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Annotation of gene product function from high-throughput studies using the Gene Ontology

Helen Attrill, Pascale Gaudet, Rachael P Huntley, Ruth C Lovering, Stacia R Engel, Sylvain Poux, Kimberly M Van Auken, George Georghiou, Marcus C Chibucos, Tanya Z Berardini, Valerie Wood, Harold Drabkin (+7 others)
2019 Database: The Journal of Biological Databases and Curation  
The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of  ...  We present an annotation framework for high-throughput studies that will facilitate good standards in GO curation and, through the use of new high-throughput evidence codes, increase the visibility of  ...  Introduction The Gene Ontology (GO) is one of the most widely used computational resources for assigning functional attributes to genes and their products (1) .  ... 
doi:10.1093/database/baz007 pmid:30715275 pmcid:PMC6355445 fatcat:zdixonld5raffapzefcqdigkku

Annotation of gene product function from high-throughput studies using the Gene Ontology

Helen Louise Attrill, Pascale Gaudet, Rachael P Huntley, Ruth C Lovering, Stacia R Engel, Sylvain Poux, Kimberly M Van Auken, George Georghiou, Marcus C Chibucos, Tanya Z Berardini, Valerie Wood, Harold Drabkin (+10 others)
2019
The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of  ...  We present an annotation framework for high-throughput studies that will facilitate good standards in GO curation and, through the use of new high-throughput evidence codes, increase the visibility of  ...  Introduction The Gene Ontology (GO) is one of the most widely used computational resources for assigning functional attributes to genes and their products (1) .  ... 
doi:10.17863/cam.36649 fatcat:hmtoawg43jefvipt76tumvafee

Gene Ontology annotations at SGD: new data sources and annotation methods

E. L. Hong, R. Balakrishnan, Q. Dong, K. R. Christie, J. Park, G. Binkley, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, B. C. Hitz (+12 others)
2007 Nucleic Acids Research  
Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational  ...  The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae  ...  ACKNOWLEDGEMENTS The SGD project is supported by a P41 grant from the NHGRI HG001315 (J.M.C.) and through the GO Consortium P41 grant from NHGRI HG002273 (co-PI J.M.C).  ... 
doi:10.1093/nar/gkm909 pmid:17982175 pmcid:PMC2238894 fatcat:kwe3m5tfdnehnctlg3ueguw2ca

Gene Ontology: A Resource for Analysis and Interpretation of Alzheimer's Disease Data [chapter]

Barbara Kramarz, Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK, Ruth C. Lovering, Functional Gene Annotation, Preclinical and Fundamental Science, UCL Institute of Cardiovascular Science, University College London, London, UK
2019 Alzheimer's Disease  
The UCL Functional Gene Annotation group focuses on GO annotation of human gene products.  ...  Gene Ontology (GO) is a universal resource for analyses and interpretation of high-throughput biological datasets.  ...  Acknowledgments: The UCL Functional Gene Annotation group has been sup-  ... 
doi:10.15586/alzheimersdisease.2019.ch2 fatcat:zfpkoabcyjbqzhql5qsknxhfcu

Improvements to cardiovascular Gene Ontology

Ruth C. Lovering, Emily C. Dimmer, Philippa J. Talmud
2009 Atherosclerosis  
GO enables the current functional knowledge of individual genes to be used to annotate genomic or proteomic datasets.  ...  Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism.  ...  Use of GO in high-throughput studies As the number of high-throughput methodologies has increased, so has the number of ways in which GO annotation data has been exploited to link experimental results  ... 
doi:10.1016/j.atherosclerosis.2008.10.014 pmid:19046747 pmcid:PMC2706316 fatcat:ytqlfpnwljakvep6uoasqoks4y

The Gene Ontology Resource: 20 years and still GOing strong

2018 Nucleic Acids Research  
The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products.  ...  New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources.  ...  The GO ribbon widget is currently used by the Alliance of Genome Resources. GO annotations from high-throughput experiments.  ... 
doi:10.1093/nar/gky1055 pmid:30395331 pmcid:PMC6323945 fatcat:cex4enabtravtnwrbbme2xhpr4

What we can learn about Escherichia coli through application of Gene Ontology

James C. Hu, Peter D. Karp, Ingrid M. Keseler, Markus Krummenacker, Deborah A. Siegele
2009 Trends in Microbiology  
Gene Ontology (GO) is one of the most successful systems for classifying biological function.  ...  An important and currently limiting step in this process is annotation: categorizing the functions of the genes that comprise the parts list of an organism.  ...  We also thank the members of the GO consortium and the EcoliHub project, without whom our efforts on GO annotation for E. coli would not have been possible.  ... 
doi:10.1016/j.tim.2009.04.004 pmid:19576778 pmcid:PMC3575750 fatcat:fqpgj7kpuje6di4ayb6o2bbo3e

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg, Christine A. Orengo
2013 PLoS Computational Biology  
However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases.  ...  Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable.  ...  We are especially grateful to Rachael Huntley for careful reading of the manuscript and for providing detailed explanations of annotation provenance and methodology in UniProt. Author Contributions  ... 
doi:10.1371/journal.pcbi.1003063 pmid:23737737 pmcid:PMC3667760 fatcat:dyez23i4n5hxjbh3lctoen3uvi

PhenoGO: an integrated resource for the multiscale mining of clinical and biological data

Lee T Sam, Eneida A Mendonça, Jianrong Li, Judith Blake, Carol Friedman, Yves A Lussier
2009 BMC Bioinformatics  
in the Gene Ontology Databases Automated natural language processing (BioMedLEE) and computational ontology (PhenOS) methods were used to derive these relationships from the literature, expanding the  ...  database with information from ten additional species to include over 600,000 phenotypic contexts spanning eleven species from five GO annotation databases.  ...  Acknowledgements Thanks to Tara Borlawsky for her help in generating the data and contributing to the evaluation.  ... 
doi:10.1186/1471-2105-10-s2-s8 pmid:19208196 pmcid:PMC2646241 fatcat:dryuzrqqqnhxviieqa5qj4isfu

The cardiovascular gene annotation initiative: current and future aims

R.C. Lovering, N.H. Campbell, A.N. Melidoni, M. Rodriguez-Lopez, R.P. Huntley, T. Sawford, C. O'Donovan, M. Martin, S. Orchard, H. Hermjakob, M. Mayr, R. Apweiler (+2 others)
2014 Atherosclerosis  
Anatomy of GO annotation GO annotation is the practice of capturing information about a gene product using terms from the Gene Ontology.  ...  Funded by the British Heart Foundation our aim is to provide high-quality annotations to the products of genes relevant to cardiovascular processes and disease. • These annotations are available through  ...  Anatomy of GO annotation GO annotation is the practice of capturing information about a gene product using terms from the Gene Ontology.  ... 
doi:10.1016/j.atherosclerosis.2014.10.062 fatcat:6bi3nthgvzduvibqj5qurjgan4

GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology

Živa Ramšak, Špela Baebler, Ana Rotter, Matej Korbar, Igor Mozetič, Björn Usadel, Kristina Gruden
2013 Nucleic Acids Research  
of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered  ...  GoMapMan is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions.  ...  the technical elements of the set-up.  ... 
doi:10.1093/nar/gkt1056 pmid:24194592 pmcid:PMC3965006 fatcat:tfwfmnboxveyrpvuzkgwvqnpvi

Towards revealing the functions of all genes in plants

Seung Yon Rhee, Marek Mutwil
2014 Trends in Plant Science  
However, functional inference to a general, high-level term in the ontology (e.g., 'binding' GO:0005488) is not useful when trying to determine the role of a gene product.  ...  Need for high-throughput experimental testing platforms Function inference methods typically use internal crossvalidation using a proportion of the gold standard data that was partitioned from the training  ... 
doi:10.1016/j.tplants.2013.10.006 pmid:24231067 fatcat:i6lf2aormbcrhbf6xwpt2l7txi

PomBase: a comprehensive online resource for fission yeast

V. Wood, M. A. Harris, M. D. McDowall, K. Rutherford, B. W. Vaughan, D. M. Staines, M. Aslett, A. Lock, J. Bahler, P. J. Kersey, S. G. Oliver
2011 Nucleic Acids Research  
The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access.  ...  PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries.  ...  ACKNOWLEDGEMENTS The authors thank members of the Ensembl and Ensembl Genomes teams for contributions to the PomBase data pipelines.  ... 
doi:10.1093/nar/gkr853 pmid:22039153 pmcid:PMC3245111 fatcat:g346pl5zdrdq7bv7wwyhu2lgia

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Brad T Sherman, Da Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki
2007 BMC Bioinformatics  
Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis.  ...  Conclusion: The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis.  ...  The contents of this tool and publication do not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations  ... 
doi:10.1186/1471-2105-8-426 pmid:17980028 pmcid:PMC2186358 fatcat:c4prreos5nhfbhkeiwn62zuxym

Muscle Research and Gene Ontology: New standards for improved data integration

Erika Feltrin, Stefano Campanaro, Alexander D Diehl, Elisabeth Ehler, Georgine Faulkner, Jennifer Fordham, Chiara Gardin, Midori Harris, David Hill, Ralph Knoell, Paolo Laveder, Lorenza Mittempergher (+7 others)
2009 BMC Medical Genomics  
The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products.  ...  Conclusion: The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease.  ...  The members of the working group were: Stefano Campanaro, Alexander D. Diehl Acknowledgements The Gene Ontology Consortium is supported by NIH -NHGRI grant HG02273 and by EMBL core funding.  ... 
doi:10.1186/1755-8794-2-6 pmid:19178689 pmcid:PMC2657163 fatcat:tr6xp5wbynbprpm2o4sqcueq7q
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