Knowledge Base Version Reintegration

Given two versions of a knowledge base (KB), independently modified, we investigated the problem of incorporating changes made to one KB version into the other. We have implemented a system that will perform such a reintegration, autonomously, using predetermined user preferences. This effort has lead to a greater insight into the version reintegration problem and has highlighted those areas where user intervention would be the most beneficial in a semi-autonomous system

An Intuitive Graphical Query Interface for Protégé Knowledge Bases

Emily is a graphical query engine for Protégé knowledge bases that was developed by the Structural Informatics Group (SIG) at the University of Washington. Currently this application is adapted for a specific knowledge model, the Foundational Model of Anatomy (FMA) [1], but it could readily be generalized for use with other Protégé knowledge bases. In developing the Emily query interface, our intent was to provide a tool that was simple and intuitive to use, like the Queries tab provided with Protégé, but with improved information retrieval capabilities. Although some more advanced query mechanisms exist, currently they are too complicated for non-expert end users. The Algernon tab [2], for example, provides extensive Protégé query capabilities but requires users to learn a query scripting language. We sought to develop a query interface that was intuitive enough for end users to operate, with only minor instruction, yet was powerful enough to gather interesting information from a knowledge base that was not easily attained by browsing alone

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

A Relation-Centric Query Engine for the Foundational Model of Anatomy

The Foundational Model of Anatomy (FMA), a detailed representation of the structural organization of the human body, was constructed to support the development of software applications requiring knowledge of anatomy. The FMA's focus on the structural relationships between anatomical entities distinguishes it from other current anatomical knowledge sources. We developed Emily, a query engine for the FMA, to enable users to explore the richness and depth of these relationships. Preliminary analysis suggests that Emily is capable of correctly processing real world anatomical queries provided they have been translated into a constrained form suitable for processing by the query engine

BodyParts3D: 3D structure database for anatomical concepts

BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a 3D whole-body model for an adult human male. It encompasses morphological and geometrical knowledge in anatomy and complements ontological representation. Moreover, BodyParts3D introduces a universal coordinate system in human anatomy, which may facilitate management of samples and data in biomedical research and clinical practice. As of today, 382 anatomical concepts, sufficient for mapping materials in most molecular medicine experiments, have been specified. Expansion of the dictionary by adding further segments and details to the whole-body model will continue in collaboration with clinical researchers until sufficient resolution and accuracy for most clinical application are achieved. BodyParts3D is accessible at: http://lifesciencedb.jp/ag/bp3d/

Mealtime Experiences of Children with Autism Spectrum Disorder from the Perspectives of Filipino Occupational Therapists in Cebu: Implications for Practice

Purpose: Occupational therapists (OTs) handle children diagnosed with autism spectrum disorder (ASD), and a common concern is how their sensory processing issues affect their feeding habits. There is limited information regarding interventions about this issue both locally and internationally. This study aims to know the experiences of OTs providing feeding interventions associated with sensory issues for children with ASD. It will also describe what approaches they used for these interventions. Method: Qualitative phenomenology using in-depth interviews with nine OTs in Cebu, Philippines was conducted, and data underwent thematic analysis. Results: Five themes emerged: 1) a family that feeds together, stays together, 2) key to mealtime challenges, 3) root of mealtime challenges, 4) highs and lows of a therapist on feeding interventions, and 5) teletherapy as a sign of times. Conclusion: OTs and parents look at foundational skill deficits of a child with ASD and relate the said skill deficits to mealtime behaviors and challenges. Results provided in-depth description of what current intervention approaches the selected therapists choose and how they are applied and combined in targeting feeding concerns and sensory issues that relate to feeding. Handling feeding issues is also an opportunity for OTs to work with other healthcare professionals

Observation of the lowest energy gamma-ray in any superdeformed nucleus : 196Bi

New results on the superdeformed $^{196}$Bi nucleus a re reported. We have observed with the EUROBALL IV $\gamma$-ray spectrometer array a superdeformed trans ition of 124 keV which is the lowest observed energy $\gamma$-ray in any superdeformed nucleus. We have de velopped microscopic cranked Hartree-Fock-Bogoliubov calculations using the SLy4 effective force and a realistic surface p airing which strongly support the $K^\pi=2^-$($\pi$[651]1/2$\otimes \nu$[752]5/2) assignment of this su perdeformed band

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

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