AIMC Topic: Molecular Sequence Annotation

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Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.

Journal of biomedical semantics Apr 12, 2018
BACKGROUND: Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardiovascular Disease Ontology (CV...
Humans Cardiovascular Diseases Deep Learning PubMed ROC Curve Biological Ontologies Molecular Sequence Annotation
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SSDOnt: An Ontology for Representing Single-Subject Design Studies.

Methods of information in medicine Apr 5, 2018
BACKGROUND: Single-Subject Design is used in several areas such as education and biomedicine. However, no suited formal vocabulary exists for annotating the detailed configuration and the results of this type of research studies with the appropriate ...
Molecular Sequence Annotation Search Engine Biological Ontologies Autistic Disorder Humans Research Design
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Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations.

Scientific reports Mar 23, 2018
Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks of this analysis - the ontolo...
Humans Reproducibility of Results Computational Biology Gene Ontology Evolution, Molecular Molecular Sequence Annotation Models, Genetic Databases, Genetic
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Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.

BMC systems biology Mar 19, 2018
BACKGROUND: Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, mos...
Gene Ontology Stochastic Processes Gene Regulatory Networks Semantics Molecular Sequence Annotation Computational Biology
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Disease Ontology: improving and unifying disease annotations across species.

Disease models & mechanisms Mar 12, 2018
Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integrating relevant model organism and/or human data often apply disparate terminologies (vocabularies and ontol...
Species Specificity Disease Rats Databases, Genetic Molecular Sequence Annotation Gene Ontology Animals Mice
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Exploring autophagy with Gene Ontology.

Autophagy Feb 17, 2018
Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular ...
Parkinson Disease Proteins Molecular Sequence Annotation Gene Ontology Autophagy Animals Databases, Genetic Humans
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Multi-label Deep Learning for Gene Function Annotation in Cancer Pathways.

Scientific reports Jan 10, 2018
The war on cancer is progressing globally but slowly as researchers around the world continue to seek and discover more innovative and effective ways of curing this catastrophic disease. Organizing biological information, representing it, and making ...
Genetic Predisposition to Disease Genetic Association Studies Databases, Genetic Molecular Sequence Annotation Computational Biology Algorithms Neoplasms Humans Machine Learning
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AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder.

Database : the journal of biological databases and curation Jan 1, 2018
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with strong genetic contributions. To provide a comprehensive resource for the genetic evidence of ASD, we have updated the Autism KnowledgeBase (AutismKB) to version 2.0. Autism...
Internet Knowledge Bases Molecular Sequence Annotation User-Computer Interface Genetic Predisposition to Disease Humans Autism Spectrum Disorder
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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...
Fuzzy Logic Molecular Sequence Annotation 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...
DNA Transposable Elements Phylogeny Databases, Genetic Knowledge Bases Molecular Sequence Annotation RNA, Untranslated MicroRNAs Plants
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