keyword
MENU ▼
Read by QxMD icon Read
search

Text mining

keyword
https://www.readbyqxmd.com/read/27915291/the-landscape-of-microbial-phenotypic-traits-and-associated-genes
#1
Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913255/using-the-bitola-system-to-identify-candidate-molecules-in-the-interaction-between-oral-lichen-planus-and-depression
#2
Yuanbo Zhan, Shuang Zhou, Ying Li, Sen Mu, Xuejing Song, Feng Lin, Ruimin Zhang, Bin Zhang
Exacerbations of oral lichen planus (OLP) have been linked to the periods of psychological stress, anxiety and depression. The specific mechanism of the interaction is unclear. The aim of this study was to explore the candidate genes or molecules that play important roles in the interaction between OLP and depression. The BITOLA system was used to search all intermediate concepts relevant to the "Gene or Gene Product" for OLP and depression, and the gene expression data and tissue-specific gene data along with manual checking were then employed to filter the intermediate concepts...
November 29, 2016: Behavioural Brain Research
https://www.readbyqxmd.com/read/27902695/text-mining-genotype-phenotype-relationships-from-biomedical-literature-for-database-curation-and-precision-medicine
#3
Ayush Singhal, Michael Simmons, Zhiyong Lu
The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27899649/protein-ontology-pro-enhancing-and-scaling-up-the-representation-of-protein-entities
#4
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899563/chimerdb-3-0-an-enhanced-database-for-fusion-genes-from-cancer-transcriptome-and-literature-data-mining
#5
Myunggyo Lee, Kyubum Lee, Namhee Yu, Insu Jang, Ikjung Choi, Pora Kim, Ye Eun Jang, Byounggun Kim, Sunkyu Kim, Byungwook Lee, Jaewoo Kang, Sanghyuk Lee
Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896985/a-new-relevance-estimator-for-the-compilation-and-visualization-of-disease-patterns-and-potential-drug-targets
#6
Modest VON Korff, Tobias Fink, Thomas Sander
A new computational method is presented to extract disease patterns from heterogeneous and text-based data. For this study, 22 million PubMed records were mined for co-occurrences of gene name synonyms and disease MeSH terms. The resulting publication counts were transferred into a matrix Mdata. In this matrix, a disease was represented by a row and a gene by a column. Each field in the matrix represented the publication count for a co-occurring disease-gene pair. A second matrix with identical dimensions Mrelevance was derived from Mdata...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896978/development-and-performance-of-text-mining-algorithms-to-extract-socioeconomic-status-from-de-identified-electronic-health-records
#7
Brittany M Hollister, Nicole A Restrepo, Eric Farber-Eger, Dana C Crawford, Melinda C Aldrich, Amy Non
Socioeconomic status (SES) is a fundamental contributor to health, and a key factor underlying racial disparities in disease. However, SES data are rarely included in genetic studies due in part to the difficultly of collecting these data when studies were not originally designed for that purpose. The emergence of large clinic-based biobanks linked to electronic health records (EHRs) provides research access to large patient populations with longitudinal phenotype data captured in structured fields as billing codes, procedure codes, and prescriptions...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896740/metabolic-pathway-mining
#8
Jan M Czarnecki, Adrian J Shepherd
Understanding metabolic pathways is one of the most important fields in bioscience in the post-genomic era, but curating metabolic pathways requires considerable man-power. As such there is a lack of reliable, experimentally verified metabolic pathways in databases and databases are forced to predict all but the most immediately useful pathways.Text-mining has the potential to solve this problem, but while sophisticated text-mining methods have been developed to assist the curation of many types of biomedical networks, such as protein-protein interaction networks, the mining of metabolic pathways from the literature has been largely neglected by the text-mining community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896584/soil-contamination-assessment-for-pb-zn-and-cd-in-a-slag-disposal-area-using-the-integration-of-geochemical-and-microbiological-data
#9
Mariana Consiglio Kasemodel, Jacqueline Zanin Lima, Isabel Kimiko Sakamoto, Maria Bernadete Amancio Varesche, Julio Cesar Trofino, Valéria Guimarães Silvestre Rodrigues
Improper disposal of mining waste is still considered a global problem, and further details on the contamination by potentially toxic metals are required for a proper assessment. In this context, it is important to have a combined view of the chemical and biological changes in the mining dump area. Thus, the objective of this study was to evaluate the Pb, Zn and Cd contamination in a slag disposal area using the integration of geochemical and microbiological data. Analyses of soil organic matter (SOM), pH, Eh, pseudo-total concentration of metals, sequential extraction and microbial community by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were conducted...
December 2016: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/27888231/text-mining-resources-for-the-life-sciences
#10
REVIEW
Piotr Przybyła, Matthew Shardlow, Sophie Aubin, Robert Bossy, Richard Eckart de Castilho, Stelios Piperidis, John McNaught, Sophia Ananiadou
Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27888133/network-pharmacology-based-study-on-the-mechanism-of-action-for-herbal-medicines-in-alzheimer-treatment
#11
Jiansong Fang, Ling Wang, Tian Wu, Cong Yang, Li Gao, Haobin Cai, Junhui Liu, Shuhuan Fang, Yunbo Chen, Wen Tan, Qi Wang
ETHNOPHARMACOLOGICAL RELEVANCE: Alzheimer's disease (AD), as the most common type of dementia, has brought a heavy economic burden to healthcare system around the world. However, currently there is still lack of effective treatment for AD patients. Herbal medicines, featured as multiple herbs, ingredients and targets, have accumulated a great deal of valuable experience in treating AD although the exact molecular mechanisms are still unclear. MATERIALS AND METHODS: In this investigation, we proposed a network pharmacology-based method, which combined large-scale text-mining, drug-likeness filtering, target prediction and network analysis to decipher the mechanisms of action for the most widely studied medicinal herbs in AD treatment...
November 23, 2016: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/27879651/prediction-of-protein-protein-interactions-by-evidence-combining-methods
#12
REVIEW
Ji-Wei Chang, Yan-Qing Zhou, Muhammad Tahir Ul Qamar, Ling-Ling Chen, Yu-Duan Ding
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of cell functions. Several experimental techniques operating in vivo or in vitro have made significant contributions to screening a large number of protein interaction partners, especially high-throughput experimental methods. However, computational approaches for PPI predication supported by rapid accumulation of data generated from experimental techniques, 3D structure definitions, and genome sequencing have boosted the map sketching of PPIs...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27876688/online-concerns-of-parents-suspecting-autism-spectrum-disorder-in-their-child-content-analysis-of-signs-and-automated-prediction-of-risk
#13
Ayelet Ben-Sasson, Elad Yom-Tov
BACKGROUND: Online communities are used as platforms by parents to verify developmental and health concerns related to their child. The increasing public awareness of autism spectrum disorders (ASD) leads more parents to suspect ASD in their child. Early identification of ASD is important for early intervention. OBJECTIVE: To characterize the symptoms mentioned in online queries posed by parents who suspect that their child might have ASD and determine whether they are age-specific...
November 22, 2016: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/27869632/p-hacking-in-orthopaedic-literature-a-twist-to-the-tail
#14
Hamid Rahmatullah Bin Abd Razak, Jin-Guang Ernest Ang, Hersh Attal, Tet-Sen Howe, John Carson Allen
BACKGROUND: "P-hacking" occurs when researchers preferentially select data or statistical analyses until nonsignificant results become significant. We wanted to evaluate if the phenomenon of p-hacking was evident in orthopaedic literature. METHODS: We text-mined through all articles published in three top orthopaedic journals in 2015. For anonymity, we cipher-coded the three journals. We included all studies that reported a single p value to answer their main hypothesis...
October 19, 2016: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/27869123/a-systems-study-reveals-concurrent-activation-of-ampk-and-mtor-by-amino-acids
#15
Piero Dalle Pezze, Stefanie Ruf, Annika G Sonntag, Miriam Langelaar-Makkinje, Philip Hall, Alexander M Heberle, Patricia Razquin Navas, Karen van Eunen, Regine C Tölle, Jennifer J Schwarz, Heike Wiese, Bettina Warscheid, Jana Deitersen, Björn Stork, Erik Fäßler, Sascha Schäuble, Udo Hahn, Peter Horvatovich, Daryl P Shanley, Kathrin Thedieck
Amino acids (aa) are not only building blocks for proteins, but also signalling molecules, with the mammalian target of rapamycin complex 1 (mTORC1) acting as a key mediator. However, little is known about whether aa, independently of mTORC1, activate other kinases of the mTOR signalling network. To delineate aa-stimulated mTOR network dynamics, we here combine a computational-experimental approach with text mining-enhanced quantitative proteomics. We report that AMP-activated protein kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR complex 2 (mTORC2) are acutely activated by aa-readdition in an mTORC1-independent manner...
November 21, 2016: Nature Communications
https://www.readbyqxmd.com/read/27856765/topic-modeling-for-untargeted-substructure-exploration-in-metabolomics
#16
Justin Johan Jozias van der Hooft, Joe Wandy, Michael P Barrett, Karl E V Burgess, Simon Rogers
The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the system under study. Unfortunately, fragmentation spectra cannot identify molecules in isolation but require authentic standards or databases of known fragmented molecules...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27843493/recognizing-chemicals-in-patents-a-comparative-analysis
#17
Maryam Habibi, David Luis Wiegandt, Florian Schmedding, Ulf Leser
Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27843447/a-new-data-representation-based-on-training-data-characteristics-to-extract-drug-name-entity-in-medical-text
#18
Mujiono Sadikin, Mohamad Ivan Fanany, T Basaruddin
One essential task in information extraction from the medical corpus is drug name recognition. Compared with text sources come from other domains, the medical text mining poses more challenges, for example, more unstructured text, the fast growing of new terms addition, a wide range of name variation for the same drug, the lack of labeled dataset sources and external knowledge, and the multiple token representations for a single drug name. Although many approaches have been proposed to overwhelm the task, some problems remained with poor F-score performance (less than 0...
2016: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/27830249/efficient-results-in-semantic-interoperability-for-health-care-findings-from-the-section-on-knowledge-representation-and-management
#19
L F Soualmia, J Charlet
OBJECTIVES: To summarize excellent current research in the field of Knowledge Representation and Management (KRM) within the health and medical care domain. METHOD: We provide a synopsis of the 2016 IMIA selected articles as well as a related synthetic overview of the current and future field activities. A first step of the selection was performed through MEDLINE querying with a list of MeSH descriptors completed by a list of terms adapted to the KRM section. The second step of the selection was completed by the two section editors who separately evaluated the set of 1,432 articles...
November 10, 2016: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/27830243/new-problems-new-solutions-a-never-ending-story-findings-from-the-clinical-information-systems-perspective-for-2015
#20
W O Hackl, T Ganslandt
OBJECTIVE: To summarize recent research and to propose a selection of best papers published in 2015 in the field of Clinical Information Systems (CIS). METHOD: The query which had been used last year to retrieve articles for the CIS section of the IMIA Yearbook of Medical Informatics 2015 was refined. It again aimed at identifying relevant publications in the field of CIS and comprised search terms from the Medical Subject Headings (MeSH) catalog as well as additional free text search terms from PubMed and Web of Science...
November 10, 2016: Yearbook of Medical Informatics
keyword
keyword
13426
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"