Semantic similarity and machine learning with ontologies

M Kulmanov, FZ Smaili, X Gao… - Briefings in …, 2021‏ - academic.oup.com
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 …

Semantic similarity in biomedical ontologies

C Pesquita, D Faria, AO Falcao, P Lord… - PLoS computational …, 2009‏ - journals.plos.org
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 …

rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms

S Sayols - microPublication biology, 2023‏ - pmc.ncbi.nlm.nih.gov
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 …

GOATOOLS: A Python library for Gene Ontology analyses

DV Klopfenstein, L Zhang, BS Pedersen, F Ramírez… - Scientific reports, 2018‏ - nature.com
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 …

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh… - Genome biology, 2019‏ - Springer
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an
ongoing, global, community-driven effort to evaluate and improve the computational …

Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease

R Bouziat, R Hinterleitner, JJ Brown… - Science, 2017‏ - science.org
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 …

ATTED-II in 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index

T Obayashi, Y Aoki, S Tadaka, Y Kagaya… - Plant and Cell …, 2018‏ - academic.oup.com
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 …

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

G Yu, F Li, Y Qin, X Bo, Y Wu, S Wang - Bioinformatics, 2010‏ - academic.oup.com
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 …

Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases

D Wang, J Wang, M Lu, F Song, Q Cui - Bioinformatics, 2010‏ - academic.oup.com
Motivation: It is popular to explore meaningful molecular targets and infer new functions of
genes through gene functional similarity measuring and gene functional network …

Identification of disease treatment mechanisms through the multiscale interactome

C Ruiz, M Zitnik, J Leskovec - Nature communications, 2021‏ - nature.com
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 …