The ontological deficiencies of process modeling in practice

Business process modeling is widely regarded as one of the most popular forms of conceptual modeling. However, little is known about the capabilities and deficiencies of process modeling grammars and how existing deficiencies impact actual process modeling practice. This paper is a first contribution towards a theory-driven, exploratory empirical investigation of the ontological deficiencies of process modeling with the industry standard Business Process Modeling Notation (BPMN). We perform an analysis of BPMN using a theory of ontological expressiveness. Through a series of semi-structured interviews with BPMN adopters we explore empirically the actual use of this grammar. Nine ontological deficiencies related to the practice of modeling with BPMN are identified, for example, the capture of business rules and the specification of process decompositions. We also uncover five contextual factors that impact on the use of process modeling grammars, such as tool support and modeling conventions. We discuss implications for research and practice, highlighting the need for consideration of representational issues and contextual factors in decisions relating to BPMN adoption in organizations.

Ontologies derived from Wikipedia : a framework for comparison

Since its debut in 2001 Wikipedia has attracted the attention of many researchers in different fields. In recent years researchers in the area of ontology learning have realised the huge potential of Wikipedia as a source of semi-structured knowledge and several systems have used it as their main source of knowledge. However, the techniques used to extract semantic information vary greatly, as do the resulting ontologies. This paper introduces a framework to compare ontology learning systems that use Wikipedia as their main source of knowledge. Six prominent systems are compared and contrasted using the framework.

Semantic search and inferencing in health informatics

Consider a person searching electronic health records, a search for the term ‘cracked skull’ should return documents that contain the term ‘cranium fracture’. A information retrieval systems is required that matches concepts, not just keywords. Further more, determining relevance of a query to a document requires inference – its not simply matching concepts. For example a document containing ‘dialysis machine’ should align with a query for ‘kidney disease’. Collectively we describe this problem as the ‘semantic gap’ – the difference between the raw medical data and the way a human interprets it. This paper presents an approach to semantic search of health records by combining two previous approaches: an ontological approach using the SNOMED CT medical ontology; and a distributional approach using semantic space vector space models. Our approach will be applied to a specific problem in health informatics: the matching of electronic patient records to clinical trials.

Do ontological deficiencies in modeling grammars matter?

Conceptual modeling grammars are a fundamental means for specifying information systems requirements. However, the actual usage of these grammars is only poorly understood. In particular, little is known about how properties of these grammars inform usage beliefs such as usefulness and ease of use. In this paper we use an ontological theory to describe conceptual modeling grammars in terms of their ontological deficiencies, and formulate two propositions in regard to how these ontological deficiencies influence primary usage beliefs. Using BPMN as an example modeling grammar, we surveyed 528 modeling practitioners to test the theorized relationships. Our results show that users of conceptual modeling grammars perceive ontological deficiencies to exist, and that these deficiency perceptions are negatively associated with usefulness and ease of use of these grammars. With our research we provide empirical evidence in support of the predictions of the ontological theory of modeling grammar expressiveness, and we identify previously unexplored links between conceptual modeling grammars and grammar usage beliefs. This work implies for practice a much closer coupling of the act of (re ) designing modeling grammars with usage-related success metrics.

Utilising semantic tags in XML clustering

This paper presents an overview of the experiments conducted using Hybrid Clustering of XML documents using Constraints (HCXC) method for the clustering task in the INEX 2009 XML Mining track. This technique utilises frequent subtrees generated from the structure to extract the content for clustering the XML documents. It also presents the experimental study using several data representations such as the structure-only, content-only and using both the structure and the content of XML documents for the purpose of clustering them. Unlike previous years, this year the XML documents were marked up using the Wiki tags and contains categories derived by using the YAGO ontology. This paper also presents the results of studying the effect of these tags on XML clustering using the HCXC method.

TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes

NF-Y is a heterotrimeric transcription factor complex. Each of the NF-Y subunits (NF-YA, NF-YB and NF-YC) in plants is encoded by multiple genes. Quantitative RT-PCR analysis revealed that five wheat NF-YC members (TaNF-YC5, 8, 9, 11 & 12) were upregulated by light in both the leaf and seedling shoot. Co-expression analysis of Affymetrix wheat genome array datasets revealed that transcript levels of a large number of genes were consistently correlated with those of the TaNF-YC11 and TaNF-YC8 genes in 3-4 separate Affymetrix array datasets. TaNF-YC11-correlated transcripts were significantly enriched with the Gene Ontology term photosynthesis. Sequence analysis in the promoters of TaNF-YC11-correlated genes revealed the presence of putative NF-Y complex binding sites (CCAAT motifs). Quantitative RT-PCR analysis of a subset of potential TaNF-YC11 target genes showed that ten out of the thirteen genes were also light-upregulated in both the leaf and seedling shoot and had significantly correlated expression profiles with TaNF-YC11. The potential target genes for TaNF-YC11 include subunit members from all four thylakoid membrane bound complexes required for the conversion of solar energy into chemical energy and rate limiting enzymes in the Calvin cycle. These data indicate that TaNF-YC11 is potentially involved in regulation of photosynthesis-related genes.

TaNF-YB3 is involved in the regulation of photosynthesis genes in Triticum aestivum

Nuclear Factor Y (NF-Y) transcription factor is a heterotrimer comprised of three subunits: NF-YA, NF-YB and NF-YC. Each of the three subunits in plants is encoded by multiple genes with differential expression profiles, implying the functional specialisation of NF-Y subunit members in plants. In this study, we investigated the roles of NF-YB members in the light-mediated regulation of photosynthesis genes. We identified two NF-YB members from Triticum aestivum (TaNF-YB3 & 7) which were markedly upregulated by light in the leaves and seedling shoots using quantitative RT-PCR. A genome-wide coexpression analysis of multiple Affymetrix Wheat Genome Array datasets revealed that TaNF-YB3-coexpressed transcripts were highly enriched with the Gene Ontology term photosynthesis. Transgenic wheat lines constitutively overexpressing TaNF-YB3 had a significant increase in the leaf chlorophyll content, photosynthesis rate and early growth rate. Quantitative RT-PCR analysis showed that the expression levels of a number of TaNF-YB3-coexpressed transcripts were elevated in the transgenic wheat lines. The mRNA level of TaGluTR encoding glutamyl-tRNA reductase, which catalyses the rate limiting step of the chlorophyll biosynthesis pathway, was significantly increased in the leaves of the transgenic wheat. Significant increases in the expression level in the transgenic plant leaves were also observed for four photosynthetic apparatus genes encoding chlorophyll a/b-binding proteins (Lhca4 and Lhcb4) and photosystem I reaction center subunits (subunit K and subunit N), as well as for a gene coding for chloroplast ATP synthase  subunit. These results indicate that TaNF-YB3 is involved in the positive regulation of a number of photosynthesis genes in wheat.

Playing with picturebooks : postmodernism and the postmodernesque

This thesis traces the influence of postmodernism on picturebooks. Through a review of current scholarship on both postmodernism and postmodern literature it examines the multiple ways in which picturebooks have responded to the influence of postmodernism. The thesis is predominantly located in the field of Cultural and Literary Studies, which informs the ways in which children’s literature is positioned within contemporary culture and how it responds to the influences which shape its production and reception. Cultural and Literary Studies also offers a useful theoretical frame for analysing issues of textuality, ideology, and originality, as well as social and political comment in the focus texts. The thesis utilises the theoretical contributions by, in particular, Linda Hutcheon, Brian McHale, and Fredric Jameson as well as reference to children’s literature studies. This thesis makes a significant contribution to the development of an understanding of the place of the postmodern picturebook within the cultural context of postmodernism. It adds to the field of children’s literature research through an awareness of the (continuing) evolution of the postmodern picturebook particularly as the current scholarship on the postmodernism picturebook does not engage with the changing form and significance of the postmodern picturebook to the same extent as this thesis. This study is significant from a methodological perspective as it draws on a wide range of theoretical perspectives across literary studies, visual semiotics, philosophy, cultural studies, and history to develop a tripartite methodological framework that utilises the methods of postclassical narratology, semiotics, and metafictive strategies to carry out the textual analysis of the focus texts. The three analysis chapters examine twenty-two picturebooks in detail with respect to the ways in which the conventions of narrative are subverted and how dominant discourses are interrogated. Chapter 4: Subverting Narrative Processes includes analysis of narrative point of view, modes of representation, and characters and the problems of identity and subjectivity. Chapter 5: Challenging Truth, History, and Unity examines questions of ontology, the difficulties of representing history, and addresses issues of difference and ‘otherness’. The final textual analysis chapter, Chapter 6: Engaging with Postmodernity, critiques texts which engage with issues of globalisation, mass media, and consumerism. Brief discussion of a further fifteen picturebooks throughout the thesis provides additional support. Children’s texts have a tradition of being both resistant and compliant. Its resistance has made a space for the development of the postmodern picturebook; its compliance is evident in its tendency to take a route around a truly radical or iconoclastic position. This thesis posits that children’s postmodern picturebooks adopt what suits their form and purposes by drawing from and reflecting on some influences of postmodernism while disregarding those that seem irrelevant to its direction. Furthermore, the thesis identifies a shift in the focus of a number of postmodern picturebooks produced since the turn of the twenty-first century. This trend has seen a shift from texts which interrogate discourses of liberal humanism to those that engage with aspects of postmodernity. These texts, postmodernesque picturebooks, offer contradictory perspectives on aspects of society emanating from the rise in global trends mentioned above.

Wellness education : an integrated theoretical framework for fostering transformative learning

Optimum Wellness involves the development, refinement and practice of lifestyle choices which resonate with personally meaningful frames of reference. Personal transformations are the means by which our frames of reference are refined across the lifespan. It is through critical reflection, supportive relationships and meaning making of our experiences that we construct and reconstruct our life paths. When individuals are able to be what they are destined to be or reach their higher purpose, then they are able to contribute to the world in positive and meaningful ways. Transformative education facilitates the changes in perspective that enable one to contemplate and travel a path in life that leads to self-actualisation. This thesis argues for an integrated theoretical framework for optimum Wellness Education. It establishes a learner centred approach to Wellness education in the form of an integrated instructional design framework derived from both Wellness and Transformative education constructs. Students’ approaches to learning and their study strategies in a Wellness education context serve to highlight convergences in the manner in which students can experience perspective transformation. As they learn to critically reflect, pursue relationships and adapt their frames of reference to sustain their pursuit of both learning and Wellness goals, strengthening the nexus between instrumental and transformative learning is a strategically important goal for educators. The aim of this exploratory research study was to examine those facets that serve to optimise the learning experiences of students in a Wellness course. This was accomplished through three research issues: 1) What are the relationships between Wellness, approaches to learning and academic success? 2) How are students approaching learning in an undergraduate Wellness subject? Why are students approaching their learning in the ways they do? 3) What sorts of transformations are students experiencing in their Wellness? How can transformative education be formulated in the context of an undergraduate Wellness subject? Subsequent to a thorough review of the literature pertaining to Wellness education, a mixed method embedded case study design was formulated to explore the research issues. This thesis examines the interrelationships between student, content and context in a one semester university undergraduate unit (a coherent set of learning activities which is assigned a unit code and a credit point value). The experiences of a cohort of 285 undergraduate students in a Wellness course formed the unit of study and seven individual students from a total of sixteen volunteers whose profiles could be constructed from complete data sets were selected for analysis as embedded cases. The introductory level course required participants to engage in a personal project involving a behaviour modification plan for a self-selected, single dimension of Wellness. Students were given access to the Standard Edition Testwell Survey to assess and report their Wellness as a part of their personal projects. To identify relationships among the constructs of Self-Regulated Learning (SRL), Wellness and Student Approaches to Learning (SAL) a blend of quantitative and qualitative methods to collect and analyse data was formulated. Surveys were the primary instruments for acquiring quantitative data. Sources included the Wellness data from Testwell surveys, SAL data from R-SPQ surveys, SRL data from MSLQ surveys and student self-evaluation data from an end of semester survey. Students’ final grades and GPA scores were used as indicators of academic performance. The sources of qualitative data included subject documentation, structured interview transcripts and open-ended responses to survey items. Subsequent to a pilot study in which survey reliability and validity were tested in context, amendments to processes for and instruments of data collection were made. Students who adopted meaning oriented (deep/achieving) approaches tended to assess their Wellness at a higher level, seek effective learning strategies and perform better in formal study. Posttest data in the main study revealed that there were significant positive statistical relationships between academic performance and total wellness scores (rs=.297, n=205, p<.01). Deep (rs=.343, n=137, p<.01) and achieving (rs=.286, n=123, p<.01) approaches to learning also significantly correlated with Wellness whilst surface approaches had negative correlations that were not significant. SRL strategies including metacognitive selfregulation, effort, help-seeking and critical thinking were increasingly correlated with Wellness. Qualitative findings suggest that while all students adopt similar patterns of day to day activities for example attending classes, taking notes, working on assignments the level of care with which these activities is undertaken varies considerably. The dominant motivational trigger for students in this cohort was the personal relevance and associated benefits of the material being learned and practiced. Students were inclined to set goals that had a positive impact on affect and used “sense of happiness” to evaluate their achievement status. Students who had a higher drive to succeed and/or understand tended to have or seek a wider range of strategies. Their goal orientations were generally learning rather than performance based and barriers presented a challenge which could be overcome as opposed to a blockage which prevented progress. Findings from an empirical analysis of the Testwell data suggest that a single third order Wellness construct exists. A revision of the instrument is necessary in order to juxtapose it with the chosen six dimensional Wellness model that forms the foundation construct in the course. Further, redevelopment should be sensitive to the Australian context and culture including choice of language, examples and scenarios used in item construction. This study concludes with an heuristic for use in Wellness education. Guided by principles of Transformative education theory and behaviour change theory, and informed by this representative case study the “CARING” heuristic is proposed as an instructional design tool for Wellness educators seeking to foster transformative learning. Based upon this study, recommendations were made for university educators to provide authentic and personal experiences in Wellness curricula. Emphasis must focus on involving students and teachers in a partnership for implementing Wellness programs both in the curriculum and co-curricularly. The implications of this research for practice are predicated on the willingness of academics to embrace transformative learning at a personal level and a professional one. To explore students’ profiles in detail is not practical however teaching students how to guide us in supporting them through the “pain” of learning is a skill which would benefit them and optimise the learning and teaching process. At a theoretical level, this research contributes to an ecological theory of Wellness education as transformational change. By signposting the wider contexts in which learning takes place, it seeks to encourage changing paradigms to ones which harness the energy of each successive contextual layer in which students live. Future research which amplifies the qualities of individuals and groups who are “Well” and seeks the refinement and development of instruments to measure Wellness constructs would be desirable for both theoretical and applied knowledge bases. Mixed method Wellness research derived and conducted by teams that incorporate expertise from multiple disciplines such as psychology, anthropology, education, and medicine would enable creative and multi-perspective programs of investigation to be designed and implemented. Congruences and inconsistencies in health promotion and education would provide valuable material for strengthening the nexus between transformational learning and behaviour change theories. Future development of and research on the effectiveness of the CARING heuristic would be valuable in advancing the understanding of pedagogies which advance rather than impede learning as a transformative process. Exploring pedagogical models that marry with transformative education may render solutions to the vexing challenge of teaching and learning in diverse contexts.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

A traffic simulation standard based on data marts

Traffic Simulation models tend to have their own data input and output formats. In an effort to standardise the input for traffic simulations, we introduce in this paper a set of data marts that aim to serve as a common interface between the necessaary data, stored in dedicated databases, and the swoftware packages, that require the input in a certain format. The data marts are developed based on real world objects (e.g. roads, traffic lights, controllers) rather than abstract models and hence contain all necessary information that can be transformed by the importing software package to their needs. The paper contains a full description of the data marts for network coding, simulation results, and scenario management, which have been discussed with industry partners to ensure sustainability.

Writing the self : the emergence of a dialogic space

While much narrative inquiry is concerned with issues of self and identity, doing study on the processes (the how) of self-making offers ongoing challenges to methodology. This article explores the creation of a dialogic space that assisted young adolescents to write about themselves and their daily lives using email journals as an alternative to face-to-face interviews. With the researcher acting as a listener-responder, and in the absence of researcher-designed questions, a dynamic field was opened up for participant-led self-making to emerge over a six month period of self-reflective written expression. The article describes a shared email relationship based on a dialogic pattern of thinking, writing, listening and response intended to foster participants’ voices as ontological narratives of self. Findings show the use of email journals created a synergy for self-disclosure and a safe space for self-expression where the willingness of participants to be themselves was encouraged. The self-representations of a specific group of gifted young adolescents thus emerged as written versions of “who” they are —offering data that differs from interview approaches and contributing to discussion of the value of ontology narratives.