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 …

The human phenotype ontology in 2017

S Köhler, NA Vasilevsky, M Engelstad… - Nucleic acids …, 2017‏ - academic.oup.com
Deep phenoty** has been defined as the precise and comprehensive analysis of
phenotypic abnormalities in which the individual components of the phenotype are observed …

Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers

D Bang, S Lim, S Lee, S Kim - Nature Communications, 2023‏ - nature.com
Computational drug repurposing aims to identify new indications for existing drugs by
utilizing high-throughput data, often in the form of biomedical knowledge graphs. However …

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 …

Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes

JT Reese, H Blau, E Casiraghi, T Bergquist… - …, 2023‏ - thelancet.com
Background Stratification of patients with post-acute sequelae of SARS-CoV-2 infection
(PASC, or long COVID) would allow precision clinical management strategies. However …

[PDF][PDF] The human phenotype ontology in 2017

S Kohler, NA Vasilevsky, M Engelstad, E Foster… - 2017‏ - repository.ubn.ru.nl
Deep phenoty** has been defined as the precise and comprehensive analysis of
phenotypic abnormalities in which the individual components of the phenotype are observed …

REVIGO summarizes and visualizes long lists of gene ontology terms

F Supek, M Bošnjak, N Škunca, T Šmuc - PloS one, 2011‏ - journals.plos.org
Outcomes of high-throughput biological experiments are typically interpreted by statistical
testing for enriched gene functional categories defined by the Gene Ontology (GO). The …

[HTML][HTML] A census of human soluble protein complexes

PC Havugimana, GT Hart, T Nepusz, H Yang… - Cell, 2012‏ - cell.com
Cellular processes often depend on stable physical associations between proteins. Despite
recent progress, knowledge of the composition of human protein complexes remains limited …

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

A Roy, J Yang, Y Zhang - Nucleic acids research, 2012‏ - academic.oup.com
We have developed a new COFACTOR webserver for automated structure-based protein
function annotation. Starting from a structural model, given by either experimental …

[ספר][B] Semantic similarity from natural language and ontology analysis

S Harispe, S Ranwez, J Montmain - 2022‏ - books.google.com
Artificial Intelligence federates numerous scientific fields in the aim of develo** machines
able to assist human operators performing complex treatments---most of which demand high …