con Carreras en Informática (RedUNCI

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

ODE: Ontology-based software Development Environment Ricardo de Almeida Falbo, Ana Candida

Software tools processing partially common set of data should share an understanding of what these data mean. Since ontologies have been used to express formally a shared understanding of information, we argue that they can be used to improve integration in Software Engineering Environments (SEE). In this paper we discuss an ontology-based approach to improve tool integration and present ODE, an ontology-based SEE