BioC: a minimalist approach to interoperability for biomedical text processing

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net

Job satisfaction of maternity care providers in the Netherlands: Does working in or with a birth centre influence job satisfaction?

Introduction In the Netherlands birth centres have recently become an alternative option as places where women with uncomplicated pregnancies can give birth. This article focusses on the job satisfaction of three groups of maternity care providers (community midwives, clinical care providers and maternity care assistants) working in or with a birth centre compared to those working only in a hospital or at home. Methods In 2015, an existing questionnaire was adapted and distributed to maternity care providers and 4073 responses were received. Using factor analyses, two composite measures were constructed, a Composite Job Satisfaction scale and an Assessment-of- Working-in-or-with-a-Birth-Centre scale. Differences between groups were tested with Student’s t-test and MANOVA with post hoc test and linear regression analyses. Results The overall score on the Composite Job Satisfaction scale did not differ between community midwives or clinical care providers working in or with a birth centre and those working in a different setting. For maternity care assistants there was a small but significantly higher score for those not working in a birth centre. Maternity care assistants’ overall job satisfaction score was higher than that of both other groups. In a linear regression analysis working or not working in or with a birth centre was related to the overall job satisfaction score, but repeated for the three professional groups separately, this relation was only found for maternity care assistants. Conclusions Job satisfaction is generally high, but, except for maternity care assistants, not related to the setting (working or not working in or with a birth centre)

Typology of birth centres in the Netherlands using the Rainbow model of integrated care: Results of the Dutch Birth Centre Study

textabstractBackground: The goal of integrated care is to offer a continuum of care that crosses the boundaries of public health, primary, secondary, and tertiary care. Integrated care is increasingly promoted for people with complex needs and has also recently been promoted in maternity care systems to improve the quality of care. Especially when located near an obstetric unit, birth centres are considered to be ideal settings for the realization of integrated care. At present, however, we know very little about the degree of integration in these centres and we do not know if increased levels of integration improve the quality of the care delivered. The Dutch Birth Centre Study is designed to evaluate birth centres and their contribution to the Dutch maternity care system. The aim of this particular sub-study is to classify birth centres in clusters with similar characteristics based on integration profiles, to support the evaluation of birth centre care. Methods: This study is based on the Rainbow Model of Integrated Care. We used a survey followed by qualitative interviews in 23 birth centres in the Netherlands to determine which integration profiles can be distinguished and to describe their discriminating characteristics. Cluster analysis was used to classify the birth centres. Results: Birth centres were classified into three clusters: 1)"Mono-disciplinary-oriented birth centres" (n = 10): which are mainly owned by primary care organizations and established as physical facilities to provide an alternative birthplace for low risk births; 2) "Multi-disciplinary-oriented birth centres" (n = 6): which are mainly multi-disciplinary oriented and can be regarded as facilities to give birth, with a focus on integrated birth care; 3) "Mixed Cluster of birth centres" (n = 7): which have a range of organizational forms that differentiate them from centres in the other clusters. Conclusion: We identified a recognizable classification, with similar characteristics between birth centres in the clusters. The results of this study can be used to relate integration profiles of birth centres to quality of care, costs, and perinatal outcomes. This assessment makes it possible to develop recommendations with regard to the type and degree of integration of Dutch birth centres in the future

Recessive dystonia-ataxia syndrome in a Turkish family caused by a COX20 (FAM36A) mutation

DYTCA is a syndrome that is characterized by predominant dystonia and mild cerebellar ataxia. We examined two affected siblings with healthy, consanguineous, Turkish parents. Both patients presented with a combination of childhood-onset cerebellar ataxia, dystonia, and sensory axonal neuropathy. In the brother, dystonic features were most pronounced in the legs, while his sister developed torticollis. Routine diagnostic investigations excluded known genetic causes. Biochemical analyses revealed a mitochondrial respiratory chain complex IV and a coenzyme Q10 deficiency in a muscle biopsy. By exome sequencing, we identified a homozygous missense mutation (c.154A>C; p.Thr52Pro) in both patients in exon 2 of the COX20 (FAM36A) gene, which encodes a complex IV assembly factor. This variant was confirmed by Sanger sequencing, was heterozygous in both parents, and was absent from 427 healthy controls. The exact same mutation was recently reported in a patient with ataxia andmuscle hypotonia. Among 128 early-onset dystonia and/ or ataxia patients, we did not detect any other patient with a COX20 mutation. cDNA sequencing and semi-quantitative analysis were performed in fibroblasts from one of our homozygous mutation carriers and six controls. In addition to the exchange of an amino acid, the mutation led to a shift in splicing. In conclusion, we extend the phenotypic spectrumof a recently identified mutation in COX20 to a recessively inherited, early-onset dystonia-ataxia syndrome that is characterized by reduced complex IV activity. Further, we confirm a pathogenic role of this mutation in cerebellar ataxia, but this mutation seems to be a rather rare cause

Additional file 2: of Typology of birth centres in the Netherlands using the Rainbow model of integrated care: results of the Dutch Birth Centre Study

Example of a topic list, used in the interviews. An example of a topic list used in the interviews. (DOCX 20 kb

BioC interoperability track overview

BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format. This promotes the development of interoperable tools for natural language processing (NLP) of biomedical text. The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format. These contributions included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format. The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format

The Dutch Birth Centre Study : study design of a programmatic evaluation of the effect of birth centre care in the Netherlands

Background: Birth centres are regarded as settings where women with uncomplicated pregnancies can give birth, assisted by a midwife and a maternity care assistant. In case of (threatening) complications referral to a maternity unit of a hospital is necessary. In the last decade up to 20 different birth centres have been instituted in the Netherlands. This increase in birth centres is attributed to various reasons such as a safe and easy accessible place of birth, organizational efficiency in integration of care and direct access to obstetric hospital care if needed, and better use of maternity care assistance. Birth centres are assumed to offer increased integration and quality of care and thus to contribute to better perinatal and maternal outcomes. So far there is no evidence for this assumption as no previous studies of birth centres have been carried out in the Netherlands. Design: The aims are 1) Identification of birth centres and measuring integration of organization and care 2) Measuring the quality of birth centre care 3) Effects of introducing a birth centre on regional quality and provision of care 4) Cost-effectiveness analysis 5) In depth longitudinal analysis of the organization and processes in birth centres. Different qualitative and quantitative methods will be used in the different sub studies. The design is a multi-centre, multi-method study, including surveys, interviews, observations, and analysis of registration data and documents. Discussion: The results of this study will enable users of maternity care, professionals, policy makers and health care financers to make an informed choice about the kind of birth location that is appropriate for their needs and wishes

The Dutch Birth Centre Study : study design of a programmatic evaluation of the effect of birth centre care in the Netherlands

Background: Birth centres are regarded as settings where women with uncomplicated pregnancies can give birth, assisted by a midwife and a maternity care assistant. In case of (threatening) complications referral to a maternity unit of a hospital is necessary. In the last decade up to 20 different birth centres have been instituted in the Netherlands. This increase in birth centres is attributed to various reasons such as a safe and easy accessible place of birth, organizational efficiency in integration of care and direct access to obstetric hospital care if needed, and better use of maternity care assistance. Birth centres are assumed to offer increased integration and quality of care and thus to contribute to better perinatal and maternal outcomes. So far there is no evidence for this assumption as no previous studies of birth centres have been carried out in the Netherlands. Design: The aims are 1) Identification of birth centres and measuring integration of organization and care 2) Measuring the quality of birth centre care 3) Effects of introducing a birth centre on regional quality and provision of care 4) Cost-effectiveness analysis 5) In depth longitudinal analysis of the organization and processes in birth centres. Different qualitative and quantitative methods will be used in the different sub studies. The design is a multi-centre, multi-method study, including surveys, interviews, observations, and analysis of registration data and documents. Discussion: The results of this study will enable users of maternity care, professionals, policy makers and health care financers to make an informed choice about the kind of birth location that is appropriate for their needs and wishes