Overview of methodologies for building ontologies

A few research groups are now proposing a series of steps and methodologies for developing ontologies. However, mainly due to the fact that Ontological Engineering is still a relatively immature discipline, each work group employs its own methodology. Our goal is to present the most representative methodologies used in ontology development and to perform an analysis of such methodologies against the same framework of reference. So, the goal of this paper is not to provide new insights about methodologies, but to put it all in one place and help people to select which methodology to use

Resource location based on precomputed partial random walks in dynamic networks

The problem of finding a resource residing in a network node (the \emph{resource location problem}) is a challenge in complex networks due to aspects as network size, unknown network topology, and network dynamics. The problem is especially difficult if no requirements on the resource placement strategy or the network structure are to be imposed, assuming of course that keeping centralized resource information is not feasible or appropriate. Under these conditions, random algorithms are useful to search the network. A possible strategy for static networks, proposed in previous work, uses short random walks precomputed at each network node as partial walks to construct longer random walks with associated resource information. In this work, we adapt the previous mechanisms to dynamic networks, where resource instances may appear in, and disappear from, network nodes, and the nodes themselves may leave and join the network, resembling realistic scenarios. We analyze the resulting resource location mechanisms, providing expressions that accurately predict average search lengths, which are validated using simulation experiments. Reduction of average search lengths compared to simple random walk searches are found to be very large, even in the face of high network volatility. We also study the cost of the mechanisms, focusing on the overhead implied by the periodic recomputation of partial walks to refresh the information on resources, concluding that the proposed mechanisms behave efficiently and robustly in dynamic networks.Comment: 39 pages, 25 figure

Is the bulbus arteriosus of fish homologous to the mamalian intrapericardial thoracic arteries?

El resumen aparece en el Program & Abstracts of the 10th International Congress of Vertebrate Morphology, Barcelona 2013.Anatomical Record, Volume 296, Special Feature — 1: P-089.Two major findings have significantly improved our understanding of the embryology and evolution of the arterial pole of the vertebrate heart (APVH): 1) a new embryonic presumptive cardiac tissue, named second heart field (SHF), forms the myocardium of the outflow tract, and the walls of the ascending aorta (AA) and the pulmonary trunk (PT) in mammals and birds; 2) the bulbus arteriosus (BA), previously thought to be an actinopterygian apomorphy, is present in all basal Vertebrates, and probably derives from the SHF. We hypothesized that the intrapericardial portions of the AA and the PT of mammals are homologous to the BA of basal vertebrates. To test this, we performed 1) a literature review of the anatomy and embryology of the APVH; 2) novel anatomical, histomorphological, and embryological analyses of the APVH, comparing basal (Galeus atlanticus), with apical (Mus musculus and Mesocricetus auratus) vertrebrates. Evidence obtained: 1) Anatomically, BA, AA, and PT are muscular tubes into the pericardial cavity, which connect the distal myocardial outflow tracts with the aortic arch system. Coronary arteries run through or originate at these anatomical structures; 2) Histologically, BA, AA, and PT show an inner layer of endothelium covered by circumferentially oriented smooth muscle cells, collagen fibers, and lamellar elastin. The histomorphological differences between the BA and the ventral aorta parallel those between intrapericardial and extrapericardial great arteries; 3) Embryologically, BA, AA, and PT are composed of smooth muscle cells derived from the SHF. They show a similar mechanism of development: incorporation of SHF‐derived cells into the pericardial cavity, and distal‐to‐proximal differentiation into an elastogenic cell linage. In conclusion, anatomical, histological and embryological evidence supports the hypothesis that SHF is a developmental unit responsible for the formation of the APVH. The BA and the intrapericardial portions of the great arteries must be considered homologous structures.Proyecto P10-CTS-6068 (Junta de Andalucía); proyecto CGL-16417 (Ministerio de Ciencia e Innovación); Fondos FEDER

Incidence and type of bicuspid aortic valve in two model species

Incidence and type of bicuspid aortic valve in two model species. MC Fernández 1,2, A López-García 1,2, MT Soto 1, AC Durán 1,2 and B Fernández 1,2. 1 Department of Animal Biology, Faculty of Science, University of Málaga, Spain. 2 Biomedical Research Institute of Málaga (IBIMA), University of Málaga, Spain. Bicuspid aortic valve (BAV) is the most frequent human congenital cardiac malformation, with an incidence of 1–2% worldwide. Two morphological types exist: type A (incidence 0.75–1.25%) and type B (incidence 0.25–0.5%), each with a distinct aetiology and natural history. Currently, ten animal models of BAV have been described in two different rodent species: one spontaneous Syrian hamster (Mesocricetus auratus) model of BAV type A and nine mutant laboratory mouse (Mus musculus) models of BAV type B. It remains to be elucidated whether the mutations leading to BAV in these models are typespecific or whether there are inter-specific differences regarding the type of BAV that hamsters, mice and humans may develop. To solve this issue, we have characterized the incidence and types of BAVs in four inbred, two outbred and two hybrid lines of Syrian hamsters (n=4,340) and in three inbred, three outbred and one hybrid lines of laboratory mice (n=1,661) by means of stereomicroscopy and scanning electron microscopy. In addition, we have reviewed and calculated the incidence and type of BAVs in the published papers dealing with this anomaly in mice. Our results indicate that the Syrian hamster develops BAVs type A and B including a variety of morphologies comparable to those of humans, whereas the mouse develops only BAVs type B with a short spectrum of valve morphologies. Thus, inter-specific differences between human and mouse aortic valves must be taken into consideration when studying valve disease in murine models. This work was supported by P10-CTS-6068.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. P10-CTS-6068

Effect of hyperlipidic diets on normal and abnormal aortic valves in the Syrian hamster: A preliminary study

Effect of hyperlipidic diets on normal and abnormal aortic valves in the Syrian hamster: A preliminary study. MC Fernández 1,2, J Moncayo-Arlandi 1, MT Soto 1, MA López-Unzu 1, B Fernández 1,2 and AC Durán 1,2. 1 Department of Animal Biology, Faculty of Science, University of Málaga, Spain. 2 Biomedical Research Institute of Málaga (IBIMA), University of Málaga, Spain. Bicuspid aortic valve (BAV) is the most frequent human congenital cardiac malformation. It frequently becomes stenotic due to calcification by an atherosclerosis-like process. Hyperlipidic diets have been classically used to induce atherosclerosis in laboratory animals, including Syrian hamsters. The aim here is to evaluate the effect of hyperlipidic diets in hamsters having different incidence of BAVs. We used a unique inbred strain of Syrian hamsters with a high ( 40%) incidence of spontaneous BAV, morphologically similar to that in man, another inbred strain with a low ( 4%) incidence of BAV, and an outbred, second control line, acquired from Charles River Laboratories. Three experimental groups were fed with standard diet supplemented with 2% cholesterol plus 15% butter during five months. In parallel, three control groups were fed with unmodified standard diet. Hyperlipidic diets induced lesions in the aortic valve and ascending aortic wall, i.e. subendothelial lipid deposits, valve sclerosis, and neo-intima in the aorta. We performed a preliminary, qualitative, comparative study of the lesions associated with the different animal populations and valvular phenotypes. Our results indicate that (1) the type and severity of the lesions varied among the three hamster populations, suggesting that genetic factors may be involved; (2) the aortic valve morphology seems not to determine the severity of the valvular lesions. We conclude that our hamster strain with high incidence of BAV is a promising animal model for studies on human aortic stenosis. This work was supported by P10-CTS-6068.Universidad de Málaga. Campus de Excelencia Andalucía Tech. P10-CTS-6068