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Neil R Smalheiser, Aaron M Cohen
Many investigators have carried out text mining of the biomedical literature for a variety of purposes, ranging from the assignment of indexing terms to the disambiguation of author names. A common approach is to define positive and negative training examples, extract features from article metadata, and employ machine learning algorithms. At present, each research group tackles each problem from scratch, and in isolation of other projects, which causes redundancy and great waste of effort. Here, we propose and describe the design of a generic platform for biomedical text mining, which can serve as a shared resource for machine learning projects, and can serve as a public repository for their outputs...
June 2018: Data and information management
Jeff Jenness, S W K van den Burg, José Aguilar-Manjarrez, Melanie Torrie
This data article provides several datasets delineating, illustrating and summarizing marine regions within exclusive economic zones (EEZs) of 69 coastal states within the Atlantic, Baltic/North Sea, Mediterranean and Caribbean marine basins. Datasets include two GIS feature classes stored in a Version 10.0 file geodatabase: (1) A polygon feature class delineating operational boundaries within EEZs based on sovereign authority, distance bands from shore, depth ranges, and whether the region lies within a recognized protected area, and (2) A polyline feature class of shorelines for each coastal state...
December 2018: Data in Brief
Christine N Spencer, Daniel K Wells, Theresa M LaVallee
Immunotherapy results in remarkable clinical benefit in a subset of cancer patients by activating the patient's own immune system. The factors determining which cancer patients will benefit are diverse. Success in realizing precision immunotherapy needs collaboration to bring together multiple diverse data sets. Defining multi-factorial biomarker algorithms for immunotherapy requires new approaches and methodologies that use deep molecular and cellular profiling of the tumor microenvironment, systemic immunity with clinical metadata from clinical trials, and other databases...
February 2019: Trends in Cancer
Alex Kuo, Dillon Chrimes, Pinle Qin, Hamid Zamani
In this paper, we report our practical experience in designing and implementing a platform with Hadoop/MapReduce framework for supporting health Big Data Analytics. Three billion of emulated health raw data was constructed and cross-referenced with data profiles and metadata based on existing health data at the Island Health Authority, BC, Canada. The patient data was stored over a Hadoop Distributed File System to simulate a presentation of an entire health authority's information system. Then, a High Performance Computing platform called WestGrid was used to benchmark the performance of the platform via several data query tests...
2019: Studies in Health Technology and Informatics
Maryam Garza, Emel Seker, Meredith Zozus
Data standards are now required for many submissions to the United States Food and Drug Administration (FDA). The required standard for submission of clinical data is the Clinical Data Interchange Standards Consortium (CDISC) Submission Data Tabulation Model (SDTM). Currently, 45 business rules and 115 associated validation rules exist for SDTM data. However, such rules have not yet been developed for therapeutic area data standards developed under the last reauthorization of the Prescription Drug User Fee Act (PDUFA V)...
2019: Studies in Health Technology and Informatics
Alexander Toet, Daisuke Kaneko, Inge de Kruijf, Shota Ushiama, Martin G van Schaik, Anne-Marie Brouwer, Victor Kallen, Jan B F van Erp
We present CROCUFID: a CROss-CUltural Food Image Database that currently contains 840 images, including 479 food images with detailed metadata and 165 images of non-food items. The database includes images of sweet, savory, natural, and processed food from Western and Asian cuisines. To create sufficient variability in valence and arousal we included images of food with different degrees of appetitiveness (fresh, unfamiliar, molded or rotten, spoiled, and partly consumed). We used a standardized photographing protocol, resulting in high resolution images depicting all food items on a standard background (a white plate), seen from a fixed viewing (45°) angle...
2019: Frontiers in Psychology
Shankai Yan, Ka-Chun Wong
The Gene Expression Omnibus (GEO) repository harbours an exponentially increasing number of gene expression studies. The expression data, as well as the related metadata, provides an abundant resource for knowledge discovery. Each study in GEO focuses on the gene expression perturbation of a specific subject (e.g. gene, drug, and disease). The identification of those subjects and the associations among them are beneficial for further in-depth studies. However, they cannot be directly inferred from the studies...
January 30, 2019: IEEE Journal of Biomedical and Health Informatics
Damon H May, Kaipo Tamura, William Stafford Noble
Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags, as well as enrichment of phosphorylated peptides, directly from a given set of mass spectra...
February 4, 2019: Journal of Proteome Research
Betty Hachard, Frédéric Noe, Antony Catherine, Sacha Zeronian, Thierry Paillard
In the metadata of the original publication of the article.
February 1, 2019: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
Manuel Rodríguez-Martínez, Cristian C Garzón-Alfonso
We present the Twitter Health Surveillance (THS) application framework. THS is designed as an integrated platform to help health officials collect tweets, determine if they are related with a medical condition, extract metadata out of them, and create a big data warehouse that can be used to further analyze the data. THS is built atop open source tools and provides the following value added services: Data Acquisition, Tweet Classification, and Big Data Warehousing. In order to validate THS, we have created a collection of roughly twelve thousands labelled tweets...
December 2018: Proceedings: IEEE International Conference on Big Data
Mak A Saito, Erin M Bertrand, Megan E Duffy, David A Gaylord, Noelle A Held, William Judson Hervey, Robert L Hettich, Pratik Jagtap, Michael G Janech, Danie B Kinkade, Dasha Leary, Matthew McIlvin, Eli Moore, Robert Morris, Benjamin A Neely, Brook Nunn, Jaclyn K Saunders, Adam Shepherd, Nicholas Symmonds, David Walsh
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, co-limitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries...
January 31, 2019: Journal of Proteome Research
Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T Morton, Molly C Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also numerous. Many tools reduce, summarize, and visualize these high-dimensional data to provide insight at the community level. However, they lose the detailed information about each taxon and can be misleading (for example, the well-known horseshoe effect in ordination plots). Thus, multiple methods at different levels of resolution are required to capture the full range of microbial patterns...
January 2019: MSystems
Scott D Nelson, Hayley H Rector, Daniel Brashear, Janos L Mathe, Haomin Wen, Stacey Lynn English, William Hedges, Christoph U Lehmann, Asli Ozdas-Weitkamp, Shane P Stenner
BACKGROUND:  Managing prescription renewal requests is a labor-intensive challenge in ambulatory care. In 2009, Vanderbilt University Medical Center developed clinic-specific standing prescription renewal orders that allowed nurses, under specific conditions, to authorize renewal requests. Formulary and authorization changes made maintaining these documents very challenging. OBJECTIVE:  This article aims to review, standardize, and restructure legacy standing prescription renewal orders into a modular, scalable, and easier to manage format for conversion and use in a new electronic health record (EHR)...
January 2019: Applied Clinical Informatics
Pierre Baillargeon, Kervin Coss-Flores, Fakhar Singhera, Justin Shumate, Hannah Williams, Lina DeLuca, Timothy P Spicer, Louis Scampavia
Microplates are an essential tool used in laboratories for storing research materials and performing assays. Many types of laboratory automation exist that greatly reduce the effort needed to utilize microplates; however, there are cases where the use of such automation is not feasible or practical. In these instances, researchers must work in an environment where liquid handling operations are performed manually with handheld pipetting devices. This type of work is tedious and error-prone as it relies on researchers to manually track a significant amount of metadata, including transfer volumes, plate barcodes, well contents, and well locations...
January 30, 2019: SLAS Technology
Theodore L Fobe, Andrei Kazakov, Demian Riccardi
Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90 degrees. In this study, we transform over 30k protein databank files (pdbs) into a single file, SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information of both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance...
January 29, 2019: Journal of Chemical Information and Modeling
Marco Govoni, Milson Munakami, Aditya Tanikanti, Jonathan H Skone, Hakizumwami B Runesha, Federico Giberti, Juan de Pablo, Giulia Galli
We propose a strategy and present a simple tool to facilitate scientific data reproducibility by making available, in a distributed manner, all data and procedures presented in scientific papers, together with metadata to render them searchable and discoverable. In particular, we describe a graphical user interface (GUI), Qresp, to curate papers (i.e. generate metadata) and to explore curated papers and automatically access the data presented in scientific publications.
January 29, 2019: Scientific Data
Chih-Yuan Huang, Hsin-Hsien Chen
Sensor Web and Internet of Things (IoT) (SW-IoT) have been attracting attention from various fields. Both of them deploy networks of embedded devices to monitor physical properties (i.e., sensing capability) or to be controlled (i.e., tasking capability). One of the most important tasks to realize the SW-IoT vision is to establish an open and interoperable architecture, across the device layer, gateway layer, service layer, and application layer. To achieve this objective, many organizations and alliances propose standards for different layers...
January 25, 2019: Sensors
Sunghee Oh, Congjun Li, Ransom L Baldwin, Seongho Song, Fang Liu, Robert W Li
Identification of differentially expressed genes has been a high priority task of downstream analyses to further advances in biomedical research. Investigators have been faced with an array of issues in dealing with more complicated experiments and metadata, including batch effects, normalization, temporal dynamics (temporally differential expression), and isoform diversity (isoform-level quantification and differential splicing events). To date, there are currently no standard approaches to precisely and efficiently analyze these moderate or large-scale experimental designs, especially with combined metadata...
January 24, 2019: Scientific Reports
Patricia Maraver, Rubén Armañanzas, Todd A Gillette, Giorgio A Ascoli
BACKGROUND: The biomedical literature is expanding at ever-increasing rates, and it has become extremely challenging for researchers to keep abreast of new data and discoveries even in their own domains of expertise. We introduce PaperBot, a configurable, modular, open-source crawler to automatically find and efficiently index peer-reviewed publications based on periodic full-text searches across publisher web portals. RESULTS: PaperBot may operate stand-alone or it can be easily integrated with other software platforms and knowledge bases...
January 24, 2019: BMC Bioinformatics
Evan C Palmer-Young, Iain W Farrell, Lynn S Adler, Nelson J Milano, Paul A Egan, Rebecca E Irwin, Philip C Stevenson
Floral chemistry mediates plant interactions with herbivores, pathogens, and pollinators. The chemistry of floral nectar and pollen-the primary food rewards for pollinators-can affect both plant reproduction and pollinator health. Although the existence and functional significance of nectar and pollen secondary metabolites has long been known, comprehensive quantitative characterizations of secondary chemistry exist for only a few species. Moreover, little is known about intraspecific variation in nectar and pollen chemical profiles...
January 22, 2019: Ecology
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