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Automated mining

Rudresh Deepak Shirwaikar, Dinesh Acharya U, Krishnamoorthi Makkithaya, Surulivelrajan Mallayaswamy, Leslie Edward Simon Lewis
Neonates who are critically ill are cared for in a neonatal intensive care unit (NICU) for continuous monitoring of their conditions. Physiological parameters such as heart rate, respiratory wave form, blood oxygen saturation, and body temperature are constantly monitored in the NICU. However, NICUs are not always equipped with a computer system for analyzing such data, identifying critical events, and providing decision support for a neonatologist. Therefore, a specialized computer system, commonly known as a data mart, should be developed for the NICU...
2018: Critical Reviews in Biomedical Engineering
Martin Komenda, Jakub Ščavnický, Petra Růžičková, Matěj Karolyi, Petr Štourač, Daniel Schwarz
This paper presents the domain of information sciences, applied informatics and biomedical engineering, proposing to develop methods for an automated detection of similarities between two particular virtual learning environments - virtual patients at and the OPTIMED curriculum management system - in order to provide support to clinically oriented stages of medical and healthcare studies. For this purpose, the authors used large amounts of text-based data collected by the system for mapping medical curricula and through the system for virtual patient authoring and delivery...
2018: Studies in Health Technology and Informatics
Karl Kreiner, Dieter Hayn, Günter Schreier
Systematic reviews are widely used as a tool for decision making to establish new clinical guidelines. Reviews can be time-consuming, potentially leaving authors with thousands of citations to screen. Software tools for assisting reviewers in this process are available, however, only few use text mining techniques to reduce screening time. In this work, we introduce Twister, a web-based tool for semi-automated literature reviews with broad research questions. We discuss how two text mining techniques can be used to (a) extract data elements from clinical abstracts and (b) how citations can be clustered based on a key phrase-extraction to help reviewers reduce screening time...
2018: Studies in Health Technology and Informatics
Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Waqar Mahmood, Hafiza Mahnoor Abbasi
Ontologies have gained a lot of popularity and recognition in the semantic web because of their extensive use in Internet-based applications. Ontologies are often considered a fine source of semantics and interoperability in all artificially smart systems. Exponential increase in unstructured data on the web has made automated acquisition of ontology from unstructured text a most prominent research area. Several methodologies exploiting numerous techniques of various fields (machine learning, text mining, knowledge representation and reasoning, information retrieval and natural language processing) are being proposed to bring some level of automation in the process of ontology acquisition from unstructured text...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Kristian Birchall, Andy Merritt, Afrah Sattikar, Catherine Kettleborough, Barbara Saxty
Building, curating, and maintaining a compound collection is an expensive operation, beyond the scope of most academic organizations. Here we describe the selection criteria used to compile the LifeArc diversity set from commercial suppliers and the process we undertook to generate our representative LifeArc index set. The aim was to avoid a "junk in, junk out" screen collection to increase chemical tractability going forward, while maximizing diversity. Using historical LifeArc screening data, we demonstrate that the index set was predictive of ligandability and that progressable hits could be identified by mining associated clusters within our larger diversity set...
October 5, 2018: SLAS Discovery
L Anand, S P Syed Ibrahim
Early detection of any sort of disease is mandatory for effective medical treatment. Medical diagnosis relies heavily on Data Mining for automated disease classification and detection. It relies on data mining algorithms to examine medical data. Liver diseases have become more common these days with many new patients being diagnosed with Heptasis B and C. Early diagnosis of Liver Disorder is essential for treatment. It can be achieved by setting up intelligent systems for early diagnose and prognosis of Liver diseases...
September 27, 2018: Journal of Medical Systems
Edward Lau, Vidya Venkatraman, Cody T Thomas, Joseph C Wu, Jennifer E Van Eyk, Maggie P Y Lam
Identifying the genes and proteins associated with a biological process or disease is a central goal of the biomedical research enterprise. However, relatively few systematic approaches are available that provide objective evaluation of the genes or proteins known to be important to a research topic, and hence researchers often rely on subjective evaluation of domain experts and laborious manual literature review. Computational bibliometric analysis, in conjunction with text mining and data curation, attempts to automate this process and return prioritized proteins in any given research topic...
October 9, 2018: Journal of Proteome Research
Khader Shameer, M Mercedes Perez-Rodriguez, Roy Bachar, Li Li, Amy Johnson, Kipp W Johnson, Benjamin S Glicksberg, Milo R Smith, Ben Readhead, Joseph Scarpa, Jebakumar Jebakaran, Patricia Kovatch, Sabina Lim, Wayne Goodman, David L Reich, Andrew Kasarskis, Nicholas P Tatonetti, Joel T Dudley
BACKGROUND: Worldwide, over 14% of individuals hospitalized for psychiatric reasons have readmissions to hospitals within 30 days after discharge. Predicting patients at risk and leveraging accelerated interventions can reduce the rates of early readmission, a negative clinical outcome (i.e., a treatment failure) that affects the quality of life of patient. To implement individualized interventions, it is necessary to predict those individuals at highest risk for 30-day readmission. In this study, our aim was to conduct a data-driven investigation to find the pharmacological factors influencing 30-day all-cause, intra- and interdepartmental readmissions after an index psychiatric admission, using the compendium of prescription data (prescriptome) from electronic medical records (EMR)...
September 14, 2018: BMC Medical Informatics and Decision Making
Olivier Clerc, Julien Mariethoz, Alain Rivet, Frédérique Lisacek, Serge Pérez, Sylvie Ricard-Blum
Mammalian glycosaminoglycans are linear complex polysaccharides comprising heparan sulfate, heparin, dermatan sulfate, chondroitin sulfate, keratan sulfate and hyaluronic acid. They bind to numerous proteins and these interactions mediate their biological activities. GAG-protein interaction data reported in the literature are curated mostly in MatrixDB database ( However, a standard nomenclature and a machine-readable format of GAGs together with bioinformatics tools for mining these interaction data are lacking...
September 18, 2018: Glycobiology
Dibyendu Dana, Satishkumar V Gadhiya, Luce G St Surin, David Li, Farha Naaz, Quaisar Ali, Latha Paka, Michael A Yamin, Mahesh Narayan, Itzhak D Goldberg, Prakash Narayan
The practice of medicine is ever evolving. Diagnosing disease, which is often the first step in a cure, has seen a sea change from the discerning hands of the neighborhood physician to the use of sophisticated machines to use of information gleaned from biomarkers obtained by the most minimally invasive of means. The last 100 or so years have borne witness to the enormous success story of allopathy, a practice that found favor over earlier practices of medical purgatory and homeopathy. Nevertheless, failures of this approach coupled with the omics and bioinformatics revolution spurred precision medicine, a platform wherein the molecular profile of an individual patient drives the selection of therapy...
September 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Bart van Beusekom, Krista Joosten, Maarten L Hekkelman, Robbie P Joosten, Anastassis Perrakis
Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and 'graft' these regions of interest...
September 1, 2018: IUCrJ
Alex Chapeaurouge, Andreza Silva, Paulo Carvalho, Ryan J R McCleary, Cassandra Marie Modahl, Jonas Perales, R Manjunatha Kini, Stephen P Mackessy
The use of -omics technologies allows for the characterization of snake venom composition at a fast rate and at high levels of detail. In the present study, we investigated the protein content of Red-headed Krait ( Bungarus flaviceps ) venom. This analysis revealed a high diversity of snake venom protein families, as evidenced by high-throughput mass spectrometric analysis. We found all six venom protein families previously reported in a transcriptome study of the venom gland of B. flaviceps , including phospholipases A₂ (PLA₂s), Kunitz-type serine proteinase inhibitors (KSPIs), three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), snaclecs, and natriuretic peptides...
September 13, 2018: Toxins
Toyofumi Fujiwara, Yasunori Yamamoto, Jin-Dong Kim, Orion Buske, Toshihisa Takagi
Recently, to speed up the differential-diagnosis process based on symptoms and signs observed from an affected individual in the diagnosis of rare diseases, researchers have developed and implemented phenotype-driven differential-diagnosis systems. The performance of those systems relies on the quantity and quality of underlying databases of disease-phenotype associations (DPAs). Although such databases are often developed by manual curation, they inherently suffer from limited coverage. To address this problem, we propose a text-mining approach to increase the coverage of DPA databases and consequently improve the performance of differential-diagnosis systems...
September 6, 2018: American Journal of Human Genetics
Aashish Jain, Daisuke Kihara
Motivation: Function annotation of proteins is fundamental in contemporary biology across fields including genomics, molecular biology, biochemistry, systems biology, and bioinformatics. Function prediction is indispensable in providing clues for interpreting omics-scale data as well as in assisting biologists to build hypotheses for designing experiments. As sequencing genomes is now routine due to the rapid advancement of sequencing technologies, computational protein function prediction methods have become increasingly important...
August 25, 2018: Bioinformatics
Ekaterina Ilgisonis, Andrey Lisitsa, Valerya Kudryavtseva, Elena Ponomarenko
Concept-centered semantic maps were created based on a text-mining analysis of PubMed using the BiblioEngine_v2018 software. The objects ("concepts") of a semantic map can be MeSH-terms or other terms (names of proteins, diseases, chemical compounds, etc.) structured in the form of controlled vocabularies. The edges between the two objects were automatically calculated based on the index of semantic similarity, which is proportional to the number of publications related to both objects simultaneously...
2018: Advances in Bioinformatics
Balachandran Manavalan, Rajiv Gandhi Govindaraj, Tae Hwan Shin, Myeong Ok Kim, Gwang Lee
Identification of B-cell epitopes (BCEs) is a fundamental step for epitope-based vaccine development, antibody production, and disease prevention and diagnosis. Due to the avalanche of protein sequence data discovered in postgenomic age, it is essential to develop an automated computational method to enable fast and accurate identification of novel BCEs within vast number of candidate proteins and peptides. Although several computational methods have been developed, their accuracy is unreliable. Thus, developing a reliable model with significant prediction improvements is highly desirable...
2018: Frontiers in Immunology
Christopher Southan, Joanna L Sharman, Elena Faccenda, Adam J Pawson, Simon D Harding, Jamie A Davies
Connecting chemistry to pharmacology has been an objective of Guide to PHARMACOLOGY (GtoPdb) and its precursor the International Union of Basic and Clinical Pharmacology Database (IUPHAR-DB) since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents, and the protein targets in the assays (D-A-R-C-P). A wide range of challenges associated with this are described in this perspective, using illustrative examples from GtoPdb entries...
July 31, 2018: ACS Omega
Elena Arsevska, Sarah Valentin, Julien Rabatel, Jocelyn de Goër de Hervé, Sylvain Falala, Renaud Lancelot, Mathieu Roche
Since 2013, the French Animal Health Epidemic Intelligence System (in French: Veille Sanitaire Internationale, VSI) has been monitoring signals of the emergence of new and exotic animal infectious diseases worldwide. Once detected, the VSI team verifies the signals and issues early warning reports to French animal health authorities when potential threats to France are detected. To improve detection of signals from online news sources, we designed the Platform for Automated extraction of Disease Information from the web (PADI-web)...
2018: PloS One
Orges Koci, Michael Logan, Vaios Svolos, Richard K Russell, Konstantinos Gerasimidis, Umer Zeeshan Ijaz
With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis...
2018: PeerJ
Benjamin Linard, Alex Crampton-Platt, Jerome Moriniere, Martijn J T N Timmermans, Carmelo Andújar, Paula Arribas, Kirsten E Miller, Julia Lipecki, Emeline Favreau, Amie Hunter, Carola Gómez-Rodríguez, Christopher Barton, Ruie Nie, Conrad P D T Gillett, Thijmen Breeschoten, Ladislav Bocak, Alfried P Vogler
A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp...
November 2018: Molecular Phylogenetics and Evolution
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