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{"title"=>"TRIP Database 2.0: A Manually Curated Information Hub for Accessing TRP Channel Interaction Network", "type"=>"journal", "authors"=>[{"first_name"=>"Young Cheul", "last_name"=>"Shin", "scopus_author_id"=>"37665952800"}, {"first_name"=>"Soo Yong", "last_name"=>"Shin", "scopus_author_id"=>"7403647087"}, {"first_name"=>"Jung Nyeo", "last_name"=>"Chun", "scopus_author_id"=>"55198006700"}, {"first_name"=>"Hyeon Sung", "last_name"=>"Cho", "scopus_author_id"=>"57198105045"}, {"first_name"=>"Jin Muk", "last_name"=>"Lim", "scopus_author_id"=>"55388624600"}, {"first_name"=>"Hong Gee", "last_name"=>"Kim", "scopus_author_id"=>"23389443700"}, {"first_name"=>"Insuk", "last_name"=>"So", "scopus_author_id"=>"35206671400"}, {"first_name"=>"Dongseop", "last_name"=>"Kwon", "scopus_author_id"=>"10143029100"}, {"first_name"=>"Ju Hong", "last_name"=>"Jeon", "scopus_author_id"=>"7202412078"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23071747", "sgr"=>"84867414333", "doi"=>"10.1371/journal.pone.0047165", "scopus"=>"2-s2.0-84867414333", "pui"=>"365840936", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"96b1823f-4380-334f-a9d8-27f94c4d192e", "abstract"=>"Transient receptor potential (TRP) channels are a family of Ca(2+)-permeable cation channels that play a crucial role in biological and disease processes. To advance TRP channel research, we previously created the TRIP (TRansient receptor potential channel-Interacting Protein) Database, a manually curated database that compiles scattered information on TRP channel protein-protein interactions (PPIs). However, the database needs to be improved for information accessibility and data utilization. Here, we present the TRIP Database 2.0 (http://www.trpchannel.org) in which many helpful, user-friendly web interfaces have been developed to facilitate knowledge acquisition and inspire new approaches to studying TRP channel functions: 1) the PPI information found in the supplementary data of referred articles was curated; 2) the PPI summary matrix enables users to intuitively grasp overall PPI information; 3) the search capability has been expanded to retrieve information from 'PubMed' and 'PIE the search' (a specialized search engine for PPI-related articles); and 4) the PPI data are available as sif files for network visualization and analysis using 'Cytoscape'. Therefore, our TRIP Database 2.0 is an information hub that works toward advancing data-driven TRP channel research.", "link"=>"http://www.mendeley.com/research/trip-database-20-manually-curated-information-hub-accessing-trp-channel-interaction-network", "reader_count"=>18, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>4, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Other"=>1, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>4, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>1, "Other"=>1, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>2, "Neuroscience"=>2, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Saudi Arabia"=>1}, "group_count"=>0}

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• http://doi.org/10.1016/j.bbrc.2016.04.138
• http://doi.org/10.1016/j.neulet.2015.10.052
• http://doi.org/10.1016/j.bbamem.2014.10.031
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• http://doi.org/10.1016/j.jcf.2013.05.008
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• http://doi.org/10.1111/febs.12302
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• http://doi.org/10.1016/j.fitote.2014.06.014
• http://doi.org/10.1007/s00424-013-1292-2
• http://doi.org/10.1016/j.bpj.2016.11.3197
• http://doi.org/10.1021/acs.accounts.9b00075

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• {"id"=>"256555447740411904", "text"=>"Our NEW TRP channel DB (TRIP DB 2.0) is published @PLOSONE http://t.co/7GgXwlGQ", "created_at"=>"2012-10-12T00:42:39Z", "user"=>"likesky3", "user_name"=>"Soo-Yong Shin", "user_profile_image"=>"http://a0.twimg.com/profile_images/1462807106/________normal.jpg"}
• {"id"=>"256599366129827841", "text"=>"RT @likesky3: Our NEW TRP channel DB (TRIP DB 2.0) is published @PLOSONE http://t.co/7GgXwlGQ", "created_at"=>"2012-10-12T03:37:10Z", "user"=>"ranzzy", "user_name"=>"Dongseop Kwon", "user_profile_image"=>"http://a0.twimg.com/profile_images/1023883991/41512_621969559_3617_n_normal.jpg"}
• {"id"=>"257449490515116032", "text"=>"#PLOSONE: TRIP Database 2.0: A Manually Curated Information Hub for Accessing TRP Channe... http://t.co/DYU4ndf8", "created_at"=>"2012-10-14T11:55:16Z", "user"=>"beasir", "user_name"=>"JinMukLim", "user_profile_image"=>"http://a0.twimg.com/profile_images/1264546001/limjinmuk_normal.jpg"}

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• {"title"=>"Transient receptor potential channel-interacting protein database", "url"=>"http://en.wikipedia.org/wiki/Transient_receptor_potential_channel-interacting_protein_database", "timestamp"=>"2017-04-20T08:39:05Z"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/559933"], "description"=>"<p>Of the total 579 PPI pairs listed in the TRIP Database 2.0, 83 PPI pairs were retrieved from only the supplementary data.</p>", "links"=>[], "tags"=>["supplementary", "referred"], "article_id"=>230419, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g002", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PPI_information_found_in_the_supplementary_data_of_referred_articles_/230419", "title"=>"PPI information found in the supplementary data of referred articles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:49:47"}
• {"files"=>["https://ndownloader.figshare.com/files/560249"], "description"=>"<p>Users can represent the TRP channel PPI data as a network using the Cytoscape program. (A) The PPI network consists of the relations between TRP channels and their interacting proteins. (B) The extended PPI network includes two different relations: one between TRP channels and their interacting proteins and the other between the interacting proteins.</p>", "links"=>[], "tags"=>["ppi"], "article_id"=>230737, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TRP_channel_PPI_network_/230737", "title"=>"TRP channel PPI network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:51:32"}
• {"files"=>["https://ndownloader.figshare.com/files/560007"], "description"=>"<p>Through clicking a specific TRP channel isotype (TRPV4 here) and then the ‘In detail’ button (A), users can see a tabular presentation, including basic information (B), external database (C), PPI pairs (D), biological process (E), and disease (F).</p>", "links"=>[], "tags"=>["links"], "article_id"=>230499, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g003", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_External_links_and_data_integration_/230499", "title"=>"External links and data integration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:50:12"}
• {"files"=>["https://ndownloader.figshare.com/files/560136"], "description"=>"<p>After clicking the ‘Download’ tab (red box), users can download various sif files according to option settings, such as TRP channel subfamily type and PPI category. In addition, our database offers the option to include the STRING DB contents for data enrichment. The TRIP Database 2.0 also provides a Microsoft Excel and a CSV file.</p>", "links"=>[], "tags"=>["sif"], "article_id"=>230628, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g004", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Downloading_sif_files_/230628", "title"=>"Downloading sif files.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:50:55"}
• {"files"=>["https://ndownloader.figshare.com/files/560490"], "description"=>"<p>The TRIP Database 2.0 provides mouse-over pop-up messages, which are indicated as red boxes, to provide brief information of some icons. (A) Current state of information contents in the ‘PPI summary matrix’. (B) References in the ‘At a glance’. (C) Symbolic names in the ‘At a glance’. (D) Show/hide mark in the ‘In detail’. (E) External databases in the ‘In detail’. (F) PPI pairs in the ‘In detail’. (G) Node in the ‘Interaction Map’ pages.</p>", "links"=>[], "tags"=>["pop-up"], "article_id"=>230981, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g007", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mouse_over_pop_up_help_messages_/230981", "title"=>"Mouse-over pop-up help messages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:52:52"}
• {"files"=>["https://ndownloader.figshare.com/files/559848"], "description"=>"<p>Users can browse the database based on TRP channel subfamilies or isotypes. If users choose to begin their search based on a specific TRP channel subfamily, they will get a summary of the subfamily, including general information (isotypes, amino acid sequences, or UniprotKB IDs) and PPI information, through the PPI summary matrix. If users choose to browse based on a specific TRP channel isotype, they will see lists of TRP channel PPI pairs. For example, the interface might provide one TRP channel with all of its interactors whereas in another instance all TRP channels with one interactor. Users also can start with a keyword search in the database or download the database contents in three formats.</p>", "links"=>[], "tags"=>["diagram", "navigating"], "article_id"=>230331, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_diagram_of_navigating_the_TRIP_Database_2_0_/230331", "title"=>"A diagram of navigating the TRIP Database 2.0.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:49:16"}
• {"files"=>["https://ndownloader.figshare.com/files/560353"], "description"=>"<p>If users click TRP channel subfamily on the left panel, they can see ‘General Information’ and ‘PPI Summary Matrix’. General information provides UniprotKB IDs and amino acid sequences with FASTA, EMBL, or GenBank format. The PPI summary matrix enables users to intuitively grasp overall PPI information. Mouse pop-up help messages (red box) show the current state of information on data contents. By clicking each symbol (S, V, C, or F), users can obtain detailed information on each PPI pair.</p>", "links"=>[], "tags"=>["matrix"], "article_id"=>230844, "categories"=>["Information And Computing Sciences", "Biochemistry", "Neuroscience", "Physiology"], "users"=>["Young-Cheul Shin", "Soo-Yong Shin", "Jung Nyeo Chun", "Hyeon Sung Cho", "Jin Muk Lim", "Hong-Gee Kim", "Insuk So", "Dongseop Kwon", "Ju-Hong Jeon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0047165.g006", "stats"=>{"downloads"=>1, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PPI_summary_matrix_table_/230844", "title"=>"PPI summary matrix table.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 21:52:06"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime