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UniProt-GOA: A Central Resource for Data Integration and GO Annotation

Mélanie Courtot, Aleksandra Shypitsyna, Elena Speretta, Alexander Holmes, Tony Sawford, Tony Wardell, Maria Jesus Martin, Claire O'Donovan
2015 Workshop on Semantic Web Applications and Tools for Life Sciences  
UniProt-GOA is the largest and most comprehensive open-source contributor of annotations to the GO Consortium annotation effort.  ...  The Gene Ontology (GO) is a well-established, structured QuickGO browser6 or downloaded in a parsable format via the EMBL-EBI [7] and GO Consortium FTP [8] sites.  ...  For many species, no experimental data is available: electronic annotations are the only source of information for biological investigation, and it is therefore critical that solid pipelines for data integration  ... 
dblp:conf/swat4ls/CourtotSSHSWMO15 fatcat:6cosb3jh5ban3g3ogwqco2354y

The UniProt-GO Annotation database in 2011

E. C. Dimmer, R. P. Huntley, Y. Alam-Faruque, T. Sawford, C. O'Donovan, M. J. Martin, B. Bely, P. Browne, W. Mun Chan, R. Eberhardt, M. Gardner, K. Laiho (+43 others)
2011 Nucleic Acids Research  
In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.  ...  The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB  ...  ACKNOWLEDGEMENTS The UniProt Consortium would like to thank all collaborating annotation groups that have enabled inclusion of their annotation data in the UniProt-GOA annotation view.  ... 
doi:10.1093/nar/gkr1048 pmid:22123736 pmcid:PMC3245010 fatcat:gdeuk363knfv5ozq2q7tn254aa

SDADB: a functional annotation database of protein structural domains

Cheng Zeng, Weihua Zhan, Lei Deng
2018 Database: The Journal of Biological Databases and Curation  
SDADB provides associations between gene ontology (GO) terms and SCOP domains calculated with an integrated framework.  ...  Annotating functional terms with individual domains is essential for understanding the functions of full-length proteins. We describe SDADB, a functional annotation database for structural domains.  ...  The GO annotations of sequence homologs are obtained from the UniProt-GOA database (37) .  ... 
doi:10.1093/database/bay064 pmid:29961821 pmcid:PMC6025185 fatcat:qez4htvrdrd65hmtev4fxxwewq

Construction of an Ortholog Database Using the Semantic Web Technology for Integrative Analysis of Genomic Data

Hirokazu Chiba, Hiroyo Nishide, Ikuo Uchiyama, Yoshihiro Yamanishi
2015 PLoS ONE  
Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data  ...  To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary.  ...  Computational resources were provided by the Data Integration and Analysis Facility, National Institute for Basic Biology.  ... 
doi:10.1371/journal.pone.0122802 pmid:25875762 pmcid:PMC4395280 fatcat:ztivbjcq7fftfo7l2ceh366phi

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  
of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation.  ...  Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation  ...  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

The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations [chapter]

Marcus C. Chibucos, Deborah A. Siegele, James C. Hu, Michelle Giglio
2016 Msphere  
The Evidence and Conclusion Ontology (ECO) is a community resource for describing the various types of evidence that are generated during the course of a scientifi c study and which are typically used  ...  Today, over 30 resources, including the Gene Ontology, use the Evidence and Conclusion Ontology to represent both evidence and how annotations are made.  ...  Number of annotations associated with that evidence type is shown at the top left  ... 
doi:10.1007/978-1-4939-3743-1_18 pmid:27812948 fatcat:l72bogmubjezxedcolzy4wn3mq

NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies

Eduardo Zúñiga-León, Ulises Carrasco-Navarro, Francisco Fierro
2018 Genes  
Here we present NeVOmics, Network-based Visualization for Omics, a functional enrichment analysis tool that identifies statistically over-represented biological terms within a given gene/protein set.  ...  NeVOmics is adapted to use updated information from the two main annotation databases: Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG).  ...  GO terms from UniProt-GOA correspond to the version released on 18 October 2018.  ... 
doi:10.3390/genes9120569 pmid:30477135 fatcat:wngulimljrevdagar4ziov7bba

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 (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces  ...  We also thank Chris Mungall for helpful discussions on Chado and GO, and we thank members of the S. pombe research community whose feedback has helped establish priorities for PomBase development.  ... 
doi:10.1093/nar/gkr853 pmid:22039153 pmcid:PMC3245111 fatcat:g346pl5zdrdq7bv7wwyhu2lgia

JaponicusDB: Rapid deployment of a model organism database for an emerging model species [article]

Kim Matthew Rutherford, Midori A Harris, Snezhana Oliferenko, Valerie Wood
2021 bioRxiv   pre-print
By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge  ...  We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to  ...  Acknowledgements 635 We are grateful to the Wellcome Trust for allowing S. O. to  ... 
doi:10.1101/2021.09.23.461587 fatcat:xdrdc3rbovacnddlaxccl3b2fy

Standardized description of scientific evidence using the Evidence Ontology (ECO)

M. C. Chibucos, C. J. Mungall, R. Balakrishnan, K. R. Christie, R. P. Huntley, O. White, J. A. Blake, S. E. Lewis, M. Giglio
2014 Database: The Journal of Biological Databases and Curation  
Also at this site is a tracker for user submission of term requests and questions.  ...  Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics  ...  ., Melissa Haendel and James A. Overton for invaluable discussion on modeling evidence.  ... 
doi:10.1093/database/bau075 pmid:25052702 pmcid:PMC4105709 fatcat:dpcrwmxwajbvbpl26mqk7vab7u

BGDB: a database of bivalent genes

Qingyan Li, Shuabin Lian, Zhiming Dai, Qian Xiang, Xianhua Dai
2013 Database: The Journal of Biological Databases and Curation  
These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently.  ...  Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells.  ...  Firstly the GO annotations in GAF 2.0 file format was downloaded from UniProt-GOA (24, 26) , and secondly, the columns of gene symbol, GO ID, GO term and GO category were extracted and stored in the database  ... 
doi:10.1093/database/bat057 pmid:23894186 pmcid:PMC3724367 fatcat:5tnyto2shrdipabs2mjxcq2swi

ZFIN, The zebrafish model organism database: Updates and new directions

Leyla Ruzicka, Yvonne M. Bradford, Ken Frazer, Douglas G. Howe, Holly Paddock, Sridhar Ramachandran, Amy Singer, Sabrina Toro, Ceri E. Van Slyke, Anne E. Eagle, David Fashena, Patrick Kalita (+8 others)
2015 Genesis  
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research.  ...  structured vocabularies (ontologies) used for data annotation and searching.  ...  Acknowledgments Grant Support: This work was supported by the National Human Genome Research Institute (HG002659, and HG004834) of the National Institutes of Health.  ... 
doi:10.1002/dvg.22868 pmid:26097180 pmcid:PMC4545674 fatcat:tba5jdejl5grxavmzhzgzjfcpa

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

S. Burge, E. Kelly, D. Lonsdale, P. Mutowo-Muellenet, C. McAnulla, A. Mitchell, A. Sangrador-Vegas, S.-Y. Yong, N. Mulder, S. Hunter
2012 Database: The Journal of Biological Databases and Curation  
The InterPro2GO mappings are comprised of the cross-references between these two resources and are the largest source of GO annotation predictions for proteins.  ...  We discuss the unique challenges involved in integrating specific GO terms with entries that may describe a diverse set of proteins, and we illustrate, with examples, how InterPro hierarchies reflect GO  ...  Acknowledgements We thank Emily Dimmer and Claire O'Donovan for their critical reading of this manuscript and Tony Sawford for assistance with protein match counts. Conflict of interest.  ... 
doi:10.1093/database/bar068 pmid:22301074 pmcid:PMC3270475 fatcat:mczeyk6qqrhxpn2aysoyqgocde

The Gene Ontology of eukaryotic cilia and flagella

Paola Roncaglia, Teunis J. P. van Dam, Karen R. Christie, Lora Nacheva, Grischa Toedt, Martijn A. Huynen, Rachael P. Huntley, Toby J. Gibson, Jane Lomax
2017 Cilia  
The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins.  ...  The revised GO and annotations, used in comparative 'before and after' analyses of representative ciliary datasets, improve enrichment results significantly.  ...  ; Dragana Mitic Potkrajac and Ana Stelkic (CCNET) for contributing to gene annotation efforts.  ... 
doi:10.1186/s13630-017-0054-8 pmid:29177046 pmcid:PMC5688719 fatcat:ohsarelpmnf5tiaz27ickkzizm

NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases

Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2015 BMC Genomics  
Enrichment analysis is a widely applied procedure for shedding light on the molecular mechanisms and functions at the basis of phenotypes, for enlarging the dataset of possibly related genes/proteins and  ...  In 143 cases (58%), the network-based procedure extracts GO terms neglected by the standard method, and in 86 cases (35%), some of the newly enriched GO terms are not included in the set of annotations  ...  Human proteins in UniProtKB were annotated with Gene ontology (GO) terms for Biological Process (BP) [26, 35] , as retrieved from the UniProt-GOA web resource [36] .  ... 
doi:10.1186/1471-2164-16-s8-s6 pmid:26110971 pmcid:PMC4480278 fatcat:5lfvejmsyvb7fcnjkrfpn4gipq
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