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Community gene annotation in practice

J. E. Loveland, J. G. R. Gilbert, E. Griffiths, J. L. Harrow
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We would like to thank Professor Christopher Tuggle and Dr Claire Rogel-Gaillard, the members of the KOMP, NorCOMM and IRAG annotation groups and the Havana annotation team.  ...  A possible next step in this community annotation effort could be the annotation of gene families across the genomes of multiple species by utilising the experience of experts in the field.  ...  The goal of both of our approaches to community annotation is to manually annotate all of the genes required by the projects, with a much depth of detail as possible.  ... 
doi:10.1093/database/bas009 pmid:22434843 pmcid:PMC3308165 fatcat:lbqygrvrwjgsjkxjov6eafakbe

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

Kathleen M. Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan M. Carland, Salvatore Loguercio, Andrew I. Su
2015 Computer applications in the biosciences : CABIOS  
This comparison revealed high overlap between the analyses, as well as novel findings due to the use of updated annotations and methods.  ...  We aggregated the individual sample results and compared them to the analysis in the original publications.  ...  in two different UCSC RefSeq releases and the number of DE genes identified by different algorithms and annotations.  ... 
doi:10.1093/bioinformatics/btv061 pmid:25637560 pmcid:PMC4443682 fatcat:3gwz4pvy7reaflqx2ojcxzlcqq

GONUTS: the Gene Ontology Normal Usage Tracking System

Daniel P. Renfro, Brenley K. McIntosh, Anand Venkatraman, Deborah A. Siegele, James C. Hu
2011 Nucleic Acids Research  
To support community annotation, GONUTS allows automated creation of gene pages for gene products in UniProt.  ...  The Gene Ontology Normal Usage Tracking System (GONUTS) is a community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins.  ...  We thank Christine Elsik for introducing us to the Gene Ontology and the many members of the GO consortium for their support and feedback. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr907 pmid:22110029 pmcid:PMC3245169 fatcat:dsrhojmevzg33jxd4gfelmei2a

The Gene Ontology (GO) project in 2006

2006 Nucleic Acids Research  
The Gene Ontology (GO) project (http://www. geneontology.org) develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see  ...  The GO Consortium continues to improve to the vocabulary content, reflecting the impact of several novel mechanisms of incorporating community input.  ...  ACKNOWLEDGEMENTS The Gene Ontology Consortium is supported by NIH/NHGRI grant HG02273 and has been supported by grants from the European Union RTD Programme 'Quality of Life and Management of Living Resources  ... 
doi:10.1093/nar/gkj021 pmid:16381878 pmcid:PMC1347384 fatcat:t4dm7drqvjcttkeiakru2iftia

READ: Practical Analysis System of Mouse Transcriptome with the FANTOM Database

Hidemasa Bono, Takeya Kasukawa, Itoshi Nikaido, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki
2001 Genome Informatics Series  
These functional annotations are described in XML, called MaXML (Mouse Annotation XML), to share them in the research community for bulk genomic analysis in silico.  ...  Introduction In addition to algorithmic development of analyzing gene expression data from microarray experiments, practical efforts are going on to get biological inference from the similarity of gene  ... 
doi:10.11234/gi1990.12.232 fatcat:ahmff4uahrdoxhsmrvha5fdhxq

ZFIN: enhancements and updates to the zebrafish model organism database

Y. Bradford, T. Conlin, N. Dunn, D. Fashena, K. Frazer, D. G. Howe, J. Knight, P. Mani, R. Martin, S. A. T. Moxon, H. Paddock, C. Pich (+11 others)
2010 Nucleic Acids Research  
ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications.  ...  Data represented in ZFIN are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations.  ...  The community wiki is powered by Atlassian Confluence software (http://www.altassian.com/software/confluence/). Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq1077 pmid:21036866 pmcid:PMC3013679 fatcat:w23trxqicjdifkyqkbpeqepale

Clinical Annotation Reference Templates: a resource for consistent variant annotation

Shawn Yost, Márton Münz, Shazia Mahamdallie, Anthony Renwick, Elise Ruark, Nazneen Rahman
2018 Wellcome Open Research  
The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome.  ...  The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM.  ...  Acknowledgements We are very grateful to the many different people we had helpful discussions with over the last three years as we were developing the CARTs, in particular within the TGMI, EBI, APPRIS,  ... 
doi:10.12688/wellcomeopenres.14924.1 fatcat:g4khooyiqfbynguuwwp4hvw4jq

Exploring the Development and Maintenance Practices in the Gene Ontology

Shuheng Wu, Besiki Stvilia
2014 Advances in Classification Research Online  
The Gene Ontology (GO) is one of the most widely used and successful bio-ontologies in biomedicine and molecular biology.  ...  What is special about GO as a knowledge organization (KO) system is its collaborative development and maintenance practices, involving diverse communities in collectively developing the Ontology and controlling  ...  For example, a user submitted a request for a new GO term to annotate several genes discussed in the literature: I need a new term for annotating several genes described in PMID 22902739 where they investigate  ... 
doi:10.7152/acro.v24i1.14675 fatcat:w7yq5zxnb5hlrbsxrrtuqvlzd4

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation

Yiannis A I Kourmpetis, Ate van der Burgt, Marco C A M Bink, Cajo J F Ter Braak, Roeland C H J van Ham
2007 In Silico Biology  
We attribute the low frequency with which multiple GO terms are used in Arabidopsis to deviating practices in the genome annotation and curation process between communities of annotators.  ...  This study shows the widespread usage of multiple hierarchically independent GO terms in the functional annotation of genes.  ...  The use of multiple hierarchically independent Gene Ontology terms in gene function prediction and genome annotation References  ... 
pmid:18467770 fatcat:n3akgt72gnedhesigzti5zxfia

Meeting Report: Towards a Critical Assessment of Functional Annotation Experiment (CAFAE) for bacterial genome annotation

Owen White, Nikos Kyrpides
2010 Standards in Genomic Sciences  
genes that could serve as the basis of reviewing in silico gene annotations from the CAFAE participants.  ...  user community. 5) All improved/refined annotations which have been validated against experimentally verified genes would also be available to the annotation community, so annotation producers could use  ... 
doi:10.4056/sigs.1323436 pmid:21304726 pmcid:PMC3035297 fatcat:zzryl2ho2vct7bqrrc6cqwoxdu

A systematic comparison of genome-scale clustering algorithms

Jeremy J Jay, John D Eblen, Yun Zhang, Mikael Benson, Andy D Perkins, Arnold M Saxton, Brynn H Voy, Elissa J Chesler, Michael A Langston
2012 BMC Bioinformatics  
These algorithms cover a broad range of approaches, from conventional techniques such as k-means and hierarchical clustering, to graphical approaches such as k-clique communities, weighted gene co-expression  ...  Jaccard similarity was used to measure each cluster's agreement with every GO and KEGG annotation set, and the highest Jaccard score was assigned to the cluster.  ...  For each annotation source, we found all annotations that match at least 2 genes in a given cluster.  ... 
doi:10.1186/1471-2105-13-s10-s7 pmid:22759431 pmcid:PMC3382433 fatcat:2fdeattqyjad7pd3b37ainkqze

A Systematic Comparison of Genome Scale Clustering Algorithms [chapter]

Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston
2011 Lecture Notes in Computer Science  
These algorithms cover a broad range of approaches, from conventional techniques such as k-means and hierarchical clustering, to graphical approaches such as k-clique communities, weighted gene co-expression  ...  Jaccard similarity was used to measure each cluster's agreement with every GO and KEGG annotation set, and the highest Jaccard score was assigned to the cluster.  ...  For each annotation source, we found all annotations that match at least 2 genes in a given cluster.  ... 
doi:10.1007/978-3-642-21260-4_39 fatcat:kjtudyxtejb7fnoz4xh3t2tfke

A quick guide for student-driven community genome annotation

Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, Mirella Flores-Gonzalez, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown, Surya Saha, Francis Ouellette
2019 PLoS Computational Biology  
Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for  ...  The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly  ...  Train annotators and formalize curation practices Recruiting annotators-Harnessing the crowd. Undergraduate annotators can be recruited by offering annotation as part of their coursework.  ... 
doi:10.1371/journal.pcbi.1006682 pmid:30943207 pmcid:PMC6447164 fatcat:brg35r3tu5grvnqgxz63qyd72u

Bovine Genome Database: new annotation tools for a new reference genome

2019 Nucleic Acids Research  
To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval.  ...  Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism  ...  A separate Apollo instance, the Bovine Apollo Demo, is available with guest login for those who wish to practice annotating genes, but the practice annotations are not permanently maintained at BGD.  ... 
doi:10.1093/nar/gkz944 pmid:31647100 pmcid:PMC7145693 fatcat:jihp4cu7fjc7xgev3btndgyvvq

A quick guide for student-driven community genome annotation [article]

Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, Mirella Flores, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'elia, Susan J. Brown, Surya Saha
2018 arXiv   pre-print
Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for  ...  The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly  ...  The entire community manually curated approximately 530 gene models.  ... 
arXiv:1805.03602v2 fatcat:ykgc4tzxfnhyhgy7ixt365mn6y
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