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Semantic similarity and machine learning with ontologies
Ontologies have long been employed in the life sciences to formally represent and reason
over domain knowledge and they are employed in almost every major biological database …
over domain knowledge and they are employed in almost every major biological database …
Semantic similarity in biomedical ontologies
In recent years, ontologies have become a mainstream topic in biomedical research. When
biological entities are described using a common schema, such as an ontology, they can be …
biological entities are described using a common schema, such as an ontology, they can be …
rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms
Gene Ontology (GO) annotation is often used to guide the biological interpretation of high-
throughput omics experiments, eg by analysing lists of differentially regulated genes for …
throughput omics experiments, eg by analysing lists of differentially regulated genes for …
GOATOOLS: A Python library for Gene Ontology analyses
The biological interpretation of gene lists with interesting shared properties, such as up-or
down-regulation in a particular experiment, is typically accomplished using gene ontology …
down-regulation in a particular experiment, is typically accomplished using gene ontology …
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an
ongoing, global, community-driven effort to evaluate and improve the computational …
ongoing, global, community-driven effort to evaluate and improve the computational …
Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease
Viral infections have been proposed to elicit pathological processes leading to the initiation
of T helper 1 (TH1) immunity against dietary gluten and celiac disease (CeD). To test this …
of T helper 1 (TH1) immunity against dietary gluten and celiac disease (CeD). To test this …
ATTED-II in 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index
Abstract ATTED-II (http://atted. jp) is a coexpression database for plant species to aid in the
discovery of relationships of unknown genes within a species. As an advanced …
discovery of relationships of unknown genes within a species. As an advanced …
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to
compute similarities between genes and gene groups, and have became important basis for …
compute similarities between genes and gene groups, and have became important basis for …
Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases
Motivation: It is popular to explore meaningful molecular targets and infer new functions of
genes through gene functional similarity measuring and gene functional network …
genes through gene functional similarity measuring and gene functional network …
Identification of disease treatment mechanisms through the multiscale interactome
Most diseases disrupt multiple proteins, and drugs treat such diseases by restoring the
functions of the disrupted proteins. How drugs restore these functions, however, is often …
functions of the disrupted proteins. How drugs restore these functions, however, is often …