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   Articles with "gene ontology" as a keyword



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A Gene Ontology Tutorial in Python.

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recommendations! Published in 2017 at "Methods in molecular biology"

DOI: 10.1007/978-1-4939-3743-1_16

Abstract: This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic similarity… read more here.

Keywords: ontology; ontology tutorial; tutorial python; biology ... See more keywords
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Combining sequence and Gene Ontology for protein module detection in the Weighted Network.

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recommendations! Published in 2017 at "Journal of theoretical biology"

DOI: 10.1016/j.jtbi.2016.10.010

Abstract: Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules.… read more here.

Keywords: protein; detection; ontology; network ... See more keywords
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Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

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recommendations! Published in 2019 at "Nature Genetics"

DOI: 10.1038/s41588-019-0500-1

Abstract: To increase the utility of Gene Ontology (GO) annotations for interpretation of genome-wide experimental data, we have developed GO-CAM, a structured framework for linking multiple GO annotations into an integrated model of a biological system.… read more here.

Keywords: cam; causal activity; ontology; ontology causal ... See more keywords

Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance

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recommendations! Published in 2020 at "Scientific Reports"

DOI: 10.1038/s41598-020-73326-3

Abstract: Gene ontology (GO) is an eminent knowledge base frequently used for providing biological interpretations for the analysis of genes or gene sets from biological, medical and clinical problems. Unfortunately, the interpretation of such results is… read more here.

Keywords: goxplorer; gene ontology; ontology; graph based ... See more keywords

Anc2vec: embedding gene ontology terms by preserving ancestors relationships

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac003

Abstract: The gene ontology (GO) provides a hierarchical structure with a controlled vocabulary composed of terms describing functions and localization of gene products. Recent works propose vector representations, also known as embeddings, of GO terms that… read more here.

Keywords: embedding gene; terms preserving; ontology; anc2vec embedding ... See more keywords
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Learning representations for gene ontology terms by jointly encoding graph structure and textual node descriptors

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac318

Abstract: Measuring the semantic similarity between Gene Ontology (GO) terms is a fundamental step in numerous functional bioinformatics applications. To fully exploit the metadata of GO terms, word embedding-based methods have been proposed recently to map… read more here.

Keywords: structure; encoding graph; ontology; gene ontology ... See more keywords
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Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery

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recommendations! Published in 2017 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbw067

Abstract: Gene Ontology (GO) semantic similarity tools enable retrieval of semantic similarity scores, which incorporate biological knowledge embedded in the GO structure for comparing or classifying different proteins or list of proteins based on their GO… read more here.

Keywords: ontology; semantic similarity; knowledge; ontology semantic ... See more keywords
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GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression.

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac147

Abstract: MOTIVATION Medical care is becoming more and more specific to patients' needs due to the increased availability of omics data. The application to these data of sophisticated machine learning models, in particular deep learning, can… read more here.

Keywords: neural network; self explaining; ontology; gene ontology ... See more keywords
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Isoform function prediction by Gene Ontology embedding

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac576

Abstract: MOTIVATION High resolution annotation of gene functions is a central task in functional genomics. Multiple proteoforms translated from alternatively spliced isoforms from a single gene are actual function performers and greatly increase the functional diversity.… read more here.

Keywords: isoform function; ontology; prediction; gene ontology ... See more keywords

SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments

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recommendations! Published in 2018 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btx716

Abstract: Motivation Gene Ontology (GO) terms are frequently used to score alignments between protein‐protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated:… read more here.

Keywords: ontology; network; measure; ontology terms ... See more keywords
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TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations

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recommendations! Published in 2019 at "Bioinformatics"

DOI: 10.1093/bioinformatics/bty625

Abstract: Summary TreeGrafter is a new software tool for annotating protein sequences using pre‐annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable to… read more here.

Keywords: ontology; tree; ontology terms; gene ontology ... See more keywords