http://www.researchonline.mq.edu.au/vital/access/services/Feed ${session.getAttribute("locale")} 5 http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:22630 Purpose: Political finance information is most often presented using a central database regime (CDR), being a system in which organizations report information to a central agency that is then made publically available via a database. I am studying the Australian Federal political finance regime to understand the extent to which it contributes to accountability. Originality: Whilst prior research has looked at what organisations report, this project explores the question of how they should report. Key literature/Theoretical Perspective and Methodology: Content analysis was used to analyse 50 submissions to the Australian Government’s 2008 Electoral Reform Green Paper titled Donations, Funding and Expenditure. Design/Methodology/approach: The qualitative characteristics inherent in the IASB’s conceptual framework were selected as the basis on which to code the data. Findings: CDRs can enhance accountability by providing a systems-level picture of political donations through the use of database searching and sorting tools. However, numerous concerns were raised by the submission-writers, including that: many donors do not produce returns; disclosure obligations may fall on unintended people, costing them time and money; and, the term ‘associated entity’ is not appropriately defined. Research limitation: Data was gathered from Parliamentary inquiry submissions, which skewed towards the provision of negative commentary. Practical and Social Implications: Corporate accountability for political donations – as well as other issues – might be enhanced by requiring disclosure in both CDRs and TBL reports. Enhancing accountability is not just a matter of improving disclosure, but also enabling disclosure to contribute to public deliberation. 2012-11-05T02:21:54.057Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:17781 Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs - determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69000 out of the world's 300000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation - but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models. 2012-05-23T21:36:09.770Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:19296 Ontology is a building block of the semantic Web. Ontology building requires a detailed domain analysis, which in turn requires financial resources, intensive domain knowledge and time. Domain models in industry are frequently stored as relational database schemas in relational databases. An ontology base underlying such schemas can represent concepts and relationships that are present in the domain of discourse. However, with ever increasing demand for wider access and domain coverage, public databases are not static and their schemas evolve over time. Ontologies generated according to these databases have to change to reflect the new situation. Once a database schema is changed, these changes in the schema should also be incorporated in any ontology generated from the database. It is not possible to generate a fresh version of the ontology using the new database schema because the ontology itself may have undergone changes that need to be preserved. To tackle this problem, this paper presents a generic framework that will help to generate and synchronize ontologies with existing data sources. In particular we address the translation between ontologies and database schemas, but our proposal is also sufficiently generic to be used to generate and maintain ontologies based on XML and object oriented databases. 2012-05-21T18:41:47.416Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:18666 P>1. Plant traits are fundamental for understanding and predicting vegetation responses to global changes, and they provide a promising basis towards a more quantitative and predictive approach to ecology. As a consequence, information on plant traits is rapidly accumulating, and there is a growing need for efficient database tools that enable the assembly and synthesis of trait data. 2. Plant traits are highly heterogeneous, exhibit a low degree of standardization and are linked and interdependent at various levels of biological organization: tissue, organ, plant and population. Therefore, they often require ancillary data for interpretation, including descriptors of the biotic and abiotic environment, methods and taxonomic relationships. 3. We introduce a generic database structure that is tailored to accommodate plant trait complexity and is consistent with current theoretical approaches to characterize the structure of observational data. The over-arching utility of the proposed database structure is illustrated based on two independent plant trait database projects. 4. The generic database structure proposed here is meant to serve as a flexible blueprint for future plant trait databases, improving data discovery, and ensuring compatibility among them. 2012-04-16T08:50:36.524Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:18605 Despite the success of several international initiatives the glycosciences still lack a managed infrastructure that contributes to the advancement of research through the provision of comprehensive structural and experimental glycan data collections. UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data. The UniCarbKB framework endeavors to support the growth of glycobioinformatics and the dissemination of knowledge through the provision of an open and unified portal to encourage the sharing of data. In order to achieve this, the framework is committed to the development of tools and procedures that support data annotation, and expanding interoperability through cross-referencing of existing databases. Database URL: http://www.unicarbkb.org. 2012-04-10T15:30:35.473Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:18357 Purpose: This paper aims to provide insight into the extent to which the Australian Federal political donation and expenditure disclosure regime is able to contribute to accountability. This is an important topic as a lack of adequate accountability concerning political donations and expenditure may serve to foster corruption. Design/Methodology: Content analysis was used to analyse 50 submissions to the Australian Government’s 2008 Electoral Reform Green Paper on Donations, Funding and Expenditure. The International Accounting Standards Board (2008) draft conceptual framework was selected as the coding framework. Findings: The AEC database can enhance accountability merely by ensuring that there is a public record of donations and expenditure, but there are issues which limit its contribution to accountability. Numerous concerns were raised by submission-writers including: many donors do not produce returns; disclosure obligations may fall on unintended people, costing them time and money; and the term ‘associated entity’ is not appropriately defined. Three issues that could most easily be acted upon are: providing the AEC with the resources necessary to cross-check donor declarations against party declarations; permitting candidates and parties to identify when donations have been returned; and increasing the frequency of disclosure and ensuring it is available prior to elections. Originality/Value: This paper contributes to the literature by expanding upon the virtually non- existent SEA research into political donation accountability and extending research into how corporate reporting should occur. 2012-03-29T21:22:12.246Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:18227 The authors have proposed using category-theoretic sketches to enhance database design and integration methodologies. The algebraic context is called the Sketch Data Model (SkDM) and mathematically describes databases, views and their updates, and other database concepts. The system described here is a freely available graphical Java environment with a module that compiles a design incorporating algebraically specified constraints into database schemas that interface directly with modern database management systems. It therefore supports, inter alia, rapid prototyping. 2012-03-22T08:57:24.400Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:16266 Maintainability and modifiability of information system software can be enhanced by the provision of comprehensive support for views, since view support allows application programs to continue to operate unchanged when the underlying information system is modified. Supporting views depend upon a solution to the view update problem. This paper presents a new treatment of view updates for formally specified semantic data models based on the category theoretic sketch data model. The sketch data model has been the basis of a number of successful major information system consultancies. We define view updates by a universal property in models of the formal specification, and explain why this indeed gives a complete and correct treatment of view updatability, including a solution to the view update problem. However, a definition of updatability which is based on models causes some inconvenience in applications, so we prove that in a variety of circumstances updatability is guaranteed independently of the current model. This is done first with a very general criterion, and then for some specific cases relevant to applications. We include some details about the sketch data model, noting that it involves extensions of algebraic data specification techniques. 2011-12-09T21:16:41.425Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:15095 Recently, an automated high-throughput HPLC platform has been developed that can be used to fully sequence and quantify low concentrations of N-linked sugars released from glycoproteins, supported by an experimental database (GlycoBase) and analytical tools (autoGU). However, commercial packages that support the operation of HPLC instruments and data storage lack platforms for the extraction of large volumes of data. The lack of resources and agreed formats in glycomics is now a major limiting factor that restricts the development of bioinformatic tools and automated workflows for high-throughput HPLC data analysis. GlycoExtractor is a web-based tool that interfaces with a commercial HPLC database/software solution to facilitate the extraction of large volumes of processed glycan profile data (peak number, peak areas, and glucose unit values). The tool allows the user to export a series of sample sets to a set of file formats (XML, JSON, and CSV) rather than a collection of disconnected files. This approach not only reduces the amount of manual refinement required to export data into a suitable format for data analysis but also opens the field to new approaches for high-throughput data interpretation and storage, including biomarker discovery and validation and monitoring of online bioprocessing conditions for next generation biotherapeutics. 2011-09-29T06:53:24.154Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:15110 We present a robust, fully automatable technology platform that includes computer software for the detailed analysis of low femtomoles of N-linked sugars released from glycoproteins. Features include (i) sample immobilization in 96-well plates, glycan release, and fluorescent labeling; (ii) quantitative HPLC analysis, including monosaccharide sequence, linkage, and arm-specific information for charged and neutral glycans; (iii) automatic structural assignment of peaks from HPLC profiles via web-based software that accesses our database (GlycoBase) of more than 350 N-glycan structures, including 117 present in the human serum glycome; and (iv) software (autoGU) that progressively analyzes data from exoglycosidase digestions to produce a refined list of final structures. The N-glycans from a plate of 96 samples can be released and purified in 2 or 3 days and profiled in 2 days. This strategy can be used for (i) identification and screening of disease biomarkers and (ii) monitoring the production of therapeutic glycoproteins, allowing optimization of production conditions. This technology is also suitable for preparing released glycans for other analytical techniques. Here we demonstrate its application to rheumatoid arthritis using 5 μl of patient serum. 2011-09-29T06:51:49.822Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:12484 Database watermarking has received significant research attention in the current decade. Although, almost all watermarking models have been either irreversible (the original relation cannot be restored from the watermarked relation) and/or non-blind (requiring original relation to detect the watermark in watermarked relation). This model has several disadvantages over reversible and blind watermarking (requiring only watermarked relation and secret key from which the watermark is detected and original relation is restored) including inability to identify rightful owner in case of successful secondary watermarking, inability to revert the relation to original data set (required in high precision industries) and requirement to store unmarked relation at a secure secondary storage. To overcome these problems, we propose a watermarking scheme that is reversible as well as blind. We utilize difference expansion on integers to achieve reversibility. The major advantages provided by our scheme are reversibility to high quality original data set, rightful owner identification, resistance against secondary watermarking attacks, and no need to store original database at a secure secondary storage. 2011-04-15T06:03:21.691Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:10980 The bioinformatic tool GlycosidIQ™ was developed for computerized interpretation of oligosaccharide mass spectrometric fragmentation based on matching experimental data with theoretically fragmented oligosaccharides generated from the database GlycoSuiteDB™. This use of the software for glycofragment mass fingerprinting obviates a large part of the manual, labor intensive, and technically challenging interpretation of oligosaccharide fragmentation. Using 130 negative ion electrospray ionization-tandem mass spectrometry fragment spectra from identified oligosaccharide structures, it was shown that the GlycosidIQ scoring algorithms were able to correctly identify oligosaccharides in the great majority of cases (correct structure top ranked in 78% of the cases and an additional 17% were ranked second highest in the sample set). 2010-12-17T01:20:19.193Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:649 Scorpion toxins are important experimental tools for characterization of vast array of ion channels and serve as scaffolds for drug design. General public database entries contain limited annotation whereby rich structure–function information from mutation studies is typically not available. SCORPION2 contains more than 800 records of native and mutant toxin sequences enriched with binding affinity and toxicity information, 624 three-dimensional structures and some 500 references. SCORPION2 has a set of search and prediction tools that allow users to extract and perform specific queries: text searches of scorpion toxin records, sequence similarity search, extraction of sequences, visualization of scorpion toxin structures, analysis of toxic activity, and functional annotation of previously uncharacterized scorpion toxins. The SCORPION2 database is available at http://sdmc.i2r.a-star.edu.sg/scorpion/. 2010-01-27T23:25:46.461Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:1740 Data produced from the MudPIT analysis of yeast (S. cerevisiae) and rice (O. sativa) were used to develop a technique to validate single-peptide protein identifications using complementary database search algorithms. This results in a considerable reduction of overall false-positive rates for protein identifications; the overall false discovery rates in yeast are reduced from near 25% to less than 1%, and the false discovery rate of yeast single-peptide protein identifications becomes negligible. This technique can be employed by laboratories utilizing a SEQUEST-based proteomic analysis platform, incorporating the XTandem algorithm as a complementary tool for verification of single-peptide protein identifications. We have achieved this using open-source software, including several data-manipulation software tools developed in our laboratory, which are freely available to download. 2010-01-27T23:12:57.108Z ]]> http://www.researchonline.mq.edu.au/vital/access/manager/Repository/mq:5937 Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive computational strategies have been developed to organize and analyse both small- and large-scale EST data for gene discovery, transcript and single nucleotide polymorphism analysis as well as functional annotation of putative gene products. We provide an overview of the significance of ESTs in the genomic era, their properties and the applications of ESTs. Methods adopted for each step of EST analysis by various research groups have been compared. Challenges that lie ahead in organizing and analysing the ever increasing EST data have also been identified. The most appropriate software tools for EST pre-processing, clustering and assembly, database matching and functional annotation have been compiled (available online from http://biolinfo.org/EST). We propose a road map for EST analysis to accelerate the effective analyses of EST data sets. An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping. 2010-01-27T22:24:25.069Z ]]>