[HTML][HTML] 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 …
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 …
Recent advances in methods of lexical semantic relatedness–a survey
Measuring lexical semantic relatedness is an important task in Natural Language
Processing (NLP). It is often a prerequisite to many complex NLP tasks. Despite an …
Processing (NLP). It is often a prerequisite to many complex NLP tasks. Despite an …
[HTML][HTML] Metrics for GO based protein semantic similarity: a systematic evaluation
Background Several semantic similarity measures have been applied to gene products
annotated with Gene Ontology terms, providing a basis for their functional comparison …
annotated with Gene Ontology terms, providing a basis for their functional comparison …
[HTML][HTML] MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
T Blum, S Briesemeister, O Kohlbacher - BMC bioinformatics, 2009 - Springer
Background Knowledge of subcellular localization of proteins is crucial to proteomics, drug
target discovery and systems biology since localization and biological function are highly …
target discovery and systems biology since localization and biological function are highly …
[HTML][HTML] An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology
Background Semantic similarity measures are useful to assess the physiological relevance
of protein-protein interactions (PPIs). They quantify similarity between proteins based on …
of protein-protein interactions (PPIs). They quantify similarity between proteins based on …
Going from where to why—interpretable prediction of protein subcellular localization
S Briesemeister, J Rahnenführer, O Kohlbacher - Bioinformatics, 2010 - academic.oup.com
Motivation: Protein subcellular localization is pivotal in understanding a protein's function.
Computational prediction of subcellular localization has become a viable alternative to …
Computational prediction of subcellular localization has become a viable alternative to …
GOASVM: a subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition
Prediction of protein subcellular localization is an important yet challenging problem.
Recently, several computational methods based on Gene Ontology (GO) have been …
Recently, several computational methods based on Gene Ontology (GO) have been …
Gene ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery
GK Mazandu, ER Chimusa… - Briefings in bioinformatics, 2017 - academic.oup.com
Gene Ontology (GO) semantic similarity tools enable retrieval of semantic similarity scores,
which incorporate biological knowledge embedded in the GO structure for comparing or …
which incorporate biological knowledge embedded in the GO structure for comparing or …
SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins
S Briesemeister, T Blum, S Brady, Y Lam… - Journal of proteome …, 2009 - ACS Publications
SherLoc2 is a comprehensive high-accuracy subcellular localization prediction system. It is
applicable to animal, fungal, and plant proteins and covers all main eukaryotic subcellular …
applicable to animal, fungal, and plant proteins and covers all main eukaryotic subcellular …