A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of similar to 240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, "preferred terms", and "structural equivalency". We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the "URI table") by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the "Analyzer") to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

Induced tooth movement: standardization of terms to describe the effects of forces on the periodontal ligament: compression/Traction instead of Pressure/Tension

There is no reason for Dentistry to use different terms for phenomena defined in Physics, the specific field in which concepts associated with forces are established and adapted. In place of pressure/tension, the compression/traction pair should be used. This study defines each one of these terms and justifies their use. Our contemporary world demands standardized criteria, methods, measures, concepts and terms to ensure that study protocols, results and applications are used in the same way in any country or area of human action.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Fourier´s law from a chain of coupled anharmonic oscillators under energy conserving shot noise.

We analyze the transport of heat along a chain of particles interacting through anharmonic potentials consisting of quartic terms in addition to harmonic quadratic terms and subject to heat reservoirs at its ends. Each particle is also subject to an impulsive shot noise with exponentially distributed waiting times whose effect is to change the sign of its velocity, thus conserving the energy of the chain. We show that the introduction of this energy conserving stochastic noise leads to Fourier's law. That is for large system size L the heat current J behaves as J ‘approximately’ 1/L, which amounts to say that the conductivity k is constant. The conductivity is related to the current by J = kΔT/L, where ΔT is the difference in the temperatures of the reservoirs. The behavior of heat conductivity k for small intensities¸ of the shot noise and large system sizes L are obtained by assuming a scaling behavior of the type k = ‘L POT a Psi’(L’lambda POT a/b’) where a and b are scaling exponents. For the pure harmonic case a = b = 1, characterizing a ballistic conduction of heat when the shot noise is absent. For the anharmonic case we found values for the exponents a and b smaller then 1 and thus consistent with a superdiffusive conduction of heat without the shot noise. We also show that the heat conductivity is not constant but is an increasing function of temperature.

A Fuzzy Ontology-Driven Approach to Semantic Interoperability in e-Government Big Data

With the increasing production of information from e-government initiatives, there is also the need to transform a large volume of unstructured data into useful information for society. All this information should be easily accessible and made available in a meaningful and effective way in order to achieve semantic interoperability in electronic government services, which is a challenge to be pursued by governments round the world. Our aim is to discuss the context of e-Government Big Data and to present a framework to promote semantic interoperability through automatic generation of ontologies from unstructured information found in the Internet. We propose the use of fuzzy mechanisms to deal with natural language terms and present some related works found in this area. The results achieved in this study are based on the architectural definition and major components and requirements in order to compose the proposed framework. With this, it is possible to take advantage of the large volume of information generated from e-Government initiatives and use it to benefit society.