AIMC Topic: Knowledge Bases

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KnowEnG: a knowledge engine for genomics.

Journal of the American Medical Informatics Association : JAMIA Jul 23, 2015
We describe here the vision, motivations, and research plans of the National Institutes of Health Center for Excellence in Big Data Computing at the University of Illinois, Urbana-Champaign. The Center is organized around the construction of "Knowled...
Humans Knowledge Bases Datasets as Topic National Institutes of Health (U.S.) Genomics United States
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IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.

mBio Jul 14, 2015
UNLABELLED: In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In...
Computational Biology Biosynthetic Pathways Knowledge Bases Secondary Metabolism Multigene Family
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Towards a Food Safety Knowledge Base Applicable in Crisis Situations and Beyond.

BioMed research international Jul 13, 2015
In case of contamination in the food chain, fast action is required in order to reduce the numbers of affected people. In such situations, being able to predict the fate of agents in foods would help risk assessors and decision makers in assessing th...
Food Safety Computer Simulation Hazard Analysis and Critical Control Points Pandemics Risk Assessment Forecasting Bioterrorism Databases, Factual Incidence Foodborne Diseases Humans Food Contamination Knowledge Bases Software Models, Statistical
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Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task.

BMC bioinformatics Jul 13, 2015
BACKGROUND: The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating system...
Gene Ontology Genes Semantics Natural Language Processing Gene Expression Regulation Knowledge Bases Information Storage and Retrieval Humans Databases, Factual Gene Regulatory Networks
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Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013.

BMC bioinformatics Jul 13, 2015
BACKGROUND: Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we pre...
Neoplasms Gene Regulatory Networks Models, Theoretical Natural Language Processing Knowledge Bases Information Storage and Retrieval Humans Genes
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Extracting biomedical events from pairs of text entities.

BMC bioinformatics Jul 13, 2015
BACKGROUND: Huge amounts of electronic biomedical documents, such as molecular biology reports or genomic papers are generated daily. Nowadays, these documents are mainly available in the form of unstructured free texts, which require heavy processin...
Models, Theoretical Support Vector Machine Natural Language Processing Knowledge Bases Data Mining Databases, Factual Biomedical Research Computational Biology Humans
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Adaptable, high recall, event extraction system with minimal configuration.

BMC bioinformatics Jul 13, 2015
BACKGROUND: Biomedical event extraction has been a major focus of biomedical natural language processing (BioNLP) research since the first BioNLP shared task was held in 2009. Accordingly, a large number of event extraction systems have been develope...
Information Storage and Retrieval Genes Models, Theoretical Natural Language Processing Knowledge Bases Neoplasms Gene Regulatory Networks Humans
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Genome Modeling System: A Knowledge Management Platform for Genomics.

PLoS computational biology Jul 9, 2015
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled...
User-Computer Interface Models, Genetic Databases, Genetic Humans Algorithms Sequence Alignment Sequence Analysis, DNA Computer Simulation Database Management Systems Knowledge Bases Chromosome Mapping Genome, Human
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Installing a Local Copy of the Reactome Web Site and Knowledgebase.

Current protocols in bioinformatics Jun 19, 2015
The Reactome project builds, maintains, and publishes a knowledgebase of biological pathways. The information in the knowledgebase is gathered from the experts in the field, peer reviewed and edited by Reactome editorial staff, and then published to ...
Knowledge Bases Databases as Topic Software Signal Transduction Internet
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An Approach for Learning Expressive Ontologies in Medical Domain.

Journal of medical systems Jun 16, 2015
The access to medical information (journals, blogs, web-pages, dictionaries, and texts) has been increased due to availability of many digital media. In particular, finding an appropriate structure that represents the information contained in texts i...
Humans Machine Learning Algorithms Vocabulary, Controlled Information Systems Internet Knowledge Bases Information Storage and Retrieval
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