AIMC Topic: Molecular Sequence Annotation
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Functional Annotation of Proteins Encoded by the Minimal Bacterial Genome Based on Secondary Structure Element Alignment.
Journal of proteome research
May 24, 2018
In synthetic biology, one of the key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0,...
Consistent prediction of GO protein localization.
Scientific reports
May 17, 2018
The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automat...
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...
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 ...
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...
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...
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...
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 ...
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 ...
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...
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