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Michael R Gryk, Bertram Ludäscher
Two barriers to computational reproducibility are the ability to record the critical metadata required for rerunning a computation, as well as translating the semantics of the metadata so that alternate approaches can easily be configured for verifying computational reproducibility. We are addressing this problem in the context of biomolecular NMR computational analysis by developing a series of linked ontologies which define the semantics of the various software tools used by researchers for data transformation and analysis...
March 2018: Transforming digital worlds: 13th International Conference, iConference 2018, Sheffield, UK, March 25-28, 2018, Proceedings
Kristen M Ogden, Yi Tan, Asmik Akopov, Laura S Stewart, Rendie McHenry, Christopher J Fonnesbeck, Bhinnata Piya, Maximilian H Carter, Nadia B Fedorova, Rebecca A Halpin, Meghan H Shilts, Kathryn M Edwards, Daniel C Payne, Mathew D Esona, Slavica Mijatovic-Rustempasic, James D Chappell, John T Patton, Natasha B Halasa, Suman R Das
Rotavirus is the leading global cause of diarrheal mortality for unvaccinated children under five years of age. The outer capsid of rotavirus virions consists of VP7 and VP4 proteins, which determine viral G and P types, respectively, and are primary targets of neutralizing antibodies. Successful vaccination depends upon generating broadly protective immune responses following exposure to rotaviruses presenting a limited number of G and P type antigens. Vaccine introduction resulted in decreased rotavirus disease burden but also coincided with emergence of uncommon G and P genotypes, including G12...
October 17, 2018: Journal of Virology
Shayoni Ray, Samrawit Gebre, Homer Fogle, Daniel C Berrios, Peter B Tran, Jonathan M Galazka, Sylvain V Costes
Motivation: - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. Results: - The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated "omics" (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms...
October 17, 2018: Bioinformatics
David B Lazarus, Johan Renaudie, Dorina Lenz, Patrick Diver, Jens Klump
Acquiring data on the occurrences of many types of difficult to identify objects are often still made by human observation, for example, in biodiversity and paleontologic research. Existing computer counting programs used to record such data have various limitations, including inflexibility and cost. We describe a new open-source program for this purpose-Raritas. Raritas is written in Python and can be run as a standalone app for recent versions of either MacOS or Windows, or from the command line as easily customized source code...
2018: PeerJ
Jason Anthony Vander Heiden, Susanna Marquez, Nishanth Marthandan, Syed Ahmad Chan Bukhari, Christian E Busse, Brian Corrie, Uri Hershberg, Steven H Kleinstein, Frederick A Matsen Iv, Duncan K Ralph, Aaron M Rosenfeld, Chaim A Schramm, Scott Christley, Uri Laserson
Increased interest in the immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to an explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). The AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of the immune repertoire. In this paper, we describe the work of the AIRR Community's Data Representation Working Group to develop standardized data representations for storing and sharing annotated antibody and T cell receptor data...
2018: Frontiers in Immunology
Niccolò Tempini, Sabina Leonelli
This paper analyses the role of information security (IS) in shaping the dissemination and re-use of biomedical data, as well as the embedding of such data in material, social and regulatory landscapes of research. We consider data management practices adopted by two UK-based data linkage infrastructures: the Secure Anonymised Information Linkage, a Welsh databank that facilitates appropriate re-use of health data derived from research and routine medical practice in the region, and the Medical and Environmental Data Mash-up Infrastructure, a project bringing together researchers to link and analyse complex meteorological, environmental and epidemiological data...
October 2018: Social Studies of Science
Antonia Lock, Kim Rutherford, Midori A Harris, Jacqueline Hayles, Stephen G Oliver, Jürg Bähler, Valerie Wood
PomBase (, the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new infrastructure supports daily data updates as well as fast, efficient querying and smoother navigation within and between pages. New pages for publications and genotypes provide routes to all data curated from a single source and to all phenotypes associated with a specific genotype, respectively...
October 13, 2018: Nucleic Acids Research
Willem G van Panhuis, Anne Cross, Donald S Burke
Objective: In 2013, we released Project Tycho, an open-access database comprising 3.6 million counts of infectious disease cases and deaths reported for over a century by public health surveillance in the United States. Our objective is to describe how Project Tycho version 1 (v1) data has been used to create new knowledge and technology and to present improvements made in the newly released version 2.0 (v2). Materials and Methods: We analyzed our user database and conducted online searches to analyze the use of Project Tycho v1 data...
October 15, 2018: Journal of the American Medical Informatics Association: JAMIA
P W Harrison, J Fan, D Richardson, L Clarke, D Zerbino, G Cochrane, A L Archibald, C J Schmidt, P Flicek
The Functional Annotation of ANimal Genomes (FAANG) project aims, through a coordinated international effort, to provide high quality functional annotation of animal genomes with an initial focus on farmed and companion animals. A key goal of the initiative is to ensure high quality and rich supporting metadata to describe the project's animals, specimens, cell cultures and experimental assays. By defining rich sample and experimental metadata standards and promoting best practices in data descriptions, deposition and openness, FAANG champions higher quality and reusability of published datasets...
October 12, 2018: Animal Genetics
Dylan Johnson, Robin Skinner, Mario Cappelli, Roger Zemek, Steven McFaull, Corrine Langill, Paula Cloutier
OBJECTIVES: To assess the performance of the Canadian Hospitals Injury Reporting and Prevention Program's newly developed self-harm surveillance tool (CHIRPP-SI) designed to improve emergency department (ED) hospital surveillance of youth self-inflicted injury (SI). METHODS: This was a prospective, single-centre cohort study from February 2015 to September 2015. Eligible participants were aged 6-17.99 years and presented to the ED with a primary mental health complaint...
October 11, 2018: Canadian Journal of Public Health. Revue Canadienne de Santé Publique
Gerd Carling, Filip Larsson, Chundra A Cathcart, Niklas Johansson, Arthur Holmer, Erich Round, Rob Verhoeven
Feature stability, time and tempo of change, and the role of genealogy versus areality in creating linguistic diversity are important issues in current computational research on linguistic typology. This paper presents a database initiative, DiACL Typology, which aims to provide a resource for addressing these questions with specific of the extended Indo-European language area of Eurasia, the region with the best documented linguistic history. The database is pre-prepared for statistical and phylogenetic analyses and contains both linguistic typological data from languages spanning over four millennia, and linguistic metadata concerning geographic location, time period, and reliability of sources...
2018: PloS One
Ann-Beth Moller, Holly Newby, Claudia Hanson, Alison Morgan, Shams El Arifeen, Doris Chou, Theresa Diaz, Lale Say, Ian Askew, Allisyn C Moran
BACKGROUND: A variety of global-level monitoring initiatives have recommended indicators for tracking progress in maternal and newborn health. As a first step supporting the work of WHO's Mother and Newborn Information for Tracking Outcomes and Results (MoNITOR) Technical Advisory Group, we aimed to compile and synthesize recommended indicators in order to document the landscape of maternal and newborn measurement and monitoring. METHODS: We conducted a scoping review of indicators proposed by global multi-stakeholder groups to suggest next steps to further support maternal and newborn measurement and monitoring...
2018: PloS One
Agnes Kirchhoff, Ulrich Bügel, Eduard Santamaria, Fabian Reimeier, Dominik Röpert, Alexander Tebbje, Anton Güntsch, Fernando Chaves, Karl-Heinz Steinke, Walter Berendsohn
Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses...
January 1, 2018: Database: the Journal of Biological Databases and Curation
John Harry Caufield, David A Liem, Anders O Garlid, Yijiang Zhou, Karol Watson, Alex A T Bui, Wei Wang, Peipei Ping
Clinical case reports (CCRs) are a valuable means of sharing observations and insights in medicine. The form of these documents varies, and their content includes descriptions of numerous, novel disease presentations and treatments. Thus far, the text data within CCRs is largely unstructured, requiring significant human and computational effort to render these data useful for in-depth analysis. In this protocol, we describe methods for identifying metadata corresponding to specific biomedical concepts frequently observed within CCRs...
September 20, 2018: Journal of Visualized Experiments: JoVE
Mark E McGovern, David Canning, Till Bärnighausen
Standard corrections for missing data rely on the strong and generally untestable assumption of missing at random. Heckman-type selection models relax this assumption, but have been criticized because they typically require a selection variable which predicts non-response but not the outcome of interest, and can impose bivariate normality. In this paper we illustrate an application using a copula methodology which does not rely on bivariate normality. We implement this approach in data on HIV testing at a demographic surveillance site in rural South Africa which are affected by non-response...
October 2018: Economics Letters
Alain Giordanengo, Pinar Øzturk, Anne Helen Hansen, Eirik Årsand, Astrid Grøttland, Gunnar Hartvigsen
BACKGROUND: Patients with diabetes use an increasing number of self-management tools in their daily life. However, health institutions rarely use the data generated by these services mainly due to (1) the lack of data reliability, and (2) medical workers spending too much time extracting relevant information from the vast amount of data produced. This work is part of the FullFlow project, which focuses on self-collected health data sharing directly between patients' tools and EHRs. OBJECTIVE: The main objective is to design and implement a prototype for extracting relevant information and documenting information gaps from self-collected health data by patients with type 1 diabetes using a context-aware approach...
July 11, 2018: JMIR diabetes
C M Fancher, C Hoffmann, V Sedov, A Parizzi, W Zhou, A J Schultz, X P Wang, D Long
Time-resolved diffraction has become a vital tool for probing dynamic responses to an applied stimulus. Such experiments traditionally use hardware solutions to histogram measured data into their respective bin. We will show that a major advantage of event-based data acquisition, which time-stamps measured diffraction data with 100 ns accuracy, is much preferred over hardware histogramming of the data by enabling postprocessing for advanced custom binning using a software solution. This approach is made even more powerful by coupling measured diffraction data with metadata about the applied stimuli and material response...
September 2018: Review of Scientific Instruments
Paul James Harvey, Phoebe Grace Peterson, Mark Patrick Taylor
VegeSafe is a national community science initiative aimed at characterising soils in Australian residential gardens and community gardens. The program has been operating for over 5 years and has generated soil metal(loid) data from over 8600 residential garden and community garden soil samples, submitted by almost 2000 community scientists. The VegeSafe program represents the largest archive of soil metal(loid) data and associated metadata for residential garden soils in Australia. Samples were collected across Australia, with 61% of samples collected from NSW (n = 5284), Victoria (VIC) 20% (n = 1688) of samples and Queensland (QLD) 7% (n = 592) of samples...
October 1, 2018: Environmental Science and Pollution Research International
Shrikant Pawar, Harshul Batra
Aim: Animal experiments tend to generate large-scale data. Some existing tools like Microsoft Excel and colony management cloud-based tools are either cumbersome or expensive. There is a need for an inexpensive and uncomplicated colony management software with specific individual database solutions. Methods: We have developed a database application named RodentSQL to meet most of the requirements of such animal colony management programs. Results: We present a user-friendly secure system for managing records of phenotype, genotype and metadata for comprehensive data analysis and mining...
September 2018: Future Science OA
Eric W Deutsch, Yasset Perez-Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P C Vissers, Dennis W Wolan, Ana Y Wang, Luis Mendoza, Jim Shofstahl, Andrew W Dowsey, Johannes Griss, Reza M Salek, Steffen Neumann, Pierre-Alain Binz, Henry Lam, Juan Antonio Vizcaíno, Nuno Bandeira, Hannes Röst
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows...
October 1, 2018: Journal of Proteome Research
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