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The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.

Singh M, Bhartiya D, Maini J, Sharma M, Singh AR, Kadarkaraisamy S, Rana R, Sabharwal A, Nanda S, Ramachandran A, Mittal A, Kapoor S, Sehgal P, Asad Z, Kaushik K, Vellarikkal SK, Jagga D, Muthuswami M, Chauhan RK, Leonard E, Priyadarshini R, Halimani M, Malhotra S, Patowary A, Vishwakarma H, Joshi P, Bhardwaj V, Bhaumik A, Bhatt B, Jha A, Kumar A, Budakoti P, Lalwani MK, Meli R, Jalali S, Joshi K, Pal K, Dhiman H, Laddha SV, Jadhav V, Singh N, Pandey V, Sachidanandan C, Ekker SC, Klee EW, Scaria V, Sivasubbu S - Database (Oxford) (2014)

Bottom Line: The credits for contributions can be tracked through a transparent microattribution system.In contrast to other wikis, the Zebrafish GenomeWiki is a 'structured wiki' or rather a 'semantic wiki'.The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search.

View Article: PubMed Central - PubMed

Affiliation: CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India, Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi 110001, India, Acharya Narendra Dev College, Delhi University, Govindpuri, Kalkaji, New Delhi 110019, India, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India, Department of Genetics, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India and Mayo Clinic, Rochester, MN, USA.

ABSTRACT
A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis that active community participation could be a viable option to address this challenge. We present here our approach to create standards for assimilation and sharing of information and a system of open standards for database intercommunication. We have attempted to address this challenge by creating a community-centric solution for zebrafish gene annotation. The Zebrafish GenomeWiki is a 'wiki'-based resource, which aims to provide an altruistic shared environment for collective annotation of the zebrafish genes. The Zebrafish GenomeWiki has features that enable users to comment, annotate, edit and rate this gene-centric information. The credits for contributions can be tracked through a transparent microattribution system. In contrast to other wikis, the Zebrafish GenomeWiki is a 'structured wiki' or rather a 'semantic wiki'. The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search. Database URL: http://genome.igib.res.in/twiki.

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Screenshot of a sample GeneCard entry. In the Zebrafish GenomeWiki, the top panel of the page consists of a genome browser interface. The GeneCard is divided into a number of fields each of which consists of information for a particular gene. All the entries highlighted in blue in the information panel are the linkouts to the respective source databases. The bottom panel of the page provides the information about the revision history of the particular gene including an option to edit the page. The information about the last annotation and the annotator is available at the bottom left corner of every page.
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bau011-F2: Screenshot of a sample GeneCard entry. In the Zebrafish GenomeWiki, the top panel of the page consists of a genome browser interface. The GeneCard is divided into a number of fields each of which consists of information for a particular gene. All the entries highlighted in blue in the information panel are the linkouts to the respective source databases. The bottom panel of the page provides the information about the revision history of the particular gene including an option to edit the page. The information about the last annotation and the annotator is available at the bottom left corner of every page.

Mentions: The Zebrafish GenomeWiki provides a seamless search interface through FishNet, a multi-resource search engine for zebrafish gene annotation. The FishNet query page in turn provides links to the corresponding GeneCard. The main GeneCard page is categorized into a number of subwebs. The subwebs attempt to cover the majority of important data related to zebrafish genomics, including but not limited to human orthologs present in zebrafish, mutants, morpholinos, diseases models, transposon insertion sites and information on noncoding RNAs (Figure 2). Each gene ID is hyperlinked to the main GeneCard entry. A GeneCard provides a vivid explanation of the gene. It consists of a number of entry points such as the Gene ID, GeneName, Transcript ID, Protein ID, Refseq ID, known GeneFunction, GeneOntology, GeneExpression and references. The reference section provides direct links to the related publications from where the information has been extracted. The highlighted entry under each category links to a new web page containing related information and has semantic linkouts wherever necessary. Each GeneCard page also provides links to external web pages. The Zebrafish GenomeWiki is also provided with a sandbox feature that guides the user on how to create new topics.Figure 2.


The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.

Singh M, Bhartiya D, Maini J, Sharma M, Singh AR, Kadarkaraisamy S, Rana R, Sabharwal A, Nanda S, Ramachandran A, Mittal A, Kapoor S, Sehgal P, Asad Z, Kaushik K, Vellarikkal SK, Jagga D, Muthuswami M, Chauhan RK, Leonard E, Priyadarshini R, Halimani M, Malhotra S, Patowary A, Vishwakarma H, Joshi P, Bhardwaj V, Bhaumik A, Bhatt B, Jha A, Kumar A, Budakoti P, Lalwani MK, Meli R, Jalali S, Joshi K, Pal K, Dhiman H, Laddha SV, Jadhav V, Singh N, Pandey V, Sachidanandan C, Ekker SC, Klee EW, Scaria V, Sivasubbu S - Database (Oxford) (2014)

Screenshot of a sample GeneCard entry. In the Zebrafish GenomeWiki, the top panel of the page consists of a genome browser interface. The GeneCard is divided into a number of fields each of which consists of information for a particular gene. All the entries highlighted in blue in the information panel are the linkouts to the respective source databases. The bottom panel of the page provides the information about the revision history of the particular gene including an option to edit the page. The information about the last annotation and the annotator is available at the bottom left corner of every page.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3936183&req=5

bau011-F2: Screenshot of a sample GeneCard entry. In the Zebrafish GenomeWiki, the top panel of the page consists of a genome browser interface. The GeneCard is divided into a number of fields each of which consists of information for a particular gene. All the entries highlighted in blue in the information panel are the linkouts to the respective source databases. The bottom panel of the page provides the information about the revision history of the particular gene including an option to edit the page. The information about the last annotation and the annotator is available at the bottom left corner of every page.
Mentions: The Zebrafish GenomeWiki provides a seamless search interface through FishNet, a multi-resource search engine for zebrafish gene annotation. The FishNet query page in turn provides links to the corresponding GeneCard. The main GeneCard page is categorized into a number of subwebs. The subwebs attempt to cover the majority of important data related to zebrafish genomics, including but not limited to human orthologs present in zebrafish, mutants, morpholinos, diseases models, transposon insertion sites and information on noncoding RNAs (Figure 2). Each gene ID is hyperlinked to the main GeneCard entry. A GeneCard provides a vivid explanation of the gene. It consists of a number of entry points such as the Gene ID, GeneName, Transcript ID, Protein ID, Refseq ID, known GeneFunction, GeneOntology, GeneExpression and references. The reference section provides direct links to the related publications from where the information has been extracted. The highlighted entry under each category links to a new web page containing related information and has semantic linkouts wherever necessary. Each GeneCard page also provides links to external web pages. The Zebrafish GenomeWiki is also provided with a sandbox feature that guides the user on how to create new topics.Figure 2.

Bottom Line: The credits for contributions can be tracked through a transparent microattribution system.In contrast to other wikis, the Zebrafish GenomeWiki is a 'structured wiki' or rather a 'semantic wiki'.The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search.

View Article: PubMed Central - PubMed

Affiliation: CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India, Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi 110001, India, Acharya Narendra Dev College, Delhi University, Govindpuri, Kalkaji, New Delhi 110019, India, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India, Department of Genetics, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India and Mayo Clinic, Rochester, MN, USA.

ABSTRACT
A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis that active community participation could be a viable option to address this challenge. We present here our approach to create standards for assimilation and sharing of information and a system of open standards for database intercommunication. We have attempted to address this challenge by creating a community-centric solution for zebrafish gene annotation. The Zebrafish GenomeWiki is a 'wiki'-based resource, which aims to provide an altruistic shared environment for collective annotation of the zebrafish genes. The Zebrafish GenomeWiki has features that enable users to comment, annotate, edit and rate this gene-centric information. The credits for contributions can be tracked through a transparent microattribution system. In contrast to other wikis, the Zebrafish GenomeWiki is a 'structured wiki' or rather a 'semantic wiki'. The Zebrafish GenomeWiki implements a semantically linked data structure, which in the future would be amenable to semantic search. Database URL: http://genome.igib.res.in/twiki.

Show MeSH