The increasing health burden of Legionella Pneumophila in NSW

BACKGROUND

Legionella pneumophila can cause severe respiratory disease and is notifiable in NSW. An analysis of notifications linked to hospitalisation and death data over the period 2010-2022 was conducted to determine the burden of disease and any association with the introduction of NSW regulatory changes in 2018.

METHODS

Cases were retrospectively identified from the Notifiable Conditions Records for Epidemiology and Surveillance (NCRES). Data on related morbidity and mortality were obtained from linked data within the NSW Communicable Disease Register (CDR). The impact of the regulatory change was evaluated by analysing monthly count data using an interrupted time series analysis.

RESULTS

A total of 928 cases were notified with 84% admitted to hospital. Annual adjusted notification and admission rates increased over the period from 4.40 to 7.92 cases and 3.72 to 7.20 admissions, per 1,000,000 population, respectively. The mean length of hospital stay (LOS) was 14 days with a median of 8 days (range 1-262 days). Time series analysis identified an underlying increasing time trend in cases notified per month with an IRR of 1.069 (95% ci 0.751-1.523) post 2018 regulatory implementation.

CONCLUSION

L. pneumophila is posing an increasing burden of disease with an underlying upward trend in notification incidence despite the introduction of regulatory changes in 2018.

IMPLICATION FOR PUBLIC HEALTH PRACTICE

This study demonstrates how linking notification, hospitalisation and death data can measure the health burden of a notifiable condition. Furthermore, time-series analysis using these data is able to identify underlying temporal trends and evaluate policy changes.

Admissions for psychosis following agency-notified child maltreatment at 40-year-follow-up: Results from the Childhood Adversity and Lifetime Morbidity (CALM) cohort

There is substantial evidence of an association between self-reported child maltreatment (CM) and subsequent psychosis in retrospective data. Such findings may be affected by recall bias. Prospective studies of notifications to statutory agencies address recall bias but are less common and subject to attrition bias. These studies may therefore be underpowered to detect significant associations for some CM types such as sexual abuse. This study therefore linked administrative health data to a large birth cohort that included notifications to child protection agencies. We assessed psychiatric outcomes of CM as measured by inpatient admissions for non-affective psychoses (ICD10 codes F20-F29) to both public and private hospitals in Brisbane, Australia. Follow-up was up to 40 years old. There were 6087 cohort participants whose data could be linked to the administrative health data. Of these, 10.1 % had been the subject of a CM notification. Seventy-two participants (1.2 %) had been admitted for non-affective psychosis by 40-year follow-up. On adjusted analysis, all notified and substantiated types of CM were associated with admissions for non-affective psychosis. This included neglect, physical, sexual or emotional abuse, as well as notifications for multiple CM types. For instance, there was a 2.72-fold increase in admissions following any agency notification (95 % CI = 1.53-4.85). All maltreatment types therefore show a significant association with subsequent admissions for psychosis up to the age of 40. Screening for CM in individuals who present with psychosis is, therefore, indicated, as well as greater awareness that survivors of CM may be at higher risk of developing psychotic symptoms.

Availability and readiness of healthcare facilities and their effects on antenatal care services uptake in Bangladesh

BACKGROUND

Sustainable Development Goal (SDG) 3.7 aims to ensure universal access to sexual and reproductive healthcare services, where antenatal care (ANC) is a core component. This study aimed to examine the influence of health facility availability and readiness on the uptake of four or more ANC visits in Bangladesh.

METHODS

The 2017/18 Bangladesh Demographic and Health Survey data were linked with the 2017 Health Facility Survey and analyzed in this study. The associations of health facility-level factors with the recommended number of ANC uptakes were determined. A multilevel mixed-effect logistic regression model was used to determine the association, adjusting for potential confounders.

RESULTS

Nearly 44% of mothers reported four or more ANC uptakes, with significant variations across several areas in Bangladesh. The average distance of mothers' homes from the nearest health facilities was 6.36 km, higher in Sylhet division (8.25 km) and lower in Dhaka division (4.45 km). The overall uptake of the recommended number of ANC visits was positively associated with higher scores for the management (adjusted odds ratio (aOR) 1.85; 95% CI, 1.16-2.82) and infrastructure (aOR, 1.59; 95% CI, 1.09-2.19) of health facilities closest to mothers' homes. The odds of using the recommended number of ANC in mothers increased by 3.02 (95% CI, 2.01-4.19) and 2.36 (95% CI, 2.09-3.16) folds for each unit increase in the availability and readiness scores to provide ANC services at the closest health facilities, respectively. Every kilometer increase in the average regional-level distance between mothers' homes and the nearest health facilities reduced the likelihood of receiving the recommended number of ANC visits by nearly 42% (aOR, 0.58, 95% CI, 0.42-0.74).

CONCLUSION

The availability of healthcare facilities close to residence, as well as their improved management, infrastructure, and readiness to provide ANC, plays a crucial role in increasing ANC services uptake. Policies and programs should prioritize increasing the availability, accessibility, and readiness of health facilities to provide ANC services.

Trajectories of homelessness and association with mental health and substance use disorders among young people transitioning from out-of-home care in Australia

BACKGROUND

Researchers have examined sub-groups that may exist among young people transitioning from out-of-home care (OHC) using various theoretical models. However, this population group has not been examined for trajectories of homelessness risk.

OBJECTIVES

To examine whether different subtypes of homelessness risk exist among young people transitioning from care and whether these trajectories of homelessness are associated with mental health and substance use disorders.

PARTICIPANTS AND SETTING

A retrospective population-based cohort study was conducted from a population of 1018 young people (aged 15-18 years) who transitioned from out-of-home in 2013 to 2014 in the state of Victoria, Australia, with follow-up to 2018.

METHODS

Latent Class Growth Analysis was conducted using linked data from homelessness data collections, child protection, mental health information systems, alcohol and drug use, and youth justice information systems.

RESULTS

Three sub-groups of young people were identified. The 'moving on' group (88 %) had the lowest levels of homelessness, with the slope of this trajectory remaining almost stable. The 'survivors' (7 %) group started off with a high risk of homelessness, followed by a sharp decrease in homelessness risk over time. The 'complex' (5 %) group started off with a low risk of homelessness but faced sharp increases in the risk of homelessness over time.

CONCLUSIONS

Our study demonstrates that subgroups of young people transitioning from care exist with distinct longitudinal trajectories of homelessness, and these classes are associated with different risk factors. Early intervention and different approaches to tackling homelessness should be considered for these three distinct groups before transitioning from care and during the first few years after leaving care.

Infants entering out-of-home care: Health, developmental needs and service provision

BACKGROUND

There are rising numbers of infants entering out-of-home care due to child protection concerns. Research has found that infants entering care are at higher risk of developmental vulnerability and poor health problems.

OBJECTIVES

To determine the prevalence of developmental vulnerability for children who entered care as infants, and the extent and likelihood of service provision in relation to their developmental vulnerability.

PARTICIPANTS AND SETTING

This study includes children who entered care before the age of 1 year for the first time between May 2010 and October 2011 in New South Wales, Australia, and who received final Children's Court care and protection orders by 30 April 2013.

METHODS

This is a prospective cohort study using interview data from the Pathways of Care Longitudinal Study (POCLS) as well as linked administrative child protection and health data. This study used standardised assessments (Age and Stages Questionnaire and the Brief Infant Toddler Social Emotional Assessment) included in the POCLS. Simple and multiple logistic regression analysis was conducted to investigate the likelihood of infants receiving professional services for developmental delays since placement.

FINDINGS

A high proportion of children who entered care as infants were identified as developmentally vulnerable through health indicators (36 %) and standardised assessments (70 %). Only 17 % of infants in care received services for developmental delay, with 20 % and 15 % of those identified as developmentally vulnerable through standardised assessments and health-related variables receiving services, respectively.

CONCLUSIONS

The findings point to the importance of developmental assessment of infants in care and the identification of developmental vulnerability and delays. The provision of early intervention services is essential for this group of high-risk infants and will be important in optimising their health, as well as social and emotional outcomes.

The hidden impact of alcohol on young victims: an analysis of alcohol-related police offences resulting in hospitalisation

BACKGROUND

Alcohol-related harm (ARH) is a significant public health concern affecting young individuals, particularly those involved in alcohol-related police incidents resulting in hospitalisation. However, the impact of alcohol on young victims remains under researched. This study aimed to identify the characteristics of offenders and victims involved in these incidents, analyse the types of offences, and understand the under-ascertainment of ARH in hospital records.

METHODS

A retrospective longitudinal study of 12-24-year-olds born between 1980 and 2005 was conducted using linked data from hospital admissions, emergency department presentations, and police incident records. Alcohol-related incidents were identified based on the attending officers' opinions in the Western Australia Police's Incident Management System (IMS). Logistic and log-binomial regression were utilised to analyse the factors associated with victimisation and under-ascertainment of ARH.

RESULTS

Our study included 22,747 individuals (11,433 victims and 11,314 offenders) involved in alcohol-related police incidents, with a small majority of victims being female (53%, n = 6,074) and a large majority of offenders being male (84.3%, n = 9,532). Most victims did not receive a diagnosis of ARH (71%, n = 760). Women were 10 times more likely to have been a victim in ARH police incidents and 2 times more likely to have an undiagnosed alcohol-related hospital admission than men. Victims and offenders predominantly came from disadvantaged areas and major cities. Aboriginal individuals were overrepresented as both offenders and victims. A significant proportion of individuals experienced emergency department presentations or hospital admissions, with head injuries being the most common. Assault causing bodily harm was the most prevalent offence resulting in hospitalisation (66%, n = 2,018).

CONCLUSIONS

There is a noteworthy disparity between the quantity of hospital admissions attributed to alcohol-related incidents and the number of cases that are formally classified as ARH in the hospital system. This disparity highlights a more profound issue of substantial under-ascertainment or inadequate identification of ARH than previously acknowledged. Our findings justify the prioritisation of prevention strategies, beyond improvement in the documentation of alcohol-related hospitalisation. Considering the scale of the problem, and the underestimation of the burden of alcohol-related hospitalisation, a proportional increase in investment is necessary to achieve population-level reductions in ARH.

Assessing resolvability, parsability, and consistency of RDF resources: a use case in rare diseases

INTRODUCTION

Healthcare data and the knowledge gleaned from it play a key role in improving the health of current and future patients. These knowledge sources are regularly represented as 'linked' resources based on the Resource Description Framework (RDF). Making resources 'linkable' to facilitate their interoperability is especially important in the rare-disease domain, where health resources are scattered and scarce. However, to benefit from using RDF, resources need to be of good quality. Based on existing metrics, we aim to assess the quality of RDF resources related to rare diseases and provide recommendations for their improvement.

METHODS

Sixteen resources of relevance for the rare-disease domain were selected: two schemas, three metadatasets, and eleven ontologies. These resources were tested on six objective metrics regarding resolvability, parsability, and consistency. Any URI that failed the test based on any of the six metrics was recorded as an error. The error count and percentage of each tested resource were recorded. The assessment results were represented in RDF, using the Data Quality Vocabulary schema.

RESULTS

For three out of the six metrics, the assessment revealed quality issues. Eleven resources have non-resolvable URIs with proportion to all URIs ranging from 0.1% (6/6,712) in the Anatomical Therapeutic Chemical Classification to 13.7% (17/124) in the WikiPathways Ontology; seven resources have undefined URIs; and two resources have incorrectly used properties of the 'owl:ObjectProperty' type. Individual errors were examined to generate suggestions for the development of high-quality RDF resources, including the tested resources.

CONCLUSION

We assessed the resolvability, parsability, and consistency of RDF resources in the rare-disease domain, and determined the extent of these types of errors that potentially affect interoperability. The qualitative investigation on these errors reveals how they can be avoided. All findings serve as valuable input for the development of a guideline for creating high-quality RDF resources, thereby enhancing the interoperability of biomedical resources.

Risk for referral to the child welfare system following parental relationship transitions in Norway

BACKGROUND

There is a lack of knowledge concerning how changes in family structures are associated with involvement in child welfare systems. Particularly little attention has been paid to the role of parental relationship transitions, which may involve major changes in the lives of children and parents in terms of housing, finances, and relationship boundaries between family members.

OBJECTIVE

To investigate how transitions in parental relationship status are linked to referrals to the child welfare system.

PARTICIPANTS AND SETTING

All children born in Norway in 1995 (N = 60,218) and 2005 (N = 56,644) and their parents.

METHODS

This retrospective birth cohort study consisted of child welfare statistics merged with various registers from Statistics Norway. Logistic panel-data models were used to examine the relationship between the occurrence of a parental relationship transition and referral to the child welfare system. Four types of relationship transitions were analyzed: (1) couple to a single mother, (2) couple to a single father, (3) single mother to a couple, and (4) single father to a couple.

RESULTS

The occurrence of any type of relationship transition increased the likelihood of referral to the child welfare system in the year that the transition occurred, with the transitions to single motherhood, to single fatherhood, and from single fatherhood to a couple associated with greater odds of referral than the transition from single motherhood to a couple.

CONCLUSIONS

Understanding how parental relationship transitions are associated with referrals to the child welfare system is important to appropriately facilitate help to families in need.

Factors associated with residential fire-related hospitalisations and deaths: A 10-year population-based study

This study aims to identify residential fire risk factors and their health outcomes in terms of hospital admissions from burns and smoke inhalation together with related readmissions, length of hospital stay (LOS), costs of hospitalisation and mortality within 30 days of the fire incidence. Residential fire-related hospitalisations from 2005 to 2014 in New South Wales, Australia were identified using linked data. Univariate and multivariable Poisson regression analyses were performed to determine factors associated with residential fires on hospital admission and loss of life. During the study period, 1862 individuals were hospitalised due to residential fires. In terms of prolonged LOS, high hospitalisation cost or mortality, fire incidents' that damaged both contents and structures of the property; were ignited by smokers' materials and/or due to mental or physical impairment of the residents had more adverse outcomes. Individuals aged 65 and over with comorbidities and/or acquired severe injuries from the fire incident were at a higher risk of long-term hospitalisation and death. This study provides information to response agencies in communicating fire safety messages and intervention programs to target vulnerable population. In addition, it also supplies indicators on hospital usage and LOS following residential fires to health administrators.

Contemporary trends in anaphylaxis burden and healthcare utilisation in Western Australia: A linked data study

Background

Anaphylaxis is a growing public health problem in Australia. To determine the extent of the problem, we linked multiple health datasets to examine temporal trends in anaphylaxis events across the health system in Western Australia (WA).

Methods

We identified an anaphylaxis cohort from 1980 to 2020 using linked datasets from ambulance, emergency departments, hospital inpatients and deaths. Age-standardised anaphylaxis event rates were calculated from 2010 to 2020. Dataset-specific rates for anaphylaxis were also examined, to show differences in health care utilisation. Annual percent change in rates (2010-2019) were estimated using age-adjusted Poisson regression models.

Results

A total of 19 140 individuals (mean age 31 years; 51% female) experienced 24 239 anaphylaxis events between 2010 and 2020. From 2010 to 2019, the average annual percent increase (95% CI) in rates was 5.3% (4.8-5.8%), from 70.3 to 113.9, with rates reducing to 76.5/100 000 population in 2020. Adolescents and young adults aged 5-14 years and 15-24 years had the greatest increase of 6.9% (5.6-8.1%) and 6.8% (5.6-8.0) respectively, with those over 25 years increasing by approximately 5% per year and children 1-4 years showing the lowest annual increase of 2.6% (1.1-4.2%). The highest absolute rates were seen in under 1 year (269.7/100 000; 2019). There has been an acceleration of trends from 2015 to 2019, underpinned by large increases in 15-24 and 25-34 years. All databases, show similar increasing trends, with ambulance attendance (33.7 per 100 000), emergency presentation (89.8 per 100 000) and hospital admissions (46.2 per 100 000), for anaphylaxis highest in 2019. However, whilst ambulance and emergency presentations have grown by 8.9% (95%CI 7.9-9.8%) and 6.6% per year (95%CI 6.0-7.2%), respectively, hospitalisations appear to be steadying with only a 0.9% (95%CI 0.2-1.6%) yearly rise.

Conclusion

Rates of anaphylaxis continue to increase, with WA having higher rates than previous estimates for Australia. Whilst rates are still high in infants, lower trends in children compared to older ages may indicate better prevention of allergy. Results show more people experiencing anaphylaxis now receive care in emergency and ambulance, rather than hospital. Further exploration of the patient care journey through prehospital and inpatient care is required, to understand the changing health demands of people who experience anaphylaxis.

Age and gender patterns in health service utilisation: Age-Period-Cohort modelling of linked health service usage records

BACKGROUND

Health service utilisation changes across the life-course and may be influenced by contextual factors at different times. There is some evidence that men engage less with preventive health services, including attending doctors' clinics, however the extent to which this varies temporally and across different age groups is unclear. This study aimed to describe age or cohort effects on engagement with GPs among employed mothers and fathers in Australia, and differences in these trends between men and women.

METHODS

We linked data from the 'Growing up in Australia: The Longitudinal Study of Australian Children' with administrative health service records from Medicare. We used a small-domain estimation Age-Period-Cohort method to describe patterns in health service use among working-age male and female parents in Australia while adjusting for employment status and controlling for time-invariant factors. Our small-domain method assumes a smooth response surface of Age, Period and Cohort.

RESULTS

Male parents have lower health service engagement than women of the same age at the same time period. Men's pattern of health service use across time is likely explained entirely by ageing. That is, we find that patterns in health service utilisation among men are largely driven by age effects, with no evidence of periods or cohort effects in health service engagement for men between 2002 and 2016.

CONCLUSIONS

Differences in health service utilisation between male and female parents at all age-period-cohort combinations highlight a need for more research to examine the extent to which this level of health service use among Australian men meets men's health needs, as well as barriers and enablers of health service engagement for men. Absence of evidence for period effects suggests that there is little shift in gendered patterns of health service utilisation during the observed period.

Automated approach for quality assessment of RDF resources

INTRODUCTION

The Semantic Web community provides a common Resource Description Framework (RDF) that allows representation of resources such that they can be linked. To maximize the potential of linked data - machine-actionable interlinked resources on the Web - a certain level of quality of RDF resources should be established, particularly in the biomedical domain in which concepts are complex and high-quality biomedical ontologies are in high demand. However, it is unclear which quality metrics for RDF resources exist that can be automated, which is required given the multitude of RDF resources. Therefore, we aim to determine these metrics and demonstrate an automated approach to assess such metrics of RDF resources.

METHODS

An initial set of metrics are identified through literature, standards, and existing tooling. Of these, metrics are selected that fulfil these criteria: (1) objective; (2) automatable; and (3) foundational. Selected metrics are represented in RDF and semantically aligned to existing standards. These metrics are then implemented in an open-source tool. To demonstrate the tool, eight commonly used RDF resources were assessed, including data models in the healthcare domain (HL7 RIM, HL7 FHIR, CDISC CDASH), ontologies (DCT, SIO, FOAF, ORDO), and a metadata profile (GRDDL).

RESULTS

Six objective metrics are identified in 3 categories: Resolvability (1), Parsability (1), and Consistency (4), and represented in RDF. The tool demonstrates that these metrics can be automated, and application in the healthcare domain shows non-resolvable URIs (ranging from 0.3% to 97%) among all eight resources and undefined URIs in HL7 RIM, and FHIR. In the tested resources no errors were found for parsability and the other three consistency metrics for correct usage of classes and properties.

CONCLUSION

We extracted six objective and automatable metrics from literature, as the foundational quality requirements of RDF resources to maximize the potential of linked data. Automated tooling to assess resources has shown to be effective to identify quality issues that must be avoided. This approach can be expanded to incorporate more automatable metrics so as to reflect additional quality dimensions with the assessment tool implementing more metrics.

Child protection system involvement in children of incarcerated mothers: A linked data study

BACKGROUND

Women prisoners are a growing portion of the prison population. Health and social outcomes of their children have been studied and found to be poor, but little is known about child protection outcomes.

OBJECTIVES

Ascertain child protection system contact of children exposed to maternal incarceration.

PARTICIPANTS AND SETTING

All children born between 1985 and 2011 exposed to the incarceration of their mothers in a Western Australian correctional facility and a matched comparison group.

METHODS

A matched cohort study using linked administrative data on 2637 mothers entering prison between 1985 and 2015 and their 6680 children. We estimated hazard ratios (HRs) and incidence rate ratios (IRRs) of child protection service (CPS) contact post maternal incarceration (four concern levels), comparing rates for children exposed to maternal incarceration with a matched non-exposed group, adjusting for maternal and child factors.

FINDINGS

Exposure to maternal incarceration increased risk of CPS contact. Unadjusted HRs exposed vs unexposed children were 7.06 (95%CI = 6.49-7.69) for substantiated child maltreatment and 12.89 (95%CI = 11.42-14.55) for out-of-home care (OOHC). Unadjusted IRRs were 6.04 (95%CI = 5.57-6.55) for number of substantiations and 12.47 (95%CI = 10.65-14.59) for number of removals to OOHC. HRs and IRRs were only slightly attenuated in adjusted models.

CONCLUSIONS

Maternal incarceration is a warning flag for a child at high risk of serious child protection concerns. Family-friendly rehabilitative women's prisons, incorporating support for more nurturing mother-child relationships could provide a placed-based public health opportunity for disrupting distressing life trajectories and intergenerational pathways of disadvantage of these vulnerable children and their mothers. This population should be a priority for trauma-informed family support services.

Air ambulance retrievals of patients with suspected appendicitis and acute abdominal pain: The patients' journeys, referral pathways and appendectomy outcomes using linked data in Central Queensland, Australia

INTRODUCTION

Acute appendicitis is the most common cause of acute abdominal pain presentations to the ED and common air ambulance transfer.

AIMS

describe how linked data can be used to explore patients' journeys, referral pathways and request-to-activation responsiveness of patients' appendectomy outcomes (minor vs major complexity).

METHODS

Data sources were linked: aeromedical, hospital and death. Request-to-activation intervals showed strong right-tailed skewness. Quantile regression examined whether the longest request-to-activation intervals were associated with appendicitis complexity in patients who underwent an appendectomy.

RESULTS

There were 684 patients in three referral pathways based on hospital capability levels. In total, 5.6 % patients were discharged from ED. 83.3 % of all rural origins entered via the ED. 3.8 % of appendicitis patients were triaged to tertiary hospitals. Appendectomy patients with major complexity outcomes were less likely to have longer request-to-activation wait times & had longer lengths of stay than patients with minor complexity outcomes.

CONCLUSIONS

Linked data highlighted four aspects of a functioning referral system: appendectomy outcomes of major complexity were less likely to have longer request-to-activation intervals compared to minor (sicker patients were identified); few were discharged from EDs (validated transfer); few were triaged to tertiary hospitals (appropriate level for need), and no deaths relating to appendectomy.

SALON ontology for the formal description of sequence alignments

BACKGROUND

Information provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and their context. Sequence alignment is a bioinformatics approach to identifying regions of similarity in DNA, RNA, or protein sequences. However, there is no consensus about the specific common terminology and representation for sequence alignments. Thus, automatically linking the wide existing knowledge about the sequences with the alignments is challenging.

RESULTS

The Sequence Alignment Ontology (SALON) defines a helpful vocabulary for representing and semantically annotating pairwise and multiple sequence alignments. SALON is an OWL 2 ontology that supports automated reasoning for alignments validation and retrieving complementary information from public databases under the Open Linked Data approach. This will reduce the effort needed by scientists to interpret the sequence alignment results.

CONCLUSIONS

SALON defines a full range of controlled terminology in the domain of sequence alignments. It can be used as a mediated schema to integrate data from different sources and validate acquired knowledge.

Querying semantic catalogues of biomedical databases

BACKGROUND

Secondary use of health data is a valuable source of knowledge that boosts observational studies, leading to important discoveries in the medical and biomedical sciences. The fundamental guiding principle for performing a successful observational study is the research question and the approach in advance of executing a study. However, in multi-centre studies, finding suitable datasets to support the study is challenging, time-consuming, and sometimes impossible without a deep understanding of each dataset.

METHODS

We propose a strategy for retrieving biomedical datasets of interest that were semantically annotated, using an interface built by applying a methodology for transforming natural language questions into formal language queries. The advantages of creating biomedical semantic data are enhanced by using natural language interfaces to issue complex queries without manipulating a logical query language.

RESULTS

Our methodology was validated using Alzheimer's disease datasets published in a European platform for sharing and reusing biomedical data. We converted data to semantic information format using biomedical ontologies in everyday use in the biomedical community and published it as a FAIR endpoint. We have considered natural language questions of three types: single-concept questions, questions with exclusion criteria, and multi-concept questions. Finally, we analysed the performance of the question-answering module we used and its limitations. The source code is publicly available at https://bioinformatics-ua.github.io/BioKBQA/.

CONCLUSION

We propose a strategy for using information extracted from biomedical data and transformed into a semantic format using open biomedical ontologies. Our method uses natural language to formulate questions to be answered by this semantic data without the direct use of formal query languages.

Comparison of causes, characteristics and consequences of residential fires in social and non-social housing dwellings in New South Wales, Australia

There are over 17,000 residential fire incidents in Australia annually, of which 6,500 occur in New South Wales (NSW). The number of state-provided accommodations for those on low incomes (social housing), is over 437,000 in Australia of which 34% are located in NSW. This study compared causes, characteristics and consequences of residential fires in social and non-social housing in NSW, Australia. This population-based study used linked fire brigade and health service data to identify those who experienced a residential fire incident from 2005 to 2014. Over the study period, 43,707 residential fires were reported, of which 5,073 (11.6%) occurred in social housing properties. Fires in social housing were more likely to occur in apartments (RR 1.85, 95%CI 1.75-1.96), caused by matches and lighters (RR 1.62, 95%CI 1.51-1.74) and smokers' materials (RR 1.51, 95%CI 1.34 - 1.71). The risk of health service utilisation or hospital admission was 16% (RR 1.16, 95%CI 1.04-1.28) and 25% (RR 1.25, 95%CI 1.02-1.51) higher in social housing respectively. Those aged 25-65 were at 40% (RR 1.40, 95%CI 1.14 - 1.73) higher risk of using residential fire-related health services. Almost 88% of social housing properties did not have a functioning fire detector of any type, and 1.2% were equipped with sprinklers. Overall, the risk of residential fire incidents and associated injuries was higher for residents in social housing. Risk mitigation strategies beyond the current provision of smoke alarms are required to reduce the impact of residential fires in social and non-social housing.

Aligning restricted access data with FAIR: a systematic review

Understanding the complexity of restricted research data is vitally important in the current new era of Open Science. While the FAIR Guiding Principles have been introduced to help researchers to make data Findable, Accessible, Interoperable and Reusable, it is still unclear how the notions of FAIR and Openness can be applied in the context of restricted data. Many methods have been proposed in support of the implementation of the principles, but there is yet no consensus among the scientific community as to the suitable mechanisms of making restricted data FAIR. We present here a systematic literature review to identify the methods applied by scientists when researching restricted data in a FAIR-compliant manner in the context of the FAIR principles. Through the employment of a descriptive and iterative study design, we aim to answer the following three questions: (1) What methods have been proposed to apply the FAIR principles to restricted data?, (2) How can the relevant aspects of the methods proposed be categorized?, (3) What is the maturity of the methods proposed in applying the FAIR principles to restricted data?. After analysis of the 40 included publications, we noticed that the methods found, reflect the stages of the Data Life Cycle, and can be divided into the following Classes: Data Collection, Metadata Representation, Data Processing, Anonymization, Data Publication, Data Usage and Post Data Usage. We observed that a large number of publications used 'Access Control' and 'Usage and License Terms' methods, while others such as 'Embargo on Data Release' and the use of 'Synthetic Data' were used in fewer instances. In conclusion, we are presenting the first extensive literature review on the methods applied to confidential data in the context of FAIR, providing a comprehensive conceptual framework for future research on restricted access data.

Rapid systematic review to identify key barriers to access, linkage, and use of local authority administrative data for population health research, practice, and policy in the United Kingdom

BACKGROUND

Improving data access, sharing, and linkage across local authorities and other agencies can contribute to improvements in population health. Whilst progress is being made to achieve linkage and integration of health and social care data, issues still exist in creating such a system. As part of wider work to create the Cambridge Child Health Informatics and Linked Data (Cam-CHILD) database, we wanted to examine barriers to the access, linkage, and use of local authority data.

METHODS

A systematic literature search was conducted of scientific databases and the grey literature. Any publications reporting original research related to barriers or enablers of data linkage of or with local authority data in the United Kingdom were included. Barriers relating to the following issues were extracted from each paper: funding, fragmentation, legal and ethical frameworks, cultural issues, geographical boundaries, technical capability, capacity, data quality, security, and patient and public trust.

RESULTS

Twenty eight articles were identified for inclusion in this review. Issues relating to technical capacity and data quality were cited most often. This was followed by those relating to legal and ethical frameworks. Issue relating to public and patient trust were cited the least, however, there is considerable overlap between this topic and issues relating to legal and ethical frameworks.

CONCLUSIONS

This rapid review is the first step to an in-depth exploration of the barriers to data access, linkage and use; a better understanding of which can aid in creating and implementing effective solutions. These barriers are not novel although they pose specific challenges in the context of local authority data.

Understanding Public Priorities and Perceptions of the Use of Linked Healthcare Data in South East England

The counties of Kent, Surrey and Sussex (KSS) in South East England are creating anonymized, linked databases of healthcare records for audit, service planning and research for the first time. We consulted with 79 citizens from KSS in 5 deliberative focus groups, asking about perceived benefits and concerns regarding these new data assets. Participants hoped the linked datasets could be used for joining up care and information, improving efficiency, and improving healthcare provision, but were concerned about missing and inaccurate data, data breaches and hacking, use of data by profit-making organisations, and stigma and discrimination. Findings will be used to underpin governance and engagement strategies for integrated datasets in KSS.

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data

BACKGROUND

The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles.

RESULTS

Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR.

CONCLUSIONS

Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.

Methodological guidelines to estimate population-based health indicators using linked data and/or machine learning techniques

BACKGROUND

The capacity to use data linkage and artificial intelligence to estimate and predict health indicators varies across European countries. However, the estimation of health indicators from linked administrative data is challenging due to several reasons such as variability in data sources and data collection methods resulting in reduced interoperability at various levels and timeliness, availability of a large number of variables, lack of skills and capacity to link and analyze big data. The main objective of this study is to develop the methodological guidelines calculating population-based health indicators to guide European countries using linked data and/or machine learning (ML) techniques with new methods.

METHOD

We have performed the following step-wise approach systematically to develop the methodological guidelines: i. Scientific literature review, ii. Identification of inspiring examples from European countries, and iii. Developing the checklist of guidelines contents.

RESULTS

We have developed the methodological guidelines, which provide a systematic approach for studies using linked data and/or ML-techniques to produce population-based health indicators. These guidelines include a detailed checklist of the following items: rationale and objective of the study (i.e., research question), study design, linked data sources, study population/sample size, study outcomes, data preparation, data analysis (i.e., statistical techniques, sensitivity analysis and potential issues during data analysis) and study limitations.

CONCLUSIONS

This is the first study to develop the methodological guidelines for studies focused on population health using linked data and/or machine learning techniques. These guidelines would support researchers to adopt and develop a systematic approach for high-quality research methods. There is a need for high-quality research methodologies using more linked data and ML-techniques to develop a structured cross-disciplinary approach for improving the population health information and thereby the population health.

Social determinants of diabetes-related foot disease among older adults in New South Wales, Australia: evidence from a population-based study

BACKGROUND

Diabetes-related foot is the largest burden to the health sector compared to other diabetes-related complications in Australia, including New South Wales (NSW). Understanding of social determinants of diabetes-related foot disease has not been definitive in Australian studies. This study aimed to investigate the social determinants of diabetes-related foot disease in NSW.

METHODOLOGY

The first wave of the 45 and Up Study survey data was linked with NSW Admitted Patient Data Collection, Emergency Department Data Collection, and Pharmaceutical Benefits Scheme data resulting in 28,210 individuals with diabetes aged 45 years and older in NSW, Australia. Three outcome variables were used: diabetes-related foot disease (DFD), diabetic foot ulcer (DFU), and diabetic foot infection (DFI). They were classified as binary, and survey logistic regression was used to determine the association between each outcome measure and associated factors after adjusting for sampling weights.

RESULTS

The prevalence of DFD, DFU and DFI were 10.8%, 5.4% and 5.2%, respectively, among people with diabetes. Multivariate analyses revealed that the common factors associated with DFD, DFU and DFI were older age (75 years or more), male, single status, background in English speaking countries, and coming from lower-income households (less than AUD 20,000 per year). Furthermore, common lifestyle and health factors associated with DFD, DFU, and DFI were low physical activity (< 150 min of moderate-to-vigorous physical activity per week), history of diabetes for over 15 years, and having cardiovascular disease.

CONCLUSION

Our study showed that about 1 in 10 adults with diabetes aged 45 years and older in NSW reported DFD. Interventions, including the provision of related health services aimed at reducing all forms of DFD in NSW, are recommended to target older individuals with a long history of diabetes, and coming from lower-income households.

Long-term outcomes following rheumatic heart disease diagnosis in Australia

Aims 

Rheumatic heart disease (RHD) is a major contributor to cardiac morbidity and mortality globally. This study aims to estimate the probability and predictors of progressing to non-fatal cardiovascular complications and death in young Australians after their first RHD diagnosis.

Methods and results 

This retrospective cohort study used linked RHD register, hospital, and death data from five Australian states and territories (covering 70% of the whole population and 86% of the Indigenous population). Progression from uncomplicated RHD to all-cause death and non-fatal cardiovascular complications (surgical intervention, heart failure, atrial fibrillation, infective endocarditis, and stroke) was estimated for people aged <35 years with first-ever RHD diagnosis between 2010 and 2018, identified from register and hospital data. The study cohort comprised 1718 initially uncomplicated RHD cases (84.6% Indigenous; 10.9% migrant; 63.2% women; 40.3% aged 5–14 years; 76.4% non-metropolitan). The composite outcome of death/cardiovascular complication was experienced by 23.3% (95% confidence interval: 19.5–26.9) within 8 years. Older age and metropolitan residence were independent positive predictors of the composite outcome; history of acute rheumatic fever was a negative predictor. Population group (Indigenous/migrant/other Australian) and sex were not predictive of outcome after multivariable adjustment.

Conclusion 

This study provides the most definitive and contemporary estimates of progression to major cardiovascular complication or death in young Australians with RHD. Despite access to the publically funded universal Australian healthcare system, one-fifth of initially uncomplicated RHD cases will experience one of the major complications of RHD within 8 years supporting the need for programmes to eradicate RHD.

Cost of intimate partner violence during pregnancy and postpartum to health services: a data linkage study in Queensland, Australia

To quantify health service costs of intimate partner violence (IPV) during pregnancy and postpartum; and to compare health service costs between women who reported IPV, versus women who did not report IPV. This was a cohort study using linked data for a publicly funded Australian tertiary hospital maternity service. Participants included all women accessing antenatal services between August 2016 and August 2018. Routinely collected IPV data were linked to women's admitted, non-admitted, emergency department, perinatal, and costing data from 6 months prior to reporting IPV through to 12 months post-birth. Of the 9889 women receiving maternity care, 280 (2.9%) reported some form of IPV with 72 (24.8%) referred to support. Women who reported IPV generated higher mean total costs than women not reporting IPV ($12,772 vs $10,166, respectively). Between-group differences were significant after adjusting for demographic and clinical factors (cost ratio 1.24, 95% CI: 1.15-1.34). There were no significant differences in mean total costs for babies where IPV was and was not reported ($4971 vs $5340, respectively). IPV is costly for health services. However, greater research is needed to comprehensively estimate the long-term health service costs associated with IPV. Furthermore, the limitations associated with routinely collected IPV data suggest that standardised screening practices and innovative data linkage and modelling approaches are required to collect data that truly represents the burden and costs associated with IPV.

Child maltreatment data: A summary of progress, prospects and challenges

BACKGROUND

In 1996, the ISPCAN Working Group on Child Maltreatment Data (ISPCAN-WGCMD) was established to provide an international forum in which individuals, who deal with child maltreatment data in their respective professional roles, can share concerns and solutions.

OBJECTIVE

This commentary describes some of the key features and the status of child maltreatment related data collection addressed by the ISPCAN-WGCMD.

METHODS

Different types of data collection methods including self-report, sentinel, and administrative data designs are described as well as how they address different needs for information to help understand child maltreatment and systems of prevention and intervention.

RESULTS

While still lacking in many parts of the world, access to child maltreatment data has become much more widespread, and in many places a very sophisticated undertaking.

CONCLUSION

The ISPCAN-WGCMD has been an important forum for supporting the continued development and improvement in the global effort to understand and combat child maltreatment thus contributing to the long term goals of the UN Convention on the Rights of the Child. Nevertheless, based on what has been learned, even greater efforts are required to improve data in order to effectively combat child maltreatment.

Pregnancy and birth characteristics of Aboriginal twins in two Australian states: a data linkage study

Introduction

Perinatal outcomes for singleton pregnancies are poorer, on average, for Aboriginal people than non-Aboriginal people, but little is known about Aboriginal multifetal pregnancies. Yet multifetal pregnancies and births are often more complicated and have poorer outcomes than singleton pregnancies. We describe the pregnancies, births and perinatal outcomes for Aboriginal twins born in Western Australia (WA) and New South Wales (NSW) with comparisons to Aboriginal singletons in both states and to non-Aboriginal births in NSW.

Materials and methods

Whole-population birth records and birth and death registrations were linked for all births during 2000–2013 (WA) and 2002–2008 (NSW). Hospital records and the WA Register of Developmental Anomalies - Cerebral Palsy were linked for all WA births and hospital records for a subset of NSW births. Descriptive statistics are reported for maternal and child demographics, maternal health, pregnancy complications, births and perinatal outcomes.

Results

Thirty-four thousand one hundred twenty-seven WA Aboriginal, 32,352 NSW Aboriginal and 601,233 NSW non-Aboriginal births were included. Pregnancy complications were more common among mothers of Aboriginal twins than Aboriginal singletons (e.g. 17% of mothers of WA twins had hypertension/pre-eclampsia/eclampsia vs 8% of mothers of singletons) but similar to mothers of NSW non-Aboriginal twins. Most Aboriginal twins were born in a principal referral, women’s or large public hospital. The hospitals were often far from the mother’s home (e.g. 31% of mothers of WA Aboriginal twins gave birth at hospitals located more than 3 h by road from their home). Outcomes were worse for Aboriginal liveborn twins than Aboriginal singletons and non-Aboriginal twins (e.g. 58% of NSW Aboriginal twins were preterm compared to 9% of Aboriginal singletons and 49% non-Aboriginal twins).

Conclusions

Mothers of Aboriginal twins faced significant challenges during the pregnancy, birth and the postnatal period in hospital and, in addition to accessible specialist medical care, these mothers may need extra practical and psychosocial support throughout their journey.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12884-021-03945-9.

Service usage of a cohort of formerly homeless women in Aotearoa New Zealand

Purpose

The aim of this paper is to explore government service usage across the domains of health, justice, and social development and tax for a cohort of formerly homeless people in Aotearoa New Zealand, focusing specifically on the experiences of women. The Integrated Data Infrastructure is used, which links our de-identified cohort data with administrative data from various Aotearoa New Zealand Government departments.

Results

Of the cohort of 390, the majority (53.8%) were women. These women were more likely to be younger (57.1% were aged 25–44), indigenous Māori (78.6%), and have children (81.4%). These women had lower incomes, and higher rates of welfare benefit receipt, when compared to men in the cohort and a control group of women from the wider population.

Conclusions

The cohort were primarily female, younger, Māori, and parents. They earned much less than their non-homeless counterparts, and relied heavily on government support. The neoliberalisation of the welfare state, high rates of women's poverty, and the gendered nature of parenthood means that women's homelessness is distinct from men's homelessness.

•

The cohort had distinct government service usage when compared to a cohort of homeless men, and non-homeless women.

•

The cohort were more likely to be Māori, younger, and parents.

•

The cohort required greater levels of income support than homeless men and non-homeless women.

FASTory digital twin data

The vast adoption of machine learning techniques in developing smart solutions increases the need of training and testing data. This data can be either collected from physical systems or created using simulation tools. In this regard, this paper presents a set of data collected using a digital twin known as the FASTory Simulator. The data contains more than 100 K events which are collected during a simulated assembly process. The FASTory simulator is a replica of a real assembly line with web-based industrial controllers. The data have been collected using specific-developed orchestrator. During the simulated process, the orchestrator was able to record all the events that occurred in the system. The provided data contains raw JavaScript Object Notation (JSON) formatted data and filtered Comma Separated Values (CSV) formatted data. This data can be exploited in machine learning for modelling the behaviour of the production systems or as testing data for optimization solution for the production system. Finally, this data has been utilized in a research for comparing different data analysis approaches including Knowledge-based systems and data-based systems.

Semantic micro-contributions with decentralized nanopublication services

While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing.

Application and evaluation of knowledge graph embeddings in biomedical data

Linked data and bio-ontologies enabling knowledge representation, standardization, and dissemination are an integral part of developing biological and biomedical databases. That is, linked data and bio-ontologies are employed in databases to maintain data integrity, data organization, and to empower search capabilities. However, linked data and bio-ontologies are more recently being used to represent information as multi-relational heterogeneous graphs, "knowledge graphs". The reason being, entities and relations in the knowledge graph can be represented as embedding vectors in semantic space, and these embedding vectors have been used to predict relationships between entities. Such knowledge graph embedding methods provide a practical approach to data analytics and increase chances of building machine learning models with high prediction accuracy that can enhance decision support systems. Here, we present a comparative assessment and a standard benchmark for knowledge graph-based representation learning methods focused on the link prediction task for biological relations. We systematically investigated and compared state-of-the-art embedding methods based on the design settings used for training and evaluation. We further tested various strategies aimed at controlling the amount of information related to each relation in the knowledge graph and its effects on the final performance. We also assessed the quality of the knowledge graph features through clustering and visualization and employed several evaluation metrics to examine their uses and differences. Based on this systematic comparison and assessments, we identify and discuss the limitations of knowledge graph-based representation learning methods and suggest some guidelines for the development of more improved methods.

Utility estimations of health states of older Australian women with atrial fibrillation using SF-6D

PURPOSE

To estimate SF-6D utility scores for older women with atrial fibrillation (AF); calculate and compare mean utility scores for women with AF with various demographic, health behaviours, and clinical characteristics; and develop a multivariable regression model to determine factors associated with SF-6D utility scores.

METHODS

This study evaluated N = 1432 women diagnosed with AF from 2000 to 2015 of the old cohort (born 1921-26) of the Australian Longitudinal Study on Women's Health (ALSWH) who remained alive for at least 12 months post first recorded AF diagnosis. Self-reported data on demographics, health behaviours, health conditions, and SF-36 were obtained from the ALSWH surveys, corresponding to within three years of the date of the first record of AF diagnosis. Linked Pharmaceutical Benefits Scheme (PBS) data determined the use of oral anticoagulants and comorbid conditions, included in CHA₂DS₂-VA (Congestive heart failure, Hypertension, Age ≥ 75 years, Diabetes, Stroke or TIA, Vascular disease and Age 65-74 years) score calculation, were assessed using state-based hospital admissions data. Utility scores were calculated for every woman from their SF-36 responses using the SF-6D algorithm with Australian population norms. Mean utility scores were then calculated for women with various demographic, health behaviours, and clinical characteristics. Ordinary Least Square (OLS) regression modelling was performed to determine factors associated with these utility scores. Two different scenarios were used for the analysis: (1) complete-case, for women with complete data on all the SF-36 items required to estimate SF-6D (N = 584 women), and (2) Multiple Imputation (MI) for missing data, applied to missing values on SF-36 items (N = 1432 women). MI scenario was included to gauge the potential bias when using complete data only.

RESULTS

The mean health utility was estimated to be 0.638 ± 0.119 for the complete dataset and 0.642 ± 0.120 for the dataset where missing values were handled using MI. Using the MI technique, living in regional and remote areas ([Formula: see text]) and the use of oral anticoagulants ([Formula: see text] were positively associated with health utility compared to living in major cities and no use of anticoagulants, respectively. Difficulty to manage on available income [Formula: see text], no/low physical activity [Formula: see text], disability [Formula: see text], history of stroke ([Formula: see text] and history of arthritis [Formula: see text] were negatively associated with health utility.

CONCLUSION

This study presents health utility estimates for older women with AF. These estimates can be used in future clinical and economic research. The study also highlights better health utilities for women living in regional and remote areas, which requires further exploration.

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

BACKGROUND

Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons." Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions.

RESULTS

As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates.

CONCLUSIONS

Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).

Vaccine coverage in children born to migrant mothers in Australia: A population-based cohort study

BACKGROUND

Overall, infant immunisation coverage is currently >90% in Australia, but there are pockets of under-immunised children including children from migrant backgrounds. This study aimed to examine whether on-time vaccination coverage of diphtheria-tetanus-pertussis dose 3 (DTP3) for children born in Australia differed by mother's region of birth and if so, what factors were associated with these differences.

METHODS

We conducted a population-based cohort study using linked data on perinatal, immunisation and birth records for 2 million children born in Western Australia and New South Wales between 1996 and 2012. We assessed on-time coverage of DTP3 (vaccination from 2 weeks prior to, and up until 30 days after, the due date) in children with mothers born overseas. Logistic regression models were developed to determine factors associated with on-time coverage for each maternal region of birth and all regions combined, adjusting for a range of demographic factors. Adjusted estimates of coverage were calculated for the different regions of birth.

RESULTS

On-time DTP3 coverage was 76.2% in children of Australian born mothers, lower in children of mothers from Oceania (66.7%) and North America (68%), and higher in children born to mothers from South-East Asia (79.9%) and Southern Asia (79.3%). While most variables were consistently associated with lower coverage in all regions of birth, higher socioeconomic status and jurisdiction of birth showed varied results. Adjusted estimates of DTP3 coverage increased in children born to mothers from Australia (78.3%), Oceania (70.5%), Northern Africa (81.5%) and the Middle East (79.6%). DTP3 coverage decreased in children born to mothers from Europe and former USSR (74.6%), North-east Asia (75.2%), Southern Asia (76.7%), North America (65.5) and South/Central America and the Caribbean (73.2%).

CONCLUSIONS

On-time vaccination rates differed by mother's region of birth. More research is needed to determine the main reasons for these remaining differences to improve vaccine uptake and also help guide policy and practice.

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects

BACKGROUND

Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability.

RESULTS

We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform.

CONCLUSIONS

Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.

Increasing anaphylaxis events in Western Australia identified using four linked administrative datasets

Background

Anaphylaxis events are increasing worldwide, based on studies of single administrative datasets including hospital admissions, emergency room presentations, and prescription and medical claims data. Linking multiple administrative datasets may provide better epidemiological estimates, by capturing a greater number of anaphylaxis events occurring at the individual level. In this linked data study in Western Australia, we combined 4 population-based datasets to identify anaphylaxis events, factors influencing occurrence, and change in event rates from 2002 to 2013.

Methods

Four linked administrative datasets from the Western Australian Data Linkage System were used, representing ambulance attendances, emergency department presentations, hospital inpatient admissions and death registrations. An anaphylaxis cohort was identified using ICD-9-CM, ICD-10-AM and additional anaphylaxis diagnosis codes, with event rates calculated. We explored the impact of age, gender, cause, Indigenous status and socioeconomic index on event rates. Standard Poisson regression models were used to examine the significance of the change in anaphylaxis event rates over time.

Results

A total 12,637 individuals (mean age 31.8 years, 49.6% female) experienced 15,462 anaphylaxis events between 2002 and 2013 (97.5% in non-Indigenous patients and 59.5% residing in the area of greatest socioeconomic advantage). Anaphylaxis event rates increased from 15.4 to 82.5/10⁵ population between 2002 and 2013. The greatest increase in anaphylaxis events was seen in those coded as unspecified anaphylaxis (all ages, males and females combined, p < 0.001), with the highest rates of unspecified anaphylaxis in males 0–4 years (171.9/10⁵ population in 2013), and females 15–19 years (104.0/10⁵ in 2013). The average annual percent increase (95% CI) for food-related anaphylaxis was 9.2% (6.6–12.0); for medication-related anaphylaxis was 5.8% (4.5–7.1); and for unspecified anaphylaxis was 10.4% (9.8–11.0); all p < 0.001. There was a significant increase in ambulance attendance, emergency presentations and inpatient admissions for anaphylaxis between 2002 and 2013, with emergency presentations (56.0/10⁵ population), inpatient admissions (43.2/10⁵), and ambulance attendance (21.6/10⁵) highest in 2013. Only 25 anaphylaxis-related deaths were recorded in the mortality register with no significant change in rates over time.

Conclusion

Using multiple linked administrative datasets, we identified significantly higher rates of total anaphylaxis than previously reported, with more than 5-fold increases in anaphylaxis events between 2002 and 2013. While the combination of 4 population-level datasets provides a more comprehensive capture of cases, even at the individual dataset level, admission rates for anaphylaxis in Western Australia are substantially higher than those previously reported for similar time periods, both in Australia and worldwide.

Accuracy of reporting of Aboriginality on administrative health data collections using linked data in NSW, Australia

BACKGROUND

Aboriginal people are under-reported on administrative health data in Australia. Various approaches have been used or proposed to improve reporting of Aboriginal people using linked records. This cross-sectional study used self-reported Aboriginality from the NSW Patient Survey Program (PSP) as a reference standard to assess the accuracy of reporting of Aboriginal people on NSW Admitted Patient (APDC) and Emergency Department Data Collections (EDDC), and compare the accuracy of selected approaches to enhance reporting Aboriginality using linked data.

METHODS

Ten PSP surveys were linked to five administrative health data collections, including APDC, EDDC, perinatal, and birth and death registration records. Accuracy of reporting of Aboriginality was assessed using sensitivity, specificity, and positive and negative predictive values (PPVs and NPVs) and F score for the EDDC and APDC as baseline and four enhancement approaches using linked records: "Most recent linked record", "Ever reported as Aboriginal", and two approaches using a weight of evidence, "Enhanced Reporting of Aboriginality (ERA) algorithm" and "Multi-stage median (MSM)".

RESULTS

There was substantial under-reporting of Aboriginality on APDC and EDDC records (sensitivities 84 and 77% respectively) with PPVs of 95% on both data collections. Overall, specificities and NPVs were above 98%. Of people who were reported as Aboriginal on the PSP, 16% were not reported as Aboriginal on any of their linked records. Record linkage approaches generally increased sensitivity, accompanied by decrease in PPV with little change in overall F score for the APDC and an increase in F score for the EDDC. The "ERA algorithm" and "MSM" approaches provided the best overall accuracy.

CONCLUSIONS

Weight of evidence approaches are preferred when record linkage is used to improve reporting of Aboriginality on administrative health data collections. However, as a substantial number of Aboriginal people are not reported as Aboriginal on any of their linked records, improvements in reporting are incomplete and should be taken into account when interpreting results of any analyses. Enhancement of reporting of Aboriginality using record linkage should not replace efforts to improve recording of Aboriginal people at the point of data collection and addressing barriers to self-identification for Aboriginal people.

Fracture-related hospitalisations and readmissions of Australian children ≤16 years: A 10-year population-based cohort study

BACKGROUND

Fractures represent the most common injury-related hospitalisations of children. Injured children often miss days from school, may experience ongoing pain and disability, as well as a reduced quality of life. To monitor temporal trends, and to enable targeted strategies to prevent fracture-related hospitalisation, an examination of the characteristics of hospitalisations by fracture-type is needed. The aim of this study was to investigate the characteristics, health outcomes and hospital treatment costs of fracture hospitalisations and readmissions of children aged ≤16 years in Australia across a 10-year period for the five most common types of fractures.

METHOD

Linked Australian hospitalisation and mortality records during 1 July 2002 to 30 June 2012 were analysed. Hospital treatment costs and length of stay were estimated, and the number and causes of hospital readmissions were identified.

RESULTS

There were 287,646 fracture-related hospital admissions in Australia for children ≤16 years. The five most common fracture regions were the forearm (48.1%), shoulder and upper arm (14.1%), lower leg including the ankle (11.3%), wrist and hand (10.4%), and the skull and face (9.0%). There was a decrease in hospitalisation rate for all fractures over the 10-year period. The hospitalisation rate for males was at least double that of females. Falls, particularly those from playground equipment, were the most common injury mechanism. Hospital readmissions within 28 days of hospitalisation were mostly due to further orthopaedic care or rehabilitation. Total treatment costs for fracture-related hospitalisations amounted to over AUD$732 million, with the median cost of readmissions being AUD$2,474.

CONCLUSION

While there is a decline in the rate of hospitalised fractures in Australian children, continued efforts are required if the rate of fractures and their associated economic costs are to be reduced. The identification of the prevalence and causes of various fracture types provides policymakers with evidence to target preventive initiatives.

Enabling ad-hoc reuse of private data repositories through schema extraction

BACKGROUND

Sharing sensitive data across organizational boundaries is often significantly limited by legal and ethical restrictions. Regulations such as the EU General Data Protection Rules (GDPR) impose strict requirements concerning the protection of personal and privacy sensitive data. Therefore new approaches, such as the Personal Health Train initiative, are emerging to utilize data right in their original repositories, circumventing the need to transfer data.

RESULTS

Circumventing limitations of previous systems, this paper proposes a configurable and automated schema extraction and publishing approach, which enables ad-hoc SPARQL query formulation against RDF triple stores without requiring direct access to the private data. The approach is compatible with existing Semantic Web-based technologies and allows for the subsequent execution of such queries in a safe setting under the data provider's control. Evaluation with four distinct datasets shows that a configurable amount of concise and task-relevant schema, closely describing the structure of the underlying data, was derived, enabling the schema introspection-assisted authoring of SPARQL queries.

CONCLUSIONS

Automatically extracting and publishing data schema can enable the introspection-assisted creation of data selection and integration queries. In conjunction with the presented system architecture, this approach can enable reuse of data from private repositories and in settings where agreeing upon a shared schema and encoding a priori is infeasible. As such, it could provide an important step towards reuse of data from previously inaccessible sources and thus towards the proliferation of data-driven methods in the biomedical domain.

Innovative use of data sources: a cross-sectional study of data linkage and artificial intelligence practices across European countries

Background

The availability of data generated from different sources is increasing with the possibility to link these data sources with each other. However, linked administrative data can be complex to use and may require advanced expertise and skills in statistical analysis. The main objectives of this study were to describe the current use of data linkage at the individual level and artificial intelligence (AI) in routine public health activities, to identify the related estimated health indicators (i.e., outcome and intervention indicators) and health determinants of non-communicable diseases and the obstacles to linking different data sources.

Method

We performed a survey across European countries to explore the current practices applied by national institutes of public health, health information and statistics for innovative use of data sources (i.e., the use of data linkage and/or AI).

Results

The use of data linkage and AI at national institutes of public health, health information and statistics in Europe varies. The majority of European countries use data linkage in routine by applying a deterministic method or a combination of two types of linkages (i.e., deterministic & probabilistic) for public health surveillance and research purposes. The use of AI to estimate health indicators is not frequent at national institutes of public health, health information and statistics. Using linked data, 46 health outcome indicators, 34 health determinants and 23 health intervention indicators were estimated in routine. The complex data regulation laws, lack of human resources, skills and problems with data governance, were reported by European countries as obstacles to routine data linkage for public health surveillance and research.

Conclusions

Our results highlight that the majority of European countries have integrated data linkage in their routine public health activities but only a few use AI. A sustainable national health information system and a robust data governance framework allowing to link different data sources are essential to support evidence-informed health policy development. Building analytical capacity and raising awareness of the added value of data linkage in national institutes is necessary for improving the use of linked data in order to improve the quality of public health surveillance and monitoring activities.

The influence of low social support and living alone on premature mortality among aging Canadians

OBJECTIVES

Among older Canadians, we examined the influence of low social support, a weak sense of belonging, and living alone to understand their role on mortality risk in Canada.

METHODS

We conducted a retrospective cohort study of older Canadians surveyed in 2001 from the Canadian Community Health Survey and followed up with death events through December 31, 2011 from the Canadian Vital Statistics Database. Analyses were stratified by age: 55-64 and 65 and older. Social support was assessed using measures developed for the Medical Outcomes Study. A sense of belonging, a binary measure, measured community integration. Living alone was a binary measure. Survival analysis was applied using a Cox proportional hazards model, adjusted for age, sex, income, smoking, and frailty.

RESULTS

Among respondents 55-64 (n = 6822), low affection (HR = 1.37; 95% CI 1.07, 1.75), low emotional/informational support (HR = 1.36; 95% CI 1.06, 1.74), and low positive social interactions (HR = 1.36; 95% CI 1.06, 1.75) were associated with mortality risk. Among respondents 65 and older (n = 8966), low affection (HR = 1.17; 95% CI 1.04, 1.31), low positive social interactions (HR = 1.20; 95% CI 1.07, 1.34), low emotional/informational support (HR = 1.19; 95% CI 1.06, 1.33), and a weak sense of belonging (HR = 1.13; 95% CI 1.05, 1.22) were associated with mortality risk.

CONCLUSION

Low social support and a weak sense of belonging are important risk factors among older Canadians and should be part of the dialogue in Canada about their roles in healthy aging.

Comparing the predictive capability of self-report and medically-verified non-fatal overdose in adults released from prison: A prospective data linkage study

BACKGROUND

Self-reported non-fatal overdose (NFOD) is a predictor of future overdose and is often used to target overdose prevention for people released from prison. However, the level of agreement between self-reported and medically-verified NFOD history remains unknown. This study aimed to determine the agreement between, and predictive value of, self-reported and medically-verified history of NFOD in people recently released from prison.

METHODS

Pre-release baseline survey data from 1307 adults in prison surveyed from 2008 to 2010 in Queensland, Australia were linked to ambulance, emergency department, and hospital records. We compared the agreement of self-reported NFOD history in the baseline survey and medically-verified NFOD ascertained through linked medical data. Unadjusted and adjusted regression models were used to determine the association between self-reported and medically verified NFOD history and medically-verified NFOD after release from prison.

RESULTS

224 (19 %) participants self-reported NFOD history only, 75 (5 %) had medically-verified NFOD history only, and 56 (4 %) both self-reported and had medically-verified NFOD history. Compared to those with no NFOD history, those who self-reported and had a medical history of NFOD (adjusted hazard ratio (AHR) 6.1, 95 %CI 3.1-11.9), those with a medical history only (AHR 3.4, 95 %CI 1.7-7.0), and those who self-reported only (AHR 1.8, 95 %CI 1.0-3.5) were at increased risk of medically-verified NFOD after release from prison.

CONCLUSIONS

Relying on self-report of NFOD is likely to miss people at increased risk of future NFOD, many of whom could be identified through medical records. Wherever possible, data related to NFOD should be triangulated from multiple sources.

An Australian study of long-term hospital admissions and costs comparing patients with unintentional burns and uninjured people

BACKGROUND

The objective of this study was to describe and quantify the long-term hospital service use (HSU) after burn injury and associated costs in a population-based cohort of patients with unintentional burns and compare with uninjured people.

METHODS

This retrospective population-based cohort study analysed de-identified linked health administrative data of all unintentional burns patients (n = 10,460) between 2000 and 2012 in Western Australia and a matched uninjured comparison cohort (n = 42,856). HSU after burn injury (annual admission counts and cumulative length of stay) was examined. HSU costs were based on the Australian Refined Diagnosis Related Groups (AR-DRGs) code on each record. Generalised linear models were used to examine and quantify associations between burn injury and long-term HSU and associated costs.

RESULTS

There were 48,728 hospitalisations after burn occurring within the study period in the burn cohort; in the uninjured comparison cohort, there were 53,244 post-study index hospitalisations. Of those in the burn cohort, 63.9% (n = 6828) had a further hospitalisation after burn injury; this compared with 40.4% (n = 17,297) in the uninjured cohort. After adjustment for socio-demographic and pre-existing health conditions the burn cohort had 2.48 times the hospitalisation rate compared to the uninjured cohort (95% CI: 2.33-2.65). The cost of post-index hospitalisations in the burn cohort totalled to $AUS248.3 million vs $AUS240.8 million in the uninjured cohort. After adjustment, the burn cohort had hospital costs 2.77 times higher than the uninjured controls (95% CI: 2.58-2.98).

CONCLUSIONS

After adjustment for covariates, burn patients experienced greater hospital use for a prolonged period after the initial injury compared with uninjured people. The mean cost per episode of care was generally higher for members of the burn cohort compared to the uninjured cohort indicating either more complicated admissions or admissions for more expensive conditions.

Driver licensing, motor-vehicle crashes, and moving violations among older adults

INTRODUCTION

Driving is important for well-being among older adults, but age-related conditions are associated with driving reduction or cessation and increased crash risk for older drivers. Our objectives were to describe population-based rates of older drivers' licensing and per-driver rates of crashes and moving violations.

METHODS

We examined individual-level statewide driver licensing, crash, and traffic citation data among all New Jersey drivers aged ≥ 65 and a 35- to 54-year-old comparison group during 2010-2014. Rate ratios (RR) of crashes and moving violations were estimated using Poisson regression.

RESULTS

Overall, 86% of males and 71% of females aged ≥ 65 held a valid driver's license. Older drivers had 27% lower per-driver crash rates than middle-aged drivers (RR: 0.73, 95% CI: 0.73, 0.74)-with appreciable differences by sex-but 40% higher fatal crash rates (RR: 1.40 [1.24, 1.58]). Moving violation rates among older drivers were 72% lower than middle-aged drivers (RR: 0.28 [0.28, 0.28]).

CONCLUSION

The majority of older adults are licensed, with substantial variation by age and sex. Older drivers have higher rates of fatal crashes but lower rates of moving violations compared with middle-aged drivers. Practical applications: Future research is needed to understand the extent to which older adults drive and to identify opportunities to further reduce risk of crashes and resultant injuries among older adults.

Older women's patterns of home and community care use and transition to residential aged care: An Australian cohort study

OBJECTIVE

To examine whether patterns of home and community care (HACC) use and person-based characteristics were associated with time to enter permanent residential aged care (RAC).

STUDY DESIGN

A prospective cohort study. The sample consisted of 8062 participants of the Australian Longitudinal Study on Women's Health who used HACC services between 2001 and 2014.

MAIN OUTCOME MEASURES

Time from first HACC use to enter permanent RAC. The median follow-up time was 63 months. Factors associated with time to enter RAC were identified using competing risk regression models.

RESULTS

Of the 8062 participants, 60% belonged to the 'basic HACC' group, who used few services minimally; 16% belonged to the 'moderate HACC' group, who predominantly used domestic assistance with moderate use of other services; and 24% belonged to the 'complex HACC' group, who used many services frequently. Being a member of the complex HACC group was associated with a lower cumulative incidence of RAC than basic or moderate HACC (chances 15% versus 30% by the median observation period, p < 0.01). Living in a remote/outer region (sub-distributional hazard ratio (sdHR) = 0.83, 95%CI: 0.74 - 0.93) was associated with delayed admission to RAC. Meanwhile, earlier admission was associated with living in an apartment (sdHR = 1.29, 95%CI: 1.20-1.40) or a retirement village (sdHR = 1.54, 95%CI = 1.38-1.72), having a physical functioning score <40 (sdHR = 1.16, 95%CI = 1.05-1.25), and falls with injury (sdHR = 1.15, 95%CI = 1.05-1.25).

CONCLUSIONS

Our findings highlight the importance of providing more community care services, age-friendly housing, falls prevention and physical activity programs to reduce inappropriate admission to RAC.

Interoperable chemical structure search service

Motivation

The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search across multiple databases provides a way to efficiently utilize these resources. To simplify such searches, many databases have adopted semantic technologies that allow interoperable querying of the datasets using SPARQL query language. However, the interoperable interfaces of the chemical databases still lack the functionality of structure-driven chemical search, which is a fundamental method of data discovery in the chemical search space.

Results

We present a SPARQL service that augments existing semantic services by making interoperable substructure and similarity searches in small-molecule databases possible. The service thus offers new possibilities for querying interoperable databases, and simplifies writing of heterogeneous queries that include chemical-structure search terms.

Availability

The service is freely available and accessible using a standard SPARQL endpoint interface. The service documentation and user-oriented demonstration interfaces that allow quick explorative querying of datasets are available at https://idsm.elixir-czech.cz.

Service usage by a New Zealand Housing First cohort prior to being housed

Background

The Ending Homelessness in New Zealand: Housing First research programme is evaluating outcomes for people housed in a Housing First programme run by The People's Project in Hamilton, New Zealand. This baseline results paper uses administrative data to look at the scope and duration of their interactions with government services.

Methods

We linked our de-identified cohort to the Integrated Data Infrastructure (IDI). This database contains administrative data on most services provided by the New Zealand Government to citizens. Linkage rates in all datasets were above 90%. This paper reports on the use of government services by the cohort before being housed. We focus on the domains of health, justice and income support.

Results

The cohort of 390 people had over 200,000 recorded interactions across a range of services in their lifetime. The most common services were health, justice and welfare. The homeless cohort had used the services at rates far in excess of the general population. Unfortunately these did not prevent them from becoming homeless.

Conclusion

These preliminary findings show the homeless population have important service delivery needs and a very high level of interaction with government services. This highlights the importance of analysing the contributing factors towards homelessness; for evaluation of interventions such as Housing First, and for understanding the need for integrated systems of government policy and practice to prevent homelessness. This paper also provides the baseline for post-Housing First evaluations.

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A homeless cohort in New Zealand had a high rate of service usage leading up to engagement with Housing First services.

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The cohort appeared in government linked data at higher rates than the general population.

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The cohort had over 200,000 interactions with government services within the five years prior to being housed by Housing First services.

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This paper shows the need for a systems-wide strategy to prevent homelessness.

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Background

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems.

Results

In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, edge2vec significantly outperforms state-of-the-art models on all three tasks.

Conclusions

We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.

Burn induced nervous system morbidity among burn and non-burn trauma patients compared with non-injured people

OBJECTIVE

Burns cause acute damage to the peripheral nervous system with published reports identifying that neurological changes after injury remain for a prolonged period. To shed some light on potential mechanisms, we assessed injury etiology and patterns of nervous system morbidity after injury by comparing long-term hospital admissions data of burns patients and other non-burn trauma patients with uninjured people.

METHODS

Linked hospital and death data of a burn patient cohort (n=30,997) in Western Australia during the period 1980-2012 were analysed along with two age and gender frequency matched comparison cohorts: non-burn trauma patients (n=28,647) and; non-injured people (n=123,399). The number of annual NS disease admissions and length of stay (LOS) were used as outcome measures. Multivariable negative binomial regression modelling was used to derive adjusted incidence rate ratios and 95% confidence intervals (IRR, 95% CI) and adjusted Cox regression models and hazard ratios (HR) were used to examine time to first nervous system admission after burn and incident admission rates.

RESULTS

The most common peripheral nervous system condition identified in each cohort (burn, non-burn trauma, uninjured) were episodic and paroxysmal disorders followed by nerve root and plexus disorders and polyneuropathies/peripheral NS conditions. Significantly elevated admission rates for NS conditions (IRR, 95% CI) were found for the burn (2.20, 1.86-2.61) and non-burn trauma (1.85, 1.51-2.27), compared to uninjured. Peripheral nervous system admission rates after injury (IRR, 95% CI) were significantly higher regardless of age at time of injury for the burn (<15years: 1.97, 1.49-2.61; 15-45: 2.70, 2.016-3.55; ≥45year: 1.62, 1.33-1.97) and non-burn trauma cohorts (<15years: 1.91, 1.55-2.35; 15-45: 1.94, 1.51-2.49; ≥45year: 1.42, 1.18-1.72), when compared to the uninjured. Significantly higher rates of incident NS hospitalisations were found for the burn cohort vs. uninjured cohort for a period of 15-years after discharge (0-5 years: HR, 95% CI: 1.97, 1.75-2.22; 5-15 years; HR, 95% CI: 1.44, 1.28-1.63). The non-burn trauma cohort had significantly higher incident nervous system admissions for 10 years after discharge (0-30 days: HR, 95% CI: 4.75, 2.44-9.23; 30days to 1-year HR, 95% CI: 2.95, 2.34-3.74; 1-5 years; HR, 95% CI: 1.47, 1.26-1.70; 5-10 years; HR, 95% CI: 1.34, 1.13-1.58).

CONCLUSIONS

Results suggest that injury patients are at increased risk of peripheral nervous system morbidity after discharge for a prolonged period of time. The time patterns associated with incident nervous system conditions suggest possible differences in underlying pathology and long-term patient care needs. Further research is needed to elucidate the underlying neuropathology.

Ozymandias: a biodiversity knowledge graph

Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com.