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

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

Proceso de desarrollo de ontologías: Ontología de Iones Monoatómicos

Dentro del campo de las Ciencias Ambientales trabajan expertos en diversos dominios tales como: Biología, Geología, Química, Derecho, Computación, etc. Cada experto utiliza vocabulario relacionado con distintas áreas de esta ciencia, no existiendo una terminología común, ni una norma que ayude a utilizar cada término con precisión. Además, desde una perspectiva terminológica, la existencia de sinónimos, el hecho de que un mismo término se pueda utilizar en distintas Ciencias y en cada una tener significado similar, pero no idéntico, y las diferencias semánticas que aparecen al utilizar un mismo término en diferentes dominios, todo ello origina que sea necesario obtener una terminología unificada, completa y coherente que pueda ser utilizada de manera consistente y precisa, de forma que sea adecuada para diferentes contextos y aplicaciones medioambientales. Para conseguir este objetivo, pueden utilizarse las ontologías