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961por Masci, Anna Maria, Arighi, Cecilia N, Diehl, Alexander D, Lieberman, Anne E, Mungall, Chris, Scheuermann, Richard H, Smith, Barry, Cowell, Lindsay G“…BACKGROUND: Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. …”
Publicado 2009
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962por Washington, Nicole L., Haendel, Melissa A., Mungall, Christopher J., Ashburner, Michael, Westerfield, Monte, Lewis, Suzanna E.“…To describe phenotypes using ontologies, we used an Entity-Quality (EQ) methodology, wherein the affected entity (E) and how it is affected (Q) are recorded using terms from a variety of ontologies. …”
Publicado 2009
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963por Huntley, Rachael P., Binns, David, Dimmer, Emily, Barrell, Daniel, O’Donovan, Claire, Apweiler, Rolf“…The Gene Ontology (GO) has proven to be a valuable resource for functional annotation of gene products. …”
Publicado 2009
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964por Dahdul, Wasila M., Balhoff, James P., Engeman, Jeffrey, Grande, Terry, Hilton, Eric J., Kothari, Cartik, Lapp, Hilmar, Lundberg, John G., Midford, Peter E., Vision, Todd J., Westerfield, Monte, Mabee, Paula M.“…A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). …”
Publicado 2010
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965por Richards, Adam J., Muller, Brian, Shotwell, Matthew, Cowart, L. Ashley, Rohrer, Bäerbel, Lu, Xinghua“…The study of gene set function most commonly makes use of controlled vocabulary in the form of ontology annotations. For a given gene set, the statistical significance of observing these annotations or ‘enrichment’ may be tested using a number of methods. …”
Publicado 2010
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966“…Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. …”
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967“…Results: Here, we introduce MedSim, a novel approach for ranking candidate genes for a particular disease based on functional comparisons involving the Gene Ontology. MedSim uses functional annotations of known disease genes for assessing the similarity of diseases as well as the disease relevance of candidate genes. …”
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968por Kupershmidt, Ilya, Su, Qiaojuan Jane, Grewal, Anoop, Sundaresh, Suman, Halperin, Inbal, Flynn, James, Shekar, Mamatha, Wang, Helen, Park, Jenny, Cui, Wenwu, Wall, Gregory D., Wisotzkey, Robert, Alag, Satnam, Akhtari, Saeid, Ronaghi, Mostafa“…The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. …”
Publicado 2010
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970por de Lima Morais, David A., Fang, Hai, Rackham, Owen J. L., Wilson, Derek, Pethica, Ralph, Chothia, Cyrus, Gough, Julian“…The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO.…”
Publicado 2011
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971“…In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. …”
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972“…This approach is applied to data in Cell System Ontology which is a comprehensive ontology that represents complex biological pathways with dynamics and visualization. …”
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973por Savarimuthu Francis, Santiyagu M., Larsen, Jill E., Pavey, Sandra J., Duhig, Edwina E., Clarke, Belinda E., Bowman, Rayleen V., Hayward, Nick K., Fong, Kwun M., Yang, Ian A.“…Our secondary aim was to identify gene ontologies common to airway obstruction, indicated by impaired FEV(1) and KCO. …”
Publicado 2011
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974por Gómez, Antonio, Cedano, Juan, Amela, Isaac, Planas, Antoni, Piñol, Jaume, Querol, Enrique“…RESULTS: In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in Mycoplasma genitalium. …”
Publicado 2011
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975“…Structured information provided by manual annotation of proteins with Gene Ontology concepts represents a high-quality reliable data source for the research community. …”
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976por Hastings, Janna, Chepelev, Leonid, Willighagen, Egon, Adams, Nico, Steinbeck, Christoph, Dumontier, Michel“…One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. …”
Publicado 2011
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977Identifying Highly Conserved and Highly Differentiated Gene Ontology Categories in Human Populationspor Jiang, Yongshuai, Zhang, Ruijie, Sun, Peng, Tang, Guoping, Zhang, Xuehong, Wang, Xing, Guo, Xiaodan, Wang, Qiuyu, Li, Xia“…In this study, we conducted a population genetic study using the HapMap genotype data to identify certain special Gene Ontology (GO) categories associated with high/low genetic difference among 11 Hapmap populations. …”
Publicado 2011
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978por Hoehndorf, Robert, Ngonga Ngomo, Axel-Cyrille, Pyysalo, Sampo, Ohta, Tomoko, Oellrich, Anika, Rebholz-Schuhmann, Dietrich“…In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. …”
Publicado 2011
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979por Prodanov, Dimiter“…Instrumental for the latter feat was the construction of a data ontology representing the common measurement data model. …”
Publicado 2011
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980“…We then briefly describe SKELETOME, a community-driven knowledge curation platform that is underpinned by the Bone Dysplasia Ontology. SKELETOME enables domain experts to use, refine and extend and apply the ontology without any prior ontology engineering experience--to advance the body of knowledge in the skeletal dysplasia field. …”
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