Model and prototype for querying multiple linked scientific datasets

Scientists need to transfer semantically similar queries across multiple heterogeneous linked datasets. These queries may require data from different locations and the results are not simple to combine due to differences between datasets. A query model was developed to make it simple to distribute queries across different datasets using RDF as the result format. The query model, based on the concept of publicly recognised namespaces for parts of each scientific dataset, was implemented with a configuration that includes a large number of current biological and chemical datasets. The configuration is flexible, providing the ability to transparently use both private and public datasets in any query. A prototype implementation of the model was used to resolve queries for the Bio2RDF website, including both Bio2RDF datasets and other datasets that do not follow the Bio2RDF URI conventions.

Linking ambulance, emergency department and hospital admissions data : understanding the emergency journey

Objective: to assess the accuracy of data linkage across the spectrum of emergency care in the absence of a unique patient identifier, and to use the linked data to examine service delivery outcomes in an emergency department setting. Design: automated data linkage and manual data linkage were compared to determine their relative accuracy. Data were extracted from three separate health information systems: ambulance, ED and hospital inpatients, then linked to provide information about the emergency journey of each patient. The linking was done manually through physical review of records and automatically using a data linking tool (Health Data Integration) developed by the CSIRO. Match rate and quality of the linking were compared. Setting: 10, 835 patient presentations to a large, regional teaching hospital ED over a two month period (August-September 2007). Results: comparison of the manual and automated linkage outcomes for each pair of linked datasets demonstrated a sensitivity of between 95% and 99%; a specificity of between 75% and 99%; and a positive predictive value of between 88% and 95%. Conclusions: Our results indicate that automated linking provides a sound basis for health service analysis, even in the absence of a unique patient identifier. The use of an automated linking tool yields accurate data suitable for planning and service delivery purposes and enables the data to be linked regularly to examine service delivery outcomes.

Open content licensing of public sector information and the risk of tortious liability for Australian Governments

There has been an increasing interest by governments worldwide in the potential benefits of open access to public sector information (PSI). However, an important question remains: can a government incur tortious liability for incorrect information released online under an open content licence? This paper argues that the release of PSI online for free under an open content licence, specifically a Creative Commons licence, is within the bounds of an acceptable level of risk to government, especially where users are informed of the limitations of the data and appropriate information management policies and principles are in place to ensure accountability for data quality and accuracy.

Assessing the concordance of health and child protection data for 'maltreated' and 'unintentionally injured' children

Objectives: To quantify the concordance of hospital child maltreatment data with child protection service (CPS) records and identify factors associated with linkage. Methods: Multivariable logistic regression analysis was conducted following retrospective medical record review and database linkage of 884 child records from 20 hospitals and the CPS in Queensland, Australia. Results: Nearly all children with hospital assigned maltreatment codes (93.1%) had a CPS record. Of these, 85.1% had a recent notification. 29% of the linked maltreatment group (n=113) were not known to CPS prior to the hospital presentation. Almost 1/3 of children with unintentional injury hospital codes were known to CPS. Just over 24% of the linked unintentional injury group (n=34) were not known to CPS prior to the hospital presentation but became known during or after discharge from hospital. These estimates are higher than the 2006/07 annual rate of 2.39% of children being notified to CPS. Rural children were more likely to link to CPS, and children were over 3 times more likely to link if the index injury documentation included additional diagnoses or factors affecting their health. Conclusions: The system for referring maltreatment cases to CPS is generally efficient, although up to 1 in 15 children had codes for maltreatment but could not be linked to CPS data. The high proportion of children with unintentional injury codes who linked to CPS suggests clinicians and hospital-based child protection staff should be supported by further education and training to ensure children at risk are being detected by the child protection system.

Sit versus stand : can sitting be accurately identified using MTI accelerometer data?

High levels of sitting have been linked with poor health outcomes. Previously a pragmatic MTI accelerometer data cut-point (100 count/min-1) has been used to estimate sitting. Data on the accuracy of this cut-point is unavailable. PURPOSE: To ascertain whether the 100 count/min-1 cut-point accurately isolates sitting from standing activities. METHODS: Participants fitted with an MTI accelerometer were observed performing a range of sitting, standing, light & moderate activities. 1-min epoch MTI data were matched to observed activities, then re-categorized as either sitting or not using the 100 count/min-1 cut-point. Self-report demographics and current physical activity were collected. Generalized estimating equation for repeated measures with a binary logistic model analyses (GEE), corrected for age, gender and BMI, were conducted to ascertain the odds of the MTI data being misclassified. RESULTS: Data were from 26 healthy subjects (8 men; 50% aged <25 years; mean BMI (SD) 22.7(3.8)m/kg2). MTI sitting and standing data mode was 0 count/min-1, with 46% of sitting activities and 21% of standing activities recording 0 count/min-1. The GEE was unable to accurately isolate sitting from standing activities using the 100 count/min-1 cut-point, since all sitting activities were incorrectly predicted as standing (p=0.05). To further explore the sensitivity of MTI data to delineate sitting from standing, the upper 95% confidence interval of the mean for the sitting activities (46 count/min-1) was used to re-categorise the data; this resulted in the GEE correctly classifying 49% of sitting, and 69% of standing activities. Using the 100 count/min-1 cut-point the data were re-categorised into a combined ‘sit/stand’ category and tested against other light activities: 88% of sit/stand and 87% of light activities were accurately predicted. Using Freedson’s moderate cut-point of 1952 count/min-1 the GEE accurately predicted 97% of light vs. 90% of moderate activities. CONCLUSION: The distributions of MTI recorded sitting and standing data overlap considerably, as such the 100 count/min -1 cut-point did not accurately isolate sitting from other static standing activities. The 100 count/min -1 cut-point more accurately predicted sit/stand vs. other movement orientated activities.

Understanding user differences in open-source workflow management system usage intentions

Open-source software systems have become a viable alternative to proprietary systems. We collected data on the usage of an open-source workflow management system developed by a university research group, and examined this data with a focus on how three different user cohorts – students, academics and industry professionals – develop behavioral intentions to use the system. Building upon a framework of motivational components, we examined the group differences in extrinsic versus intrinsic motivations on continued usage intentions. Our study provides a detailed understanding of the use of open-source workflow management systems in different user communities. Moreover, it discusses implications for the provision of workflow management systems, the user-specific management of open-source systems and the development of services in the wider user community.

Open source innovation in physical products : advantages and disadvantages, a corporate perspective

A better understanding of Open Source Innovation in Physical Product (OSIP) might allow project managers to mitigate risks associated with this innovation model and process, while developing the right strategies to maximise OSIP outputs. In the software industry, firms have been highly successful using Open Source Innovation (OSI) strategies. However, OSI in the physical world has not been studied leading to the research question: What advantages and disadvantages do organisations incur from using OSI in physical products? An exploratory research methodology supported by thirteen semi-structured interviews helped us build a seven-theme framework to categorise advantages and disadvantages elements linked with the use of OSIP. In addition, factors impacting advantage and disadvantage elements for firms using OSIP were identified as: „h Degree of openness in OSIP projects; „h Time of release of OSIP in the public domain; „h Use of Open Source Innovation in Software (OSIS) in conjunction with OSIP; „h Project management elements (Project oversight, scope and modularity); „h Firms. Corporate Social Responsibility (CSR) values; „h Value of the OSIP project to the community. This thesis makes a contribution to the body of innovation theory by identifying advantages and disadvantages elements of OSIP. Then, from a contingency perspective it identifies factors which enhance or decrease advantages, or mitigate/ or increase disadvantages of OSIP. In the end, the research clarifies the understanding of OSI by clearly setting OSIP apart from OSIS. The main practical contribution of this paper is to provide manager with a framework to better understand OSIP as well as providing a model, which identifies contingency factors increasing advantage and decreasing disadvantage. Overall, the research allows managers to make informed decisions about when they can use OSIP and how they can develop strategies to make OSIP a viable proposition. In addition, this paper demonstrates that advantages identified in OSIS cannot all be transferred to OSIP, thus OSIP decisions should not be based upon OSIS knowledge.

Estimation and control for an open-source quadcopter

This paper describes modelling, estimation and control of the horizontal translational motion of an open-source and cost effective quadcopter — the MikroKopter. We determine the dynamics of its roll and pitch attitude controller, system latencies, and the units associated with the values exchanged with the vehicle over its serial port. Using this we create a horizontal-plane velocity estimator that uses data from the built-in inertial sensors and an onboard laser scanner, and implement translational control using a nested control loop architecture. We present experimental results for the model and estimator, as well as closed-loop positioning.

Facilitating Malaysia towards innovative society : arguing the case for open access policy

The Malaysian National Innovation Model blueprint states that there is an urgent need to pursue an innovation-oriented economy to improve the nation’s capacity for knowledge, creativity and innovation. In nurturing a pervasive innovation culture, the Malaysian government has declared the year 2010 as an Innovative Year whereby creativity among its population is highly celebrated. However, while Malaysian citizens are encouraged to be creative and innovative, scientific data and information generated from publicly funded research in Malaysia is locked up because of rigid intellectual property licensing regimes and traditional publishing models. Reflecting on these circumstances, this paper looks at, and argue why, scientific data and information should be made available, accessible and re-useable freely to promote the grassroots level of innovation in Malaysia. Using innovation theory as its platform of argument, this paper calls for an open access policy for publicly funded research output to be adopted and implemented in Malaysia. Simultaneously, a normative analytic approach is used to determine the types of open access policy that ought to be adopted to spur greater innovation among Malaysians.

Tools and methods for capturing Twitter data during natural disasters

During the course of several natural disasters in recent years, Twitter has been found to play an important role as an additional medium for many–to–many crisis communication. Emergency services are successfully using Twitter to inform the public about current developments, and are increasingly also attempting to source first–hand situational information from Twitter feeds (such as relevant hashtags). The further study of the uses of Twitter during natural disasters relies on the development of flexible and reliable research infrastructure for tracking and analysing Twitter feeds at scale and in close to real time, however. This article outlines two approaches to the development of such infrastructure: one which builds on the readily available open source platform yourTwapperkeeper to provide a low–cost, simple, and basic solution; and, one which establishes a more powerful and flexible framework by drawing on highly scaleable, state–of–the–art technology.

Cyclic imides and an open-chain amide carboxylic acid from the facile reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with the isomeric monofluoroanilines

The structures of the cyclic imides cis-2-(2-fluorophenyl)-3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione, C14H14FNO2, (I), and cis-2-(4-fluorophenyl)-3a,4,5,6,7,7a-hexahydroisoindoline-1,3-dione, C14H14FNO2, (III), and the open-chain amide acid rac-cis-2-[(3-fluorophenyl)carbamoyl]cyclohexane-1-carboxylic acid, C14H16FNO3, (II), are reported. Cyclic imides (I) and (III) are conformationally similar, with comparable ring rotations about the imide N-Car bond [the dihedral angles between the benzene ring and the five-membered isoindole ring are 55.40 (8)° for (I) and 51.83 (7)° for (III)]. There are no formal intermolecular hydrogen bonds involved in the crystal packing of either (I) or (III). With the acid (II), in which the meta-related F-atom substituent is rotationally disordered (0.784:0.216), the amide group lies slightly out of the benzene plane [the interplanar dihedral angle is 39.7 (1)°]. Intermolecular amide-carboxyl N-HO hydrogen-bonding interactions between centrosymmetrically related molecules form stacks extending down b, and these are linked across c by carboxyl-amide O-HO hydrogen bonds, giving two-dimensional layered structures which lie in the (011) plane. The structures reported here represent examples of compounds analogous to the phthalimides or phthalanilic acids and have little precedence in the crystallographic literature.

Business Process Data Compliance

Most approaches to business process compliance are restricted to the analysis of the structure of processes. It has been argued that full regulatory compliance requires information on not only the structure of processes but also on what the tasks in a process do. To this end Governatori and Sadiq[2007] proposed to extend business processes with semantic annotations. We propose a methodology to automatically extract one kind of such annotations; in particular the annotations related to the data schema and templates linked to the various tasks in a business process.

System identification, estimation and control for a cost effective open-source quadcopter

This paper describes system identification, estimation and control of translational motion and heading angle for a cost effective open-source quadcopter — the MikroKopter. The dynamics of its built-in sensors, roll and pitch attitude controller, and system latencies are determined and used to design a computationally inexpensive multi-rate velocity estimator that fuses data from the built-in inertial sensors and a low-rate onboard laser range finder. Control is performed using a nested loop structure that is also computationally inexpensive and incorporates different sensors. Experimental results for the estimator and closed-loop positioning are presented and compared with ground truth from a motion capture system.

Association between prostinogen (KLK15) genetic variants and prostate cancer risk and aggressiveness in Australia and a meta-analysis of GWAS data

Background: Kallikrein 15 (KLK15)/Prostinogen is a plausible candidate for prostate cancer susceptibility. Elevated KLK15 expression has been reported in prostate cancer and it has been described as an unfavorable prognostic marker for the disease. Objectives: We performed a comprehensive analysis of association of variants in the KLK15 gene with prostate cancer risk and aggressiveness by genotyping tagSNPs, as well as putative functional SNPs identified by extensive bioinformatics analysis. Methods and Data Sources: Twelve out of 22 SNPs, selected on the basis of linkage disequilibrium pattern, were analyzed in an Australian sample of 1,011 histologically verified prostate cancer cases and 1,405 ethnically matched controls. Replication was sought from two existing genome wide association studies (GWAS): the Cancer Genetic Markers of Susceptibility (CGEMS) project and a UK GWAS study. Results: Two KLK15 SNPs, rs2659053 and rs3745522, showed evidence of association (p, 0.05) but were not present on the GWAS platforms. KLK15 SNP rs2659056 was found to be associated with prostate cancer aggressiveness and showed evidence of association in a replication cohort of 5,051 patients from the UK, Australia, and the CGEMS dataset of US samples. A highly significant association with Gleason score was observed when the data was combined from these three studies with an Odds Ratio (OR) of 0.85 (95% CI = 0.77-0.93; p = 2.7610 24). The rs2659056 SNP is predicted to alter binding of the RORalpha transcription factor, which has a role in the control of cell growth and differentiation and has been suggested to control the metastatic behavior of prostate cancer cells. Conclusions: Our findings suggest a role for KLK15 genetic variation in the etiology of prostate cancer among men of European ancestry, although further studies in very large sample sets are necessary to confirm effect sizes.

Validation of de-identified record linkage to ascertain hospital admissions in a cohort study

Background Cohort studies can provide valuable evidence of cause and effect relationships but are subject to loss of participants over time, limiting the validity of findings. Computerised record linkage offers a passive and ongoing method of obtaining health outcomes from existing routinely collected data sources. However, the quality of record linkage is reliant upon the availability and accuracy of common identifying variables. We sought to develop and validate a method for linking a cohort study to a state-wide hospital admissions dataset with limited availability of unique identifying variables. Methods A sample of 2000 participants from a cohort study (n = 41 514) was linked to a state-wide hospitalisations dataset in Victoria, Australia using the national health insurance (Medicare) number and demographic data as identifying variables. Availability of the health insurance number was limited in both datasets; therefore linkage was undertaken both with and without use of this number and agreement tested between both algorithms. Sensitivity was calculated for a sub-sample of 101 participants with a hospital admission confirmed by medical record review. Results Of the 2000 study participants, 85% were found to have a record in the hospitalisations dataset when the national health insurance number and sex were used as linkage variables and 92% when demographic details only were used. When agreement between the two methods was tested the disagreement fraction was 9%, mainly due to "false positive" links when demographic details only were used. A final algorithm that used multiple combinations of identifying variables resulted in a match proportion of 87%. Sensitivity of this final linkage was 95%. Conclusions High quality record linkage of cohort data with a hospitalisations dataset that has limited identifiers can be achieved using combinations of a national health insurance number and demographic data as identifying variables.