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Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
BACKGROUND: The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a “Wiki-based” approach to take ad...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847265/ https://www.ncbi.nlm.nih.gov/pubmed/27118214 http://dx.doi.org/10.1186/s12864-016-2629-y |
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author | Chen, I-Min A. Markowitz, Victor M. Palaniappan, Krishna Szeto, Ernest Chu, Ken Huang, Jinghua Ratner, Anna Pillay, Manoj Hadjithomas, Michalis Huntemann, Marcel Mikhailova, Natalia Ovchinnikova, Galina Ivanova, Natalia N. Kyrpides, Nikos C. |
author_facet | Chen, I-Min A. Markowitz, Victor M. Palaniappan, Krishna Szeto, Ernest Chu, Ken Huang, Jinghua Ratner, Anna Pillay, Manoj Hadjithomas, Michalis Huntemann, Marcel Mikhailova, Natalia Ovchinnikova, Galina Ivanova, Natalia N. Kyrpides, Nikos C. |
author_sort | Chen, I-Min A. |
collection | PubMed |
description | BACKGROUND: The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a “Wiki-based” approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation. RESULTS: Here, we present a different approach, relying on tightly integrated method rather than “Wiki-based” method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existing IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review. CONCLUSION: By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies. |
format | Online Article Text |
id | pubmed-4847265 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-48472652016-04-28 Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system Chen, I-Min A. Markowitz, Victor M. Palaniappan, Krishna Szeto, Ernest Chu, Ken Huang, Jinghua Ratner, Anna Pillay, Manoj Hadjithomas, Michalis Huntemann, Marcel Mikhailova, Natalia Ovchinnikova, Galina Ivanova, Natalia N. Kyrpides, Nikos C. BMC Genomics Software BACKGROUND: The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a “Wiki-based” approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation. RESULTS: Here, we present a different approach, relying on tightly integrated method rather than “Wiki-based” method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existing IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review. CONCLUSION: By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies. BioMed Central 2016-04-26 /pmc/articles/PMC4847265/ /pubmed/27118214 http://dx.doi.org/10.1186/s12864-016-2629-y Text en © Chen et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Chen, I-Min A. Markowitz, Victor M. Palaniappan, Krishna Szeto, Ernest Chu, Ken Huang, Jinghua Ratner, Anna Pillay, Manoj Hadjithomas, Michalis Huntemann, Marcel Mikhailova, Natalia Ovchinnikova, Galina Ivanova, Natalia N. Kyrpides, Nikos C. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system |
title | Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system |
title_full | Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system |
title_fullStr | Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system |
title_full_unstemmed | Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system |
title_short | Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system |
title_sort | supporting community annotation and user collaboration in the integrated microbial genomes (img) system |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847265/ https://www.ncbi.nlm.nih.gov/pubmed/27118214 http://dx.doi.org/10.1186/s12864-016-2629-y |
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