Semantic metrics

In the context of the Semantic Web, many ontology-related operations, e.g. ontology ranking, segmentation, alignment, articulation, reuse, evaluation, can be boiled down to one fundamental operation: computing the similarity and?or dissimilarity among ontological entities, and in some cases among ontologies themselves. In this paper, we review standard metrics for computing distance measures and we propose a series of semantic metrics. We give a formal account of semantic metrics drawn from a variety of research disciplines, and enrich them with semantics based on standard Description Logic constructs. We argue that concept-based metrics can be aggregated to produce numeric distances at ontology-level and we speculate on the usability of our ideas through potential areas

Resistance of Eucalyptus pellita to rust (Puccinia psidii).

Eucalypts rust (Puccinia psidii) is currently one of the major diseases in commercial eucalypt plantations in Brazil. The primary method of disease control is the use of resistant genotypes, and, among the different species of Eucalyptus, E. pellita is indicated as a promising source of resistance. In this work, the genetic control of rust resistance in E. pellita through inoculations under controlled conditions of 441 plants from four full-sibling families was studied. Inoculations were performed using the monopostular isolate UFV-2, race 1. All families tested segregated for rust resistance, and the number of resistant plants was higher than susceptible in all crosses. Inheritance models based on few genes did not fully explain the observed segregation patterns, and the narrow-sense heritability of rust resistance was estimated between 32.7% and 37.3%. The results suggested that rust resistance in E. pellita is complex and is controlled by major- and minor-effect genes

Analytic Metaphysics versus Naturalized Metaphysics: The Relevance of Applied Ontology

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field

SNPs and INDELs in genes involved in lipid metabolism of mammary gland of Zebu breeds identified by whole genome sequencing.

In this context, the objective of this study was to sequence and to map the genome of three Guzerá bulls and three Gir bulls in order to identify zebu-specific variations involved in the lipid metabolism of the mammary gland.ISMB/ECCB 2015. Pôster G28

Work-Unit Absenteeism: Effects of Satisfaction, Commitment, Labor Market Conditions, and Time

Prior research is limited in explaining absenteeism at the unit level and over time. We developed and tested a model of unit-level absenteeism using five waves of data collected over six years from 115 work units in a large state agency. Unit-level job satisfaction, organizational commitment, and local unemployment were modeled as time-varying predictors of absenteeism. Shared satisfaction and commitment interacted in predicting absenteeism but were not related to the rate of change in absenteeism over time. Unit-level satisfaction and commitment were more strongly related to absenteeism when units were located in areas with plentiful job alternatives

Identification of candidate genes for reactivity in Guzerat (Bos indicus) cattle: a genome-wide association study.

Temperament is fundamental to animal production due to its direct influence on the animal-herdsman relationship. When compared to calm animals, the aggressive, anxious or fearful ones exhibit less weight gain, lower reproductive efficiency, decreased milk production and higher herd maintenance costs, all of which contribute to reduced profits. However, temperament is a trait that is complex and difficult to assess. Recently, a new quantitative system, REATEST®, for assessing reactivity, a phenotype of temperament, was developed. Herein, we describe the results of a Genome-wide association study for reactivity, assessed using REATEST® with a sample of 754 females from five dual-purpose (milk and meat production) Guzerat (Bos indicus) herds. Genotyping was performed using a 50k SNP chip and a two-step mixed model approach (Grammar-Gamma) with a one-by-one marker regression was used to identify QTLs. QTLs for reactivity were identified on chromosomes BTA1, BTA5, BTA14, and BTA25. Five intronic and two intergenic markers were significantly associated with reactivity. POU1F1, DRD3, VWA3A, ZBTB20, EPHA6, SNRPF and NTN4 were identified as candidate genes. Previous QTL reports for temperament traits, covering areas surrounding the SNPs/genes identified here, further corroborate these associations. The seven genes identified in the present study explain 20.5% of reactivity variance and give a better understanding of temperament biology

Computational neuroanatomy: ontology-based representation of neural components and connectivity

Background: A critical challenge in neuroscience is organizing, managing, and accessing the explosion in neuroscientific knowledge, particularly anatomic knowledge. We believe that explicit knowledge-based approaches to make neuroscientific knowledge computationally accessible will be helpful in tackling this challenge and will enable a variety of applications exploiting this knowledge, such as surgical planning. Results: We developed ontology-based models of neuroanatomy to enable symbolic lookup, logical inference and mathematical modeling of neural systems. We built a prototype model of the motor system that integrates descriptive anatomic and qualitative functional neuroanatomical knowledge. In addition to modeling normal neuroanatomy, our approach provides an explicit representation of abnormal neural connectivity in disease states, such as common movement disorders. The ontology-based representation encodes both structural and functional aspects of neuroanatomy. The ontology-based models can be evaluated computationally, enabling development of automated computer reasoning applications. Conclusion: Neuroanatomical knowledge can be represented in machine-accessible format using ontologies. Computational neuroanatomical approaches such as described in this work could become a key tool in translational informatics, leading to decision support applications that inform and guide surgical planning and personalized care for neurological disease in the future

Polymorphisms in genes coding milk proteins and protein hormones involved in milk production traits in Brazilian Guzerá cattle.

Research on genes affecting phenotypic variation in milk production and composition from indicine (Bos indicus) cattle is imperative, since these breeds are important tropical genetic resources, and there have been few studies investigating the genetic basis of these traits. We identified polymorphisms in k-casein (CSN3), b-lactoglobulin (LGB), thyroglobulin (TG) and prolactin (PRL) and examined their effect on milk and composition traits in the Guzerá breed. DNA samples of 260 Guzerá cattle selected for dual purpose use were genotyped. Allele frequencies observed for the A allele were 0.83, 0.18 and 0.25 respectively for CSN3, LGB and PRL genes, while for the TG gene T allele had an allele frequency of 0.09. For all polymorphisms evaluated, observed genotypic frequencies were in agreement with those expected according to the Hardy-Weinberg Equilibrium hypothesis. A polymorphism association study evaluated breeding values (BV) for 305-day milk (BV-M), fat (BV-F), and protein (BV-P) production, employing the allele substitution model using a sample of 139 cows belonged to 27 full and half-sib families of a MOET (multiple ovulation and embryo transfer) selection nucleus. Association was found between the LGB polymorphism and BV-M, BV-F and BV-P. Animals with LGB AA genotype have, on average, higher BV when compared to animals with LGB AB and BB genotypes (277.85 kg for BV-M, 12.09 kg for BV-F and 9.33 kg for BV-P). These findings contribute to a better understanding on the influence of these polymorphisms on milk production traits in Guzerá cattle

Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities

BACKGROUND: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. METHODOLOGY/PRINCIPAL FINDINGS: Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. CONCLUSIONS/SIGNIFICANCE: We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle