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Custom search engine

Hadyl Asfari, Julien Souvignet, Agnès Lillo-Le Louët, Béatrice Trombert, Marie-Christine Jaulent, Cédric Bousquet
AIM: To propose an alternative approach for building custom groupings of terms that complements the usual approach based on both hierarchical method (selection of reference groupings in medical dictionary for regulatory activities [MedDRA]) and/or textual method (string search), for case reports extraction from a pharmacovigilance database in response to a safety problem. Here we take cardiac valve fibrosis as an example. METHODS: The list of terms obtained by an automated approach, based on querying ontology of adverse drug reactions (OntoADR), a knowledge base defining MedDRA terms through relationships with systematized nomenclature of medicine-clinical terms (SNOMED CT) concepts, was compared with the reference list consisting of 53 preferred terms obtained by hierarchical and textual method...
July 21, 2016: Thérapie
Michele Diana, Luigi Schiraldi, Yu-Yin Liu, Riccardo Memeo, Didier Mutter, Patrick Pessaux, Jacques Marescaux
BACKGROUND: High intensity focused ultrasound (HIFU) is emerging as a valid minimally-invasive image-guided treatment of malignancies. We aimed to review to current state of the art of HIFU therapy applied to the digestive system and discuss some promising avenues of the technology. METHODS: Pertinent studies were identified through PubMed and Embase search engines using the following keywords, combined in different ways: HIFU, esophagus, stomach, liver, pancreas, gallbladder, colon, rectum, and cancer...
August 2016: Hepatobiliary Surgery and Nutrition
Alberto G Jácome, Florentino Fdez-Riverola, Anália Lourenço
BACKGROUND AND OBJECTIVES: Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces...
July 2016: Computer Methods and Programs in Biomedicine
Christopher J Mitchell, Min-Sik Kim, Chan Hyun Na, Akhilesh Pandey
Quantitative mass spectrometry data necessitates an analytical pipeline that captures the accuracy and comprehensiveness of the experiments. Currently, data analysis is often coupled to specific software packages, which restricts the analysis to a given workflow and precludes a more thorough characterization of the data by other complementary tools. To address this, we have developed PyQuant, a cross-platform mass spectrometry data quantification application that is compatible with existing frameworks and can be used as a stand-alone quantification tool...
August 2016: Molecular & Cellular Proteomics: MCP
Yuxin Li, Xusheng Wang, Ji-Hoon Cho, Timothy I Shaw, Zhiping Wu, Bing Bai, Hong Wang, Suiping Zhou, Thomas G Beach, Gang Wu, Jinghui Zhang, Junmin Peng
Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMPg creates multiple databases of DNA polymorphisms, mutations, splice junctions, partially trypticity, as well as protein fragments translated from the whole transcriptome in all six frames upon RNA-seq de novo assembly...
July 1, 2016: Journal of Proteome Research
Vardeep Singh Dhillon, Dilpreet Kaur
Climate change is a reality, and the modern healthcare sector not just contributes towards this grave phenomenon but is itself being affected by it. The present review was thus conducted to understand the meaning of 'Green Hospital', to identify the many ways in which health sector is contributing towards climate change, to explore possibilities for countering this grave trend and last of all to look for institutions that are pioneering change. Data for the review was extracted from multiple online sources using the Google search engine...
December 2015: Journal of Clinical and Diagnostic Research: JCDR
Pradeep Anand Ravindranath, Stefano Forli, David S Goodsell, Arthur J Olson, Michel F Sanner
Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; and 2) increased number of false positives, calling for scoring functions tailored for flexible receptor docking...
December 2015: PLoS Computational Biology
Shuai Zheng, James J Lu, Christina Appin, Daniel Brat, Fusheng Wang
BACKGROUND: Structural reporting enables semantic understanding and prompt retrieval of clinical findings about patients. While synoptic pathology reporting provides templates for data entries, information in pathology reports remains primarily in narrative free text form. Extracting data of interest from narrative pathology reports could significantly improve the representation of the information and enable complex structured queries. However, manual extraction is tedious and error-prone, and automated tools are often constructed with a fixed training dataset and not easily adaptable...
2015: Journal of Pathology Informatics
Heeyoun Hwang, Gun Wook Park, Kwang Hoe Kim, Ju Yeon Lee, Hyun Kyoung Lee, Eun Sun Ji, Sung-Kyu Robin Park, Tao Xu, John R Yates, Kyung-Hoon Kwon, Young Mok Park, Hyoung-Joo Lee, Young-Ki Paik, Jin Young Kim, Jong Shin Yoo
The goal of the Chromosome-Centric Human Proteome Project (C-HPP) is to fully provide proteomic information from each human chromosome, including novel proteoforms, such as novel protein-coding variants expressed from noncoding genomic regions, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). In the 144 LC/MS/MS raw files from human hippocampal tissues of control, epilepsy, and Alzheimer's disease, we identified the novel proteoforms with a workflow including integrated proteomic pipeline using three different search engines, MASCOT, SEQUEST, and MS-GF+...
December 4, 2015: Journal of Proteome Research
Rajiv Karbhal, Sangeeta Sawant, Urmila Kulkarni-Kale
BACKGROUND: Diverse types of biological data, primary as well as derived, are available in various formats and are stored in heterogeneous resources. Database-specific as well as integrated search engines are available for carrying out efficient searches of databases. These search engines however, do not support extraction of subsets of data with the same level of granularity that exists in typical database entries. In order to extract fine grained subsets of data, users are required to download complete or partial database entries and write scripts for parsing and extraction...
2015: BioData Mining
Katelyn Godin, Jackie Stapleton, Sharon I Kirkpatrick, Rhona M Hanning, Scott T Leatherdale
BACKGROUND: Grey literature is an important source of information for large-scale review syntheses. However, there are many characteristics of grey literature that make it difficult to search systematically. Further, there is no 'gold standard' for rigorous systematic grey literature search methods and few resources on how to conduct this type of search. This paper describes systematic review search methods that were developed and applied to complete a case study systematic review of grey literature that examined guidelines for school-based breakfast programs in Canada...
October 22, 2015: Systematic Reviews
S Abdullah, K Karunamoorthi
OBJECTIVE: The deadly Ebola virus has been first known to mankind since 1976. In the past decades, Ebola outbreaks has often been ignored/neglected as erupted in the rural remote/isolated areas of Africa. The recent 2013-2014 epidemic is the most wide-spread with high incidence rates, morbidity and, mortality in the Ebola history. Eventually, the World Health Organization (WHO) has declared it as a 'Public Health Concern of the International Community'. This scrutiny was conducted to initiate a serious debate on various aspects of Ebola, particularly blood transfusion as an empirical therapeutic modality...
August 2015: European Review for Medical and Pharmacological Sciences
Gregory A Abel, Angel M Cronin, Kristofer Earles, Stacy W Gray
Although the Internet may help to increase cancer patients' awareness of clinical trials, little is known about the accessibility and quality of online clinical trial information. We simulated the experience of a naïve cancer patient without clinical trial knowledge by searching three popular search engines for treatment information for breast, lung, and prostate cancer, and myelodysplastic syndromes (MDS). Two coders independently evaluated website content for accessibility and quality. We screened 120 websites and identified 40 unique sites for analysis...
October 2015: Cancer Epidemiology, Biomarkers & Prevention
Ashraf Ayoub, Randa Al-Fotawei
Reconstruction of maxillofacial bones has proven to be complex due to the aesthetic requirements and functional demands of the jaw. Although autogenous bone grafts and a wide range of biomaterials are routinely used for facial bone reconstruction, these methods are associated with a number of drawbacks, including the limited availability of autogenous grafts and the morbidity associated with bone graft harvesting, whilst biomaterials are also linked with a high failure rate. These limitations have inspired the search for innovative techniques for bone bioengineering and the development of more reliable biomaterials...
2015: Frontiers of Oral Biology
Viness Pillay, Yahya E Choonara
No abstract text is available yet for this article.
2015: Recent Patents on Drug Delivery & Formulation
Matthias Munz, Sascha Tönnies, Wolf-Tilo Balke, Eric Simon
The high abundance of genetic information enables researchers to gain new insights from the comparison of human genes according to their similarities. However, existing tools that allow the exploration of such gene-to-gene relationships, apply each similarity independently. To make use of multidimensional scoring, we developed a new search engine named Genehopper. It can handle two query types: (i) the typical use case starts with a term-to-gene search, i.e. an optimized full-text search for an anchor gene of interest...
July 1, 2015: Nucleic Acids Research
Todd Raine, Brent Thoma, Teresa M Chan, Michelle Lin
The number of online resources read by and pertinent to clinicians has increased dramatically. However, most healthcare professionals still use mainstream search engines as their primary port of entry to the resources on the Internet. These search engines use algorithms that do not make it easy to find clinician-oriented resources. FOAMSearch, a custom search engine (CSE), was developed to find relevant, high-quality online resources for emergency medicine and critical care (EMCC) clinicians. Using Google™ algorithms, it searches a vetted list of >300 blogs, podcasts, wikis, knowledge translation tools, clinical decision support tools and medical journals...
August 2015: Emergency Medicine Australasia: EMA
Angelo Duarte, Artur T L Queiroz, Rafael Tosta, Augusto M Carvalho, Carlos Henrique Barbosa, Maria Bellio, Camila I de Oliveira, Manoel Barral-Netto
BACKGROUND: Leishmaniasis is caused by intracellular Leishmania parasites that induce a T-cell mediated response associated with recognition of CD4+ and CD8+ T cell Line 1Lineepitopes. Identification of CD8+ antigenic determinants is crucial for vaccine and therapy development. Herein, we developed an open-source software dedicated to search and compile data obtained from currently available on line prediction algorithms. METHODOLOGY/PRINCIPAL FINDINGS: We developed a two-phase algorithm and implemented in an open source software called EPIBOT, that consolidates the results obtained with single prediction algorithms, generating a final output in which epitopes are ranked...
2015: PloS One
Thilo Muth, Carolin A Kolmeder, Jarkko Salojärvi, Salla Keskitalo, Markku Varjosalo, Froukje J Verdam, Sander S Rensen, Udo Reichl, Willem M de Vos, Erdmann Rapp, Lennart Martens
Metaproteomic research involves various computational challenges during the identification of fragmentation spectra acquired from the proteome of a complex microbiome. These issues are manifold and range from the construction of customized sequence databases, the optimal setting of search parameters to limitations in the identification search algorithms themselves. In order to assess the importance of these individual factors, we studied the effect of strategies to combine different search algorithms, explored the influence of chosen database search settings, and investigated the impact of the size of the protein sequence database used for identification...
October 2015: Proteomics
Tzu-Hsien Yang, Hong-Tsun Chang, Eric Sl Hsiao, Juo-Ling Sun, Chung-Ching Wang, Hsin-Yi Wu, Pao-Chi Liao, Wei-Sheng Wu
BACKGROUND: Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work...
2014: BMC Bioinformatics
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