MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison
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{"title"=>"MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison", "type"=>"journal", "authors"=>[{"first_name"=>"Baoxing", "last_name"=>"Song", "scopus_author_id"=>"55482027600"}, {"first_name"=>"Xiaoquan", "last_name"=>"Su", "scopus_author_id"=>"53872101500"}, {"first_name"=>"Jian", "last_name"=>"Xu", "scopus_author_id"=>"57102076500"}, {"first_name"=>"Kang", "last_name"=>"Ning", "scopus_author_id"=>"8887034300"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23145044", "sgr"=>"84869066862", "doi"=>"10.1371/journal.pone.0048998", "scopus"=>"2-s2.0-84869066862", "pui"=>"366041892", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"b1e00e15-3524-3559-8dcb-6ba5daa80d3c", "abstract"=>"The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects.", "link"=>"http://www.mendeley.com/research/metasee-interactive-extendable-visualization-toolbox-metagenomic-sample-analysis-comparison", "reader_count"=>79, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>27, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>2, "Student > Master"=>8, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>27, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>2, "Student > Master"=>8, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>7, "Mathematics"=>1, "Agricultural and Biological Sciences"=>55, "Medicine and Dentistry"=>2, "Social Sciences"=>1, "Computer Science"=>3, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>55}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>6}}, "reader_count_by_country"=>{"Canada"=>2, "Sweden"=>1, "Netherlands"=>1, "Belgium"=>1, "United States"=>3, "Brazil"=>1, "France"=>3, "Portugal"=>1, "Germany"=>1, "India"=>1, "Russia"=>1, "Spain"=>2}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4434613", "https://ndownloader.figshare.com/files/4434628"], "description"=>"<div><p>The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects.</p></div>", "links"=>[], "tags"=>["data sample sources", "visualization tool", "NGS", "data visualization", "core visualization engine", "Extendable Visualization Toolbox", "Metagenomic Sample Analysis", "metagenomic data visualization", "MetaSee", "III", "II", "visualization effects", "metagenomic samples"], "article_id"=>1083675, "categories"=>["Microbiology", "Genetics", "Biotechnology", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Baoxing Song", "Xiaoquan Su", "Jian Xu", "Kang Ning"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048998.s001", "https://dx.doi.org/10.1371/journal.pone.0048998.s002"], "stats"=>{"downloads"=>4, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MetaSee_An_Interactive_and_Extendable_Visualization_Toolbox_for_Metagenomic_Sample_Analysis_and_Comparison_/1083675", "title"=>"MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-08 14:50:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/4434766"], "description"=>"<p>(A) Global view, (B) Taxa view with pie-chart format, (C) Taxa view with bar-chart format.</p>", "links"=>[], "tags"=>["data sample sources", "visualization tool", "NGS", "data visualization", "core visualization engine", "Extendable Visualization Toolbox", "Metagenomic Sample Analysis", "metagenomic data visualization", "MetaSee", "III", "II", "visualization effects", "metagenomic samples"], "article_id"=>216054, "categories"=>["Microbiology", "Genetics", "Biotechnology", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Baoxing Song", "Xiaoquan Su", "Jian Xu", "Kang Ning"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048998.g004"], "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_across_multiple_samples_/216054", "title"=>"Comparison across multiple samples.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-08 14:50:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/4434658"], "description"=>"<p>(A) The visualization result of MEGAN with taxonomy components of two metagenomic samples. (B) The visualization user interface of Strainer (The visualization of components of metagenomics in micro-perspective). The comparison between a component of a metagenome sample and a genome. (C) The visualization user interface of BLASTatla (The visualization of components of metagenomics in macro-perspective: The comparison among a component of metagenome and multiple genomes). (D) Contig and gene annotation visualization of IMG/M. (E) The visualization user interface of Krona. This is the user interface of comparison of four saliva microbiomes. (F) The metagenome visualization result of iTOL with default parameters.</p>", "links"=>[], "tags"=>["data sample sources", "visualization tool", "NGS", "data visualization", "core visualization engine", "Extendable Visualization Toolbox", "Metagenomic Sample Analysis", "metagenomic data visualization", "MetaSee", "III", "II", "visualization effects", "metagenomic samples"], "article_id"=>215626, "categories"=>["Microbiology", "Genetics", "Biotechnology", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Baoxing Song", "Xiaoquan Su", "Jian Xu", "Kang Ning"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0048998.g001"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Screenshot_of_current_metagenomic_visualization_effects_/215626", "title"=>"Screenshot of current metagenomic visualization effects.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-08 14:50:43"}
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Relative Metric

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