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The Gene Ontology resource: enriching a GOld mine

Gene Ontology Consortium
2020 Nucleic Acids Research  
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products.  ...  for both the ontology and annotations.  ...  ACKNOWLEDGEMENTS We want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/ page/acknowledgments-contributors), and all the authors  ... 
doi:10.1093/nar/gkaa1113 pmid:33290552 pmcid:PMC7779012 fatcat:socxl3x5svamfoc2sobzyvjjoy

The Gene Ontology resource: enriching a GOld mine

Gene Ontology Consortium, Apollo-University Of Cambridge Repository
2021
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products.  ...  for both the ontology and annotations.  ...  INTRODUCTION The Gene Ontology (GO) resource is the world's most comprehensive source of information about the function of genes and gene products (proteins and non-coding RNAs).  ... 
doi:10.17863/cam.64435 fatcat:pwjvycwsjzanxgyuxxflzlk5ly

Overview of the gene ontology task at BioCreative IV

Y. Mao, K. Van Auken, D. Li, C. N. Arighi, P. McQuilton, G. T. Hayman, S. Tweedie, M. L. Schaeffer, S. J. F. Laulederkind, S.-J. Wang, J. Gobeill, P. Ruch (+14 others)
2014 Database: The Journal of Biological Databases and Curation  
Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles.  ...  for the genes in a given article (a concept-recognition task).  ...  Acknowledgements The authors would like to thank Lynette Hirschman, John Wilbur, Cathy Wu  ... 
doi:10.1093/database/bau086 pmid:25157073 pmcid:PMC4142793 fatcat:e72af2fpcnczbbj3hdtidnyy2u

Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

Lei Yang, Xianglong Tang
2014 The Scientific World Journal  
Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO) annotations to overcome the shortcoming and improve the accuracy of predictions.  ...  The false-positive and false-negative interactions in a network usually interfere with prediction.  ...  Acknowledgment The authors thank the editors for valuable comments and suggestions. This paper is supported by the National Science  ... 
doi:10.1155/2014/523634 pmid:24578640 pmcid:PMC3919085 fatcat:fajenv2ct5bobmq3kkbxgi6see

A robust data-driven approach for gene ontology annotation

Y. Li, H. Yu
2014 Database: The Journal of Biological Databases and Curation  
Gene ontology (GO) and GO annotation are important resources for biological information management and knowledge discovery, but the speed of manual annotation became a major bottleneck of database curation  ...  In the post-submission evaluation, we obtained a 10.6% F1 using a simpler setting. Overall, the experimental analysis showed our approaches were robust in both the two tasks.  ...  During the past decades, various ontology resources such as gene ontology (GO) (1) and medical subject headings (MeSH) (2), have been developed and shown great advantage to accelerate the process of biological  ... 
doi:10.1093/database/bau113 pmid:25425037 pmcid:PMC4243380 fatcat:7cfhl42k25cvrl7ia32fpojkee

Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways

Lei Chen, Yu-Hang Zhang, ShaoPeng Wang, YunHua Zhang, Tao Huang, Yu-Dong Cai, Bin Liu
2017 PLoS ONE  
OPEN ACCESS Citation: (2017) Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. PLoS ONE 12(9): e0184129. https://doi.org/10.  ...  Acknowledgments This study was supported by the National Natural Science  ...  Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds.  ... 
doi:10.1371/journal.pone.0184129 pmid:28873455 pmcid:PMC5584762 fatcat:6hu2at6yevenhlsluobzqjncwm

A novel method to quantify gene set functional association based on gene ontology

S. Lv, Y. Li, Q. Wang, S. Ning, T. Huang, P. Wang, J. Sun, Y. Zheng, W. Liu, J. Ai, X. Li
2011 Journal of the Royal Society Interface  
We improved the measurement of semantic similarity to quantify the functional association between gene sets in the context of gene ontology and developed a web toolkit named Gene Set Functional Similarity  ...  Numerous gene sets have been used as molecular signatures for exploring the genetic basis of complex disorders.  ...  to the ontology structure.  ... 
doi:10.1098/rsif.2011.0551 pmid:21998111 pmcid:PMC3306647 fatcat:azziaxcdo5a55lhaubjsryh5hm

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

Sushma Naithani, Daemon Dikeman, Priyanka Garg, Noor Al-Bader, Pankaj Jaiswal
2021 PeerJ  
Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins  ...  Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI.  ...  Grant Disclosures The following grant information was disclosed by the authors: National Science Foundation: NSF IOS-1127112.  ... 
doi:10.7717/peerj.11052 pmid:33777532 pmcid:PMC7971086 fatcat:hn23sqonojgflfxl4rimczazfq

Shared resources, shared costs—leveraging biocuration resources

Sandra Orchard, Henning Hermjakob
2015 Database: The Journal of Biological Databases and Curation  
Approaches taken by two of these, the Gene Ontology annotation effort and the IntAct molecular interaction database, are reviewed in more detail.  ...  Sharing curation effort is a model already being adopted by several data resources.  ...  Similar observations can be made when looking at the granularity of Gene Ontology (GO) annotation added computationally to gene products by automated annotation.  ... 
doi:10.1093/database/bav009 pmid:25776020 pmcid:PMC4360620 fatcat:hqo72b6gbnerzgodftpd4ofvmm

Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer's and other neurological diseases

Shirin C C Saverimuttu, Barbara Kramarz, Milagros Rodríguez-López, Penelope Garmiri, Helen Attrill, Katherine E Thurlow, Marios Makris, Sandra de Miranda Pinheiro, Sandra Orchard, Ruth C Lovering
2021 Database: The Journal of Biological Databases and Curation  
The GO Consortium provides a gold-standard bioinformatics resource used for analysis and interpretation of large biomedical data sets.  ...  However, those studies using high-throughput methods have been compromised by the lack of Gene Ontology (GO) annotations describing the role of proteins in the normal function of the BBB.  ...  and ontology development on an ongoing basis.  ... 
doi:10.1093/database/baab067 pmid:34697638 pmcid:PMC8546235 fatcat:p46an54utbghfb72qyrjwpxfzu

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

Clement Jonquet, Paea LePendu, Sean Falconer, Adrien Coulet, Natasha F. Noy, Mark A. Musen, Nigam H. Shah
2011 Social Science Research Network  
Users often prefer labels from ontologies because they provide a clear point of reference during their search and mining tasks [4, 5, 6] .  ...  Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index-a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources  ...  The NCBO Resource Index won the First prize in the Semantic Web Challenge 2010 (http:// challenge.semanticweb.org/).  ... 
doi:10.2139/ssrn.3199526 fatcat:pjp4jwykt5d23juzfnnnlhxkvu

NCBO Resource Index: Ontology-based search and mining of biomedical resources

Clement Jonquet, Paea LePendu, Sean Falconer, Adrien Coulet, Natalya F. Noy, Mark A. Musen, Nigam H. Shah
2011 Journal of Web Semantics  
Users often prefer labels from ontologies because they provide a clear point of reference during their search and mining tasks [4, 5, 6] .  ...  Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index-a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources  ...  The NCBO Resource Index won the First prize in the Semantic Web Challenge 2010 (http:// challenge.semanticweb.org/).  ... 
doi:10.1016/j.websem.2011.06.005 pmid:21918645 pmcid:PMC3170774 fatcat:4rbicvxpdrf3bgzol2ferrolda

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome

Chisato Yamasaki, Chisato Yamasaki, Jun-ichi Takeda, Takuya Habara, Makoto Ogawa, Akiko Noda, Ryuichi Sakate, Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori
2010 Nature Precedings  
/hinvNaviTop.jsp) and "H-InvDB Enrichment Analysis Tool (HEAT)" , a data mining tool for automatically identifying features specific to a given human gene set (http://hinv.jp/HEAT/ ).  ...  H-InvDB consists of three main views, the Transcript view, the Locus view and the Protein view, and six sub-databases; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view  ...  lang=en H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set.  ... 
doi:10.1038/npre.2010.5272.1 fatcat:nog5ihdzzbfcfgotrucnv45awa

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome

Chisato Yamasaki, Chisato Yamasaki, Jun-ichi Takeda, Takuya Habara, Makoto Ogawa, Akiko Noda, Ryuichi Sakate, Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori
2010 Nature Precedings  
/hinvNaviTop.jsp) and "H-InvDB Enrichment Analysis Tool (HEAT)" , a data mining tool for automatically identifying features specific to a given human gene set (http://hinv.jp/HEAT/ ).  ...  H-InvDB consists of three main views, the Transcript view, the Locus view and the Protein view, and six sub-databases; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view  ...  lang=en H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set.  ... 
doi:10.1038/npre.2010.5272 fatcat:wcqjysxtbvchxm2ukgzobdnjoq

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome

Chisato Yamasaki, Chisato Yamasaki, Jun-ichi Takeda, Takuya Habara, Makoto Ogawa, Akiko Noda, Ryuichi Sakate, Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori
2010 Nature Precedings  
/hinvNaviTop.jsp) and "H-InvDB Enrichment Analysis Tool (HEAT)" , a data mining tool for automatically identifying features specific to a given human gene set (http://hinv.jp/HEAT/ ).  ...  H-InvDB consists of three main views, the Transcript view, the Locus view and the Protein view, and six sub-databases; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view  ...  lang=en H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set.  ... 
doi:10.1038/npre.2010.5271 fatcat:natwwhqmqrb6zkpbzq4j3vzr2y
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