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Automated mining

George Karystianis, Armita Adily, Peter W Schofield, David Greenberg, Louisa Jorm, Goran Nenadic, Tony Butler
BACKGROUND: The police attend numerous domestic violence events each year, recording details of these events as both structured (coded) data and unstructured free-text narratives. Abuse types (including physical, psychological, emotional, and financial) conducted by persons of interest (POIs) along with any injuries sustained by victims are typically recorded in long descriptive narratives. OBJECTIVE: We aimed to determine if an automated text mining method could identify abuse types and any injuries sustained by domestic violence victims in narratives contained in a large police dataset from the New South Wales Police Force...
March 12, 2019: Journal of Medical Internet Research
Şenay Kafkas, Robert Hoehndorf
Gene-phenotype associations play an important role in understanding the disease mechanisms which is a requirement for treatment development. A portion of gene-phenotype associations are observed mainly experimentally and made publicly available through several standard resources such as MGI. However, there is still a vast amount of gene-phenotype associations buried in the biomedical literature. Given the large amount of literature data, we need automated text mining tools to alleviate the burden in manual curation of gene-phenotype associations and to develop comprehensive resources...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Alexander J Sundermann, James K Miller, Jane W Marsh, Melissa I Saul, Kathleen A Shutt, Marissa Pacey, Mustapha M Mustapha, Ashley Ayres, A William Pasculle, Jieshi Chen, Graham M Snyder, Artur W Dubrawski, Lee H Harrison
BACKGROUND: Identifying routes of transmission among hospitalized patients during a healthcare-associated outbreak can be tedious, particularly among patients with complex hospital stays and multiple exposures. Data mining of the electronic health record (EHR) has the potential to rapidly identify common exposures among patients suspected of being part of an outbreak. METHODS: We retrospectively analyzed 9 hospital outbreaks that occurred during 2011-2016 and that had previously been characterized both according to transmission route and by molecular characterization of the bacterial isolates...
February 18, 2019: Infection Control and Hospital Epidemiology
Dominic P Morgan, David Muscatello, Andrew Hayen, Joanne Travaglia
OBJECTIVE: Programmes that reduce the time to defibrillation are likely to improve overall survival rates from out-of-hospital cardiac arrests (OHCAs). This research sought to identify human factors common among community responders taking an automated external defibrillator (AED) to a victim of an OHCA that are either barriers or enablers of desired behaviour. METHODS: A qualitative methodology was used. Community members who had access to an AED and who had been notified of an incident of OHCA near them were approached to participate in the research...
February 13, 2019: Emergency Medicine Australasia: EMA
Min Xu, Jitin Singla, Elitza I Tocheva, Yi-Wei Chang, Raymond C Stevens, Grant J Jensen, Frank Alber
Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called "Multi-Pattern Pursuit" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures...
January 31, 2019: Structure
Zhen Yang, Jing Li, Carl E Zipper, Yingying Shen, Hui Miao, Patricia F Donovan
Surface coal mining disturbances affect the local ecology, human populations and environmental quality. Thus, much public attention has been focused on mining issues and the need for monitoring of environmental disturbances in mining areas. An automated method for identifying mining disturbances, and for characterizing recovery of vegetative cover on disturbed areas using multitemporal Landsat imagery is described. The method analyzes normalized difference vegetation index (NDVI) data to identify sample points with multitemporal spectral characteristics ("trajectories") that indicate the presence of environmental disturbances caused by mining...
December 10, 2018: Science of the Total Environment
Minh-Son To, Alistair Jukes
OBJECTIVEThe objective of this study was to evaluate the trends in reporting of p values in the neurosurgical literature from 1990 through 2017.METHODSAll abstracts from the Journal of Neurology, Neurosurgery, and Psychiatry (JNNP), Journal of Neurosurgery (JNS) collection (including Journal of Neurosurgery: Spine and Journal of Neurosurgery: Pediatrics), Neurosurgery (NS), and Journal of Neurotrauma (JNT) available on PubMed from 1990 through 2017 were retrieved. Automated text mining was performed to extract p values from relevant abstracts...
February 8, 2019: Journal of Neurosurgery
Deepak R Bharti, Anmol J Hemrom, Andrew M Lynn
BACKGROUND: Traditional drug discovery approaches are time-consuming, tedious and expensive. Identifying a potential drug-like molecule using high throughput screening (HTS) with high confidence is always a challenging task in drug discovery and cheminformatics. A small percentage of molecules that pass the clinical trial phases receives FDA approval. This whole process takes 10-12 years and millions of dollar of investment. The inconsistency in HTS is also a challenge for reproducible results...
February 4, 2019: BMC Bioinformatics
Donald C Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu
Summary: Interest in text mining full text biomedical research articles is growing. To facilitate automated processing of nearly 3 million full-text articles (in PMC Open Access and Author Manuscript subsets) and to improve interoperability, we convert these articles to BioC, a community-driven simple data structure in either XML or JSON format for conveniently sharing text and annotations. Results: The resultant articles can be downloaded via both ftp for bulk access and a Web API for updates or a more focused collection...
January 31, 2019: Bioinformatics
Ross W Filice, Charles E Kahn
An ontology offers a human-readable and machine-computable representation of the concepts in a domain and the relationships among them. Mappings between ontologies enable the reuse and interoperability of biomedical knowledge. We sought to map concepts of the Radiology Gamuts Ontology (RGO), an ontology that links diseases and imaging findings to support differential diagnosis in radiology, to terms in three key vocabularies for clinical radiology: the International Classification of Diseases, version 10, Clinical Modification (ICD-10-CM), the Radiological Society of North America's radiology lexicon (RadLex), and the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT)...
January 31, 2019: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
Saber A Akhondi, Hinnerk Rey, Markus Schwörer, Michael Maier, John Toomey, Heike Nau, Gabriele Ilchmann, Mark Sheehan, Matthias Irmer, Claudia Bobach, Marius Doornenbal, Michelle Gregory, Jan A Kors
In commercial research and development projects, public disclosure of new chemical compounds often takes place in patents. Only a small proportion of these compounds are published in journals, usually a few years after the patent. Patent authorities make available the patents but do not provide systematic continuous chemical annotations. Content databases such as Elsevier's Reaxys provide such services mostly based on manual excerptions, which are time-consuming and costly. Automatic text-mining approaches help overcome some of the limitations of the manual process...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Gabriel Muñoz, W Daniel Kissling, E Emiel van Loon
Background: A considerable portion of primary biodiversity data is digitally locked inside published literature which is often stored as pdf files. Large-scale approaches to biodiversity science could benefit from retrieving this information and making it digitally accessible and machine-readable. Nonetheless, the amount and diversity of digitally published literature pose many challenges for knowledge discovery and retrieval. Text mining has been extensively used for data discovery tasks in large quantities of documents...
2019: Biodiversity Data Journal
Ali El-Naggar, Sabry M Shaheen, Zeng-Yei Hseu, Shan-Li Wang, Yong Sik Ok, Jörg Rinklebe
This study assessed the impact of pre-definite redox potential (EH ) on the release dynamics and distribution of As, Co, and Mo between the dissolved and colloidal phases as well as their potential mobility and phytoavailability in the sediment phase of a mining soil treated with rice hull biochar (BC). The experiment was conducted from controlled moderately-reducing to oxidizing conditions using an automated biogeochemical microcosm system. Arsenic and Mo were more abundant in the dissolved phase due to their predominant in potential mobile fractions, while Co was more abundant in the colloidal phase due to its association with Fe-(hydr)oxides...
March 20, 2019: Science of the Total Environment
Julien Rabatel, Elena Arsevska, Mathieu Roche
Monitoring animal health worldwide, especially the early detection of outbreaks of emerging pathogens, is one of the means of preventing the introduction of infectious diseases in countries (Collier et al., 2008) [3]. In this context, we developed PADI-web, a Platform for Automated extraction of animal Disease Information from the Web (Arsevska et al., 2016, 2018). PADI-web is a text-mining tool that automatically detects, categorizes and extracts disease outbreak information from Web news articles. PADI-web currently monitors the Web for five emerging animal infectious diseases, i...
February 2019: Data in Brief
Neil R Smalheiser, Mengqi Luo, Sidharth Addepalli, Xiaokai Cui
Clinical case reports are the `eyewitness reports' of medicine and provide a valuable, unique, albeit noisy and underutilized type of evidence. Generally a case report has a single main finding that represents the reason for writing up the report in the first place. In the present study, we present the results of manual annotation carried out by two individuals on 500 randomly sampled case reports. This corpus contains main finding sentences extracted from title, abstract and full-text of the same article that can be regarded as semantically related and are often paraphrases...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Philippe M Burlina, Neil J Joshi, Elise Ng, Seth D Billings, Alison W Rebman, John N Aucott
Lyme disease can lead to neurological, cardiac, and rheumatologic complications when untreated. Timely recognition of the erythema migrans rash of acute Lyme disease by patients and clinicians is crucial to early diagnosis and treatment. Our objective in this study was to develop deep learning approaches using deep convolutional neural networks for detecting acute Lyme disease from erythema migrans images of varying quality and acquisition conditions. This study used a cross-sectional dataset of images to train a model employing a deep convolutional neural network to perform classification of erythema migrans versus other skin conditions including tinea corporis and herpes zoster, and normal, non-pathogenic skin...
February 2019: Computers in Biology and Medicine
Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W Jim Zheng, Hulin Wu
Motivation: Gene Expression Omnibus (GEO) and other publicly available data store their metadata in the format of unstructured English text, which is very difficult for automated reuse. Results: We employed text mining techniques to analyze the metadata of GEO and developed Restructured GEO database (ReGEO). ReGEO reorganizes and categorizes GEO series and makes them searchable by two new attributes extracted automatically from each series' metadata. These attributes are the number of time points tested in the experiment and the disease being investigated...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Nigel W Moriarty, Paul D Adams
Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4 S4 cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4 S4 : coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Julien Boccard, David Tonoli, Petra Strajhar, Fabienne Jeanneret, Alex Odermatt, Serge Rudaz
The human adrenal cell line H295R constitutes a well-established model to evaluate potential alterations of steroidogenic pathways as a result of chemical exposure. However, to date most assays are based on the targeted investigation of a limited number of steroid hormones, thus preventing in-depth mechanistic interpretation with respect to steroidogenesis. In that context, analytical strategies coupling liquid chromatography and high-resolution mass spectrometry (LC-HRMS) have been reported as promising methods for an extended monitoring of steroid metabolites...
April 1, 2019: Talanta
Michael T Finke, Ross W Filice, Charles E Kahn
Mappings between ontologies enable reuse and interoperability of biomedical knowledge. The Radiology Gamuts Ontology (RGO)-an ontology of 16 918 diseases, interventions, and imaging observations-provides a resource for differential diagnosis and automated textual report understanding in radiology. An automated process with subsequent manual review was used to identify exact and partial matches of RGO entities to the Disease Ontology (DO) and the Human Phenotype Ontology (HPO). Exact mappings identified equivalent concepts; partial mappings identified subclass and superclass relationships...
January 8, 2019: Journal of the American Medical Informatics Association: JAMIA
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