gene ontology
Semantic Searching Of Biological Documents Using Gene Ontology
... biological_process. Regulation of DNA recombination is any process that modulates the frequency, rate or extent of DNA recombination. Regulation of DNA recombination is a subset of gosubset_prok. Regulation of DNA ...
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Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria
... on Gene Ontology (GO), which defines genes/ proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular ...
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Semi-bipartite graph visualization for gene ontology networks
... measure gene expression level—the activity level of genes—in biological ...the gene expression levels of diseased ...The Gene Ontology [3] is a directed acyclic graph containing known ...
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Semi-bipartite graph visualization for gene ontology networks
... the gene nodes. The reason is that each new gene usually annotates to several new terms, and each new term in turn introduces several new ...are Gene Ontology terms that have no gene ...
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The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
... the Gene Ontology Consortium and by the European Union RTD Programme ‘ Quality of Life and Management of Living Resources ’ QLRI-CT-2001-00981 and QLRI-CT-2001-00015 to GO and UniProtKB-GOA groups at ...
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Disjunctive shared information between ontology concepts: application to Gene Ontology
... two ontology concepts, based on the information content of the disjunctive common ancestors of the concepts being ...to Gene Ontology and its performance was evaluated against state-of-the-art ...
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Empirical study of Gene Ontology based Microarray clustering.
... The Gene Ontology is a graph with 111,672 ...each gene is annotated averagely by 5 GO terms on average, and each term has 15 ...the Gene Ontology, they can form a small graph with the ...
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A task-based approach for Gene Ontology evaluation
... 1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, ...
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Automatic clustering of gene ontology by genetic algorithm
... Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the ...
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Quantifying Protein Function Specificity in the Gene Ontology
... Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures be- tween protein ...
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A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL
... There has been a steady increase of data in ChEMBL over time. There has been a fourfold increase in the total numbers of assays from the first ChEMBL release (ChEMBL1) to the current release (ChEMBL21) which has 1.2 ...
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The Gene Ontology of eukaryotic cilia and flagella
... the Gene Ontology ...of gene function, and the relationships between these ...specific gene products (proteins and RNAs) to capture experimental findings from the scientific lit- erature [7, ...
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The classification of gene products in the molecular biology domain: Realism, objectivity, and the limitations of the Gene Ontology
... the Gene Ontology finds in terms of specificity is that it aims, ultimately, to cover all of molecular biology with the same ...the ontology, worked over by domain experts at ontology ...
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Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
... Using similar patterns, we can also begin to imagine more complex class descriptions that utilise additional expressivity in OWL, such as the use of complement classes to query for genes that is_capable_of_function some ...
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Semi-bipartite graph visualization for gene ontology networks
... Abstract: In this paper we proposed three layout algorithms for semi-bipartite graphs-bipartite graphs with edges within one partition-that emerges from the gene function analysis in bioinformatics. The algorithms ...
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Ontological Realism and Classification: Structures and Concepts in the Gene Ontology
... This paper, and a companion paper (Mayor and Robinson 2013), report an examination of the GO from a variety of perspectives, focusing on two aspects in particular. First, the GO is explicitly rooted in ontological ...
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Fast Gene Ontology based clustering for microarray experiments
... We re-analysed the data set with the goal of finding differ- entially expressed genes (DEGs) between four undifferen- tiated samples (EC_0502, EC_0564, EC_1017 and EC_1740) and 10 differentiated samples (Cc_0915, N_9013, ...
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Fast and simple semantic class assignment for biomedical text
... the Gene Ontology and Cell Type Ontology ...Sequence Ontology false negatives in the data re- flected in the P/R/F values in Table 1, a full 2,050 are due to the single character +, which does ...
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Discovery of MicroRNAs and Transcription Factors Co-Regulatory Modules by integrating Multiple Types of Genomic Data
... ABSTARCT: Gene Ontology (GO) is a structured repository of conception that are associated to one or more gene products through a process referred to as ...from Ontology Based annotated ...
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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
... the Gene Ontology Consortium, for quality control and validation [8, ...the ontology (for example, a cell that is lo- cated in two disconnected locations, or two cell classes that share the same ...
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