AI Medical Compendium Journal:
Database : the journal of biological databases and curation

Showing 11 to 20 of 151 articles

Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach.

Database : the journal of biological databases and curation Jan 1, 2018
The precision medicine (PM) initiative promises to identify individualized treatment depending on a patients' genetic profile and their related responses. In order to help health professionals and researchers in the PM endeavor, BioCreative VI organi...
Neural Networks, Computer Algorithms Protein Interaction Maps Databases, Protein Mutation
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Large-scale automated machine reading discovers new cancer-driving mechanisms.

Database : the journal of biological databases and curation Jan 1, 2018
PubMed, a repository and search engine for biomedical literature, now indexes >1 million articles each year. This exceeds the processing capacity of human domain experts, limiting our ability to truly understand many diseases. We present Reach, a sys...
Publications Automation Algorithms Neoplasms Humans Machine Learning
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An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
The BioCreative VI Track IV (mining protein interactions and mutations for precision medicine) challenge was organized in 2017 with the goal of applying biomedical text mining methods to support advancements in precision medicine approaches. As part ...
Algorithms Protein Interaction Maps Mutation Databases, Protein Neural Networks, Computer Machine Learning
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Assisting document triage for human kinome curation via machine learning.

Database : the journal of biological databases and curation Jan 1, 2018
In the era of data explosion, the increasing frequency of published articles presents unorthodox challenges to fulfill specific curation requirements for bio-literature databases. Recognizing these demands, we designed a document triage system with a...
Documentation Statistics as Topic Protein Kinases Data Mining Machine Learning Proteome Humans
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Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling.

Database : the journal of biological databases and curation Jan 1, 2018
We present a system for automatically identifying a multitude of biomedical entities from the literature. This work is based on our previous efforts in the BioCreative VI: Interactive Bio-ID Assignment shared task in which our system demonstrated sta...
Molecular Sequence Annotation Algorithms Fuzzy Logic
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Improved ontology for eukaryotic single-exon coding sequences in biological databases.

Database : the journal of biological databases and curation Jan 1, 2018
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryo...
Base Sequence Protein Isoforms Databases, Genetic Exons Open Reading Frames Gene Ontology Eukaryota
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Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
In this paper, we describe a hierarchical bi-directional attention-based Re-current Neural Network (RNN) as a reusable sequence encoder architecture, which is used as sentence and document encoder for document classification. The sequence encoder is ...
Data Mining Models, Theoretical Support Vector Machine Databases, Protein Mutation Reproducibility of Results Protein Interaction Maps Neural Networks, Computer Algorithms
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PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants.

Database : the journal of biological databases and curation Jan 1, 2018
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although th...
Databases, Genetic MicroRNAs Phylogeny Molecular Sequence Annotation RNA, Untranslated DNA Transposable Elements Plants Knowledge Bases
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Automatic query generation using word embeddings for retrieving passages describing experimental methods.

Database : the journal of biological databases and curation Jan 10, 2017
Information regarding the physical interactions among proteins is crucial, since protein-protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing...
Proteins Databases, Protein Data Curation Data Mining Biological Ontologies
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Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Database : the journal of biological databases and curation Dec 26, 2016
We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO ann...
Molecular Sequence Annotation Gene Ontology Models, Genetic Apoptosis Evolution, Molecular Autophagy Animals Phylogeny Humans Software
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