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Community gene annotation in practice
2012
Database: The Journal of Biological Databases and Curation
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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
2015
Computer applications in the biosciences : CABIOS
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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
2011
Nucleic Acids Research
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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
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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
2001
Genome Informatics Series
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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
2010
Nucleic Acids Research
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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
2018
Wellcome Open Research
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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
2014
Advances in Classification Research Online
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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
2007
In Silico Biology
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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
2010
Standards in Genomic Sciences
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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
2012
BMC Bioinformatics
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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]
2011
Lecture Notes in Computer Science
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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
2019
PLoS Computational Biology
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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
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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]
2018
arXiv
pre-print
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Other Versions
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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