语义Web中描述逻辑本体的可伸缩推理和非一致处理

随着Web信息的与日俱增，使用机器处理这种信息成为一种必然的趋势。语义Web应运而生，成为当前研究的热点之一。它以本体为核心，为不同领域提供共享的词汇，以便机器处理Web信息。表达本体的标准语言OWL以描述逻辑为基础。OWL本体的推理可伸缩性差，难以适应规模较大的本体应用，因此推理可伸缩性问题是一个重要的实际问题。此外，OWL本体是一个逻辑系统，在生成、维护和集成等过程中，都很容易出现非一致现象，导致标准的推理机制不能正常运作。因此本体非一致问题是另一个重要的实际问题。针对上述两个实际问题，本文分别在实现可伸缩推理、修复非一致本体、以及进行非一致容忍推理三个方面提出了解决办法。 [可伸缩推理方面] 本文提出了一种本体断言公理集的划分方法，使本体推理能够在独立的划分子集中进行，以此提高本体推理的可伸缩性。 [本体修复方面] 本文提出了一种计算具有最小删除代价的本体子集的方法；通过删除这种本体子集，可以恢复本体的一致性。该方法将计算上述本体子集的问题归约为在命题逻辑程序中计算某种最优模型的问题，以调用现有的可满足性问题求解器来解决。 [非一致容忍推理方面] 本文将命题逻辑中字典序推理方法应用到描述逻辑中，以提供针对非一致本体的查询机制。本文还提出了一种在描述逻辑本体中进行字典序推理的方法。该方法将字典序结论的判定问题归约为命题可满足性判定问题，以调用现有的可满足性问题求解器来解决。

How well do we understand the clusters found in microarray data?

Clare, A. and King R.D. (2002) How well do we understand the clusters found in microarray data? In In Silico Biol. 2, 0046

ART: An ontology based tool for the translation of papers into Semantic Web format

To be presented at SIG/ISMB07 ontology workshop: http://bio-ontologies.org.uk/index.php To be published in BMC Bioinformatics. Sponsorship: JISC

Merleau-Ponty and Nishida: Artistic expression as 'motor-perceptual faith'

This dissertation carries out a dialogue between Maurice Merleau-Ponty and Nishida Kitarō concerning their theories of artistic expression and faith. Both philosophers go through remarkably similar trajectories in their philosophic projects: In their early works they focus on the motor-perceptual body of the artist, and as they move towards the mature articulation of their ontologies, the concept of faith becomes central. I propose the term “motor-perceptual faith” to bring these seemingly diverse sets of concerns into a conceptual continuity. My study explores this connection, and argues that the artist’s motor-perceptual expressive body, as colourfully and sometimes poetically articulated in their early works, enacts the form of faith developed more abstractly in their later writings. Exploring these relations fosters a mutual expansion of the early by the later works, thus thickening the concept of faith by seeing it as enacted by the artist, while enlarging the concept of artistic expression by understanding it as a practice of motor‐perceptual faith. Framing these philosophers as putting forth a traditionally religious concept as illustrated by way of artistic expression, offers a new articulation of both of their writings, an important conceptual bridge between the two, while challenging un-ambiguous distinctions between art, philosophy and religion, and ultimately philosophy East and West.

Phenex: ontological annotation of phenotypic diversity.

BACKGROUND: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. CONCLUSIONS/SIGNIFICANCE: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

A unified anatomy ontology of the vertebrate skeletal system.

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

BACKGROUND: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. DEVELOPMENT AND TESTING OF THE ONTOLOGY: Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. RESULTS AND SIGNIFICANCE: Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

I wanna be a protocol: online media and electronic structures of kinship

Heidegger famously identified Modernity with a technological leveling of being to a single order of a “standing reserve.” In a radically different tone, Gilles Deleuze articulated a single “plane of immanence” within which ontological distinctions between mind and body, God and world, interiority and exteriority become indiscernible. Taking such philosophical declarations as points of departure, this panel will consider how a collapse of ontological distinction emerged as a thematic and structural trope in literary and cinematic modernisms. We hope to consider how writers and film-makers of the 20th c. utilize the resources of their media to ask “the question of being” that troubled their philosophical contemporaries and heirs. In this vein, we will examine how these modernist ontologies of immanence describe the crisis of a subject saturated and eclipsed by a world which comprises her while also remaining strange or opaque. Papers will ask what is lost with the departure of a distinctly human sense of “being” and how the historical arrival of an alternative ontological order may be evident in the lived experience of modernity. In this sense, the relationship to departures and arrivals becomes the modern subject’s suspicion that he is unable to do either vis á vis the world.

Engineering design knowledge management in de-centralised virtual enterprises

The problems of collaborative engineering design and knowledge management at the conceptual stage in a network of dissimilar enterprises was investigated. This issue in engineering design is a result of the supply chain and virtual enterprise (VE) oriented industry that demands faster time to market and accurate cost/manufacturing analysis from conception. The solution consisted of a de-centralised super-peer net architecture to establish and maintain communications between enterprises in a VE. In the solution outlined below, the enterprises are able to share knowledge in a common format and nomenclature via the building-block shareable super-ontology that can be tailored on a project by project basis, whilst maintaining the common nomenclature of the ‘super-ontology’ eliminating knowledge interpretation issues. The two-tier architecture layout of the solution glues together the peer-peer and super-ontologies to form a coherent system for both internal and virtual enterprise knowledge management and product development.

La Web Semántica y los archivos de televisión: estado de la cuestión

Se analizan y describen las principales líneas de trabajo de la Web Semántica en el ámbito de los archivos de televisión. Para ello, se analiza y contextualiza la web semántica desde una perspectiva general para posteriormente analizar las principales iniciativas que trabajan con lo audiovisual: Proyecto MuNCH, Proyecto S5T, Semantic Television y VideoActive.

A Data Model for Content Modelling of Temporal Media

This paper describes a data model for content representation of temporal media in an IP based sensor network. The model is formed by introducing the idea of semantic-role from linguistics into the underlying concepts of formal event representation with the aim of developing a common event model. The architecture of a prototype system for a multi camera surveillance system, based on the proposed model is described. The important aspects of the proposed model are its expressiveness, its ability to model content of temporal media, and its suitability for use with a natural language interface. It also provides a platform for temporal information fusion, as well as organizing sensor annotations by help of ontologies.

Wind Power Planning: Problems and Perceptions in Practice and Procedure

Despite the fact that the UK has highest potential in the EU to generate renewable energy from wind, it lags behind its European partners. The departure point for this study is provided by the fact that the land use planning system has been perceived by some to create difficulties in pursuit of the achievement of National Action Plan targets. In the course of a review of literature, legislation, policy and case files a number of issues emerge relating not only to operational practice but structural concerns regarding knowledge, legitimacy and ethics. These are scrutinised in an empirical investigation which provides insights into the ontologies behind how knowledge is used and abused. Concerns are highlighted regarding the tactical manipulation of knowledges and the difficulties associated with objectifying evidence so that it can be understood, validated and authenticated. The paper concludes by reflecting on the implications for the regulatory framework, the legitimisation of decisions and the ethics of the profession and how these, in turn, are conditioned by the production, use and transparency of planning knowledge.

Meta-analysis of Positive and Negative Symptoms Reveals Schizophrenia Modifier Genes

BACKGROUND: Evidence suggests that genetic factors may influence both schizophrenia (Scz) and its clinical presentation. In recent years, genome-wide association studies (GWAS) have demonstrated considerable success in identifying risk loci. Detection of "modifier loci" has the potential to further elucidate underlying disease processes.

METHODS: We performed GWAS of empirically derived positive and negative symptom scales in Irish cases from multiply affected pedigrees and a larger, independent case-control sample, subsequently combining these into a large Irish meta-analysis. In addition to single-SNP associations, we considered gene-based and pathway analyses to better capture convergent genetic effects, and to facilitate biological interpretation of these findings. Replication and testing of aggregate genetic effects was conducted using an independent European-American sample.

RESULTS: Though no single marker met the genome-wide significance threshold, genes and ontologies/pathways were significantly associated with negative and positive symptoms; notably, NKAIN2 and NRG1, respectively. We observed limited overlap in ontologies/pathways associated with different symptom profiles, with immune-related categories over-represented for negative symptoms, and addiction-related categories for positive symptoms. Replication analyses suggested that genes associated with clinical presentation are generalizable to non-Irish samples.

CONCLUSIONS: These findings strongly support the hypothesis that modifier loci contribute to the etiology of distinct Scz symptom profiles. The finding that previously implicated "risk loci" actually influence particular symptom dimensions has the potential to better delineate the roles of these genes in Scz etiology. Furthermore, the over-representation of distinct gene ontologies/pathways across symptom profiles suggests that the clinical heterogeneity of Scz is due in part to complex and diverse genetic factors.