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SALON ontology for the formal description of sequence alignments
BackgroundInformation provided by high-throughput sequencing platforms allows the collection of content-rich data about biological sequences and...
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The Ontology of Biological Attributes (OBA)—computational traits for the life sciences
Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or...
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The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
BackgroundWith the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that...
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A process ontology of organisms and its connection to biological individuality concepts
Recent research uncovering extraordinary organismal complexity (e.g., extent of symbiotic associations, genetic exchange between organisms) has led...
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Integrative comparative analysis of avian chromosome evolution by in-silico map** of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions
Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds....
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Automatic consistency assurance for literature-based gene ontology annotation
BackgroundLiterature-based gene ontology (GO) annotation is a process where expert curators use uniform expressions to describe gene functions...
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Identification of Chemical–Disease Associations Through Integration of Molecular Fingerprint, Gene Ontology and Pathway Information
AbstractThe identification of chemical–disease association types is helpful not only to discovery lead compounds and study drug repositioning, but...
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A Power Law Semantic Similarity from Gene Ontology
Currently, there is a massive data generation in the most diverse areas of knowledge, as bioinformatics that generates huge amounts of data,...
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MetaTron: advancing biomedical annotation empowering relation annotation and collaboration
BackgroundThe constant growth of biomedical data is accompanied by the need for new methodologies to effectively and efficiently extract...
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Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images
BackgroundImmunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple...
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NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding
Machine reading (MR) is essential for unlocking valuable knowledge contained in millions of existing biomedical documents. Over the last two decades
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Food system resilience: ontology development and impossible trinities
BackgroundGiven the polysemy of the concept resilience, is it possible to have a unified conceptualisation of food system resilience? This paper...
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Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data
BackgroundWith the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts...
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TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction
BackgroundDatabases are fundamental to advance biomedical science. However, most of them are populated and updated with a great deal of human effort....
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Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations
BackgroundThe hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell...
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Finding Gene Associations by Text Mining and Annotating it with Gene Ontology
Digitalization of the research articles and their maintenance in a database was the first stage toward the development of biomedical research. With...
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Transcriptomics for Drought Stress Mediated by Biological Processes in-relation to Key Regulated Pathways in Gossypium darwinii
BackgroundWild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and...
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Man in Relation to the World: Umwelt–Welt Transition
In the corpus of phenomenological philosophy (as far as it is influenced by the works of Jacob von Uexküll and the debate of phenomenologists with...
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The Relation Between Ashaninka Amazonian Society and Cultivated Acanthaceae Plants
The article discusses the relationships between Ashaninka people from Peruvian Amazonia and the ibinishi ethnotaxon corresponding to several species...
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Proteome alterations in human autopsy tissues in relation to time after death
Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its...
