{"id":"https://openalex.org/W1968632482","doi":"https://doi.org/10.1186/1471-2105-13-s9-s7","title":"DTome: a web-based tool for drug-target interactome construction","display_name":"DTome: a web-based tool for drug-target interactome construction","publication_year":2012,"publication_date":"2012-06-01","ids":{"openalex":"https://openalex.org/W1968632482","doi":"https://doi.org/10.1186/1471-2105-13-s9-s7","mag":"1968632482"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s9-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s9-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S9-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S9-S7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052779340","display_name":"Jingchun Sun","orcid":"https://orcid.org/0000-0002-3284-7973"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jingchun Sun","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010253402","display_name":"Yonghui Wu","orcid":"https://orcid.org/0000-0002-6780-6135"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yonghui Wu","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084072550","display_name":"Hua Xu","orcid":"https://orcid.org/0000-0002-5274-4672"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hua Xu","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006688612","display_name":"Zhongming Zhao","orcid":"https://orcid.org/0000-0002-3477-0914"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]},{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhongming Zhao","raw_affiliation_strings":["Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA"],"affiliations":[{"raw_affiliation_string":"Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5052779340"],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.1831,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.95618202,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"S9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9790999889373779,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/drugbank","display_name":"DrugBank","score":0.870202362537384},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.683198869228363},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6147692203521729},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6007212400436401},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5946875810623169},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.5167517066001892},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.511683464050293},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4445188641548157},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3938448429107666},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3586702346801758},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.21392866969108582},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15071028470993042},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.14973163604736328},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09175309538841248}],"concepts":[{"id":"https://openalex.org/C155261790","wikidata":"https://www.wikidata.org/wiki/Q1122544","display_name":"DrugBank","level":3,"score":0.870202362537384},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.683198869228363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6147692203521729},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6007212400436401},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5946875810623169},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.5167517066001892},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.511683464050293},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4445188641548157},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3938448429107666},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3586702346801758},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.21392866969108582},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15071028470993042},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.14973163604736328},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09175309538841248},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1471-2105-13-s9-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s9-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S9-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2378161","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3372450","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s9-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s9-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S9-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1070438488","display_name":null,"funder_award_id":"NARSAD","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4838924695","display_name":null,"funder_award_id":"NCI R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320311440","display_name":"National Alliance for Research on Schizophrenia and Depression","ror":"https://ror.org/03a63f080"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1968632482.pdf","grobid_xml":"https://content.openalex.org/works/W1968632482.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1504533062","https://openalex.org/W1544009106","https://openalex.org/W1895993106","https://openalex.org/W1980548655","https://openalex.org/W2002915579","https://openalex.org/W2009313526","https://openalex.org/W2009405916","https://openalex.org/W2010768245","https://openalex.org/W2017274683","https://openalex.org/W2037442572","https://openalex.org/W2061136308","https://openalex.org/W2062533676","https://openalex.org/W2069676201","https://openalex.org/W2070925211","https://openalex.org/W2076764146","https://openalex.org/W2085360366","https://openalex.org/W2086078635","https://openalex.org/W2087698552","https://openalex.org/W2094791588","https://openalex.org/W2097698606","https://openalex.org/W2099787654","https://openalex.org/W2103205725","https://openalex.org/W2108069034","https://openalex.org/W2110065044","https://openalex.org/W2113072832","https://openalex.org/W2124757426","https://openalex.org/W2130687290","https://openalex.org/W2134672568","https://openalex.org/W2138512826","https://openalex.org/W2144656637","https://openalex.org/W2146653758","https://openalex.org/W2150065588","https://openalex.org/W2150934340","https://openalex.org/W2152285853","https://openalex.org/W2153121902","https://openalex.org/W2154896031","https://openalex.org/W2154947819","https://openalex.org/W2155142785","https://openalex.org/W2159636537","https://openalex.org/W2163480486","https://openalex.org/W2164928285","https://openalex.org/W2166963829","https://openalex.org/W2170146596","https://openalex.org/W2184417913","https://openalex.org/W2917431650","https://openalex.org/W4237095724"],"related_works":["https://openalex.org/W2137827821","https://openalex.org/W2803206732","https://openalex.org/W2431109715","https://openalex.org/W1964657534","https://openalex.org/W2070692310","https://openalex.org/W2017360600","https://openalex.org/W4200184670","https://openalex.org/W2402340532","https://openalex.org/W2908134064","https://openalex.org/W2226749982"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Understanding":[2],"drug":[3,9,29,66,146,190,209,241,252,255],"bioactivities":[4],"is":[5,18,48,106,178],"crucial":[6],"for":[7,60,199],"early-stage":[8],"discovery,":[10],"toxicology":[11],"studies":[12],"and":[13,44,86,112,127,135,152,162,170,197,214,254],"clinical":[14],"trials.":[15],"Network":[16],"pharmacology":[17],"a":[19,32,57,72,97,109,113,130,158,246],"promising":[20,198],"approach":[21],"to":[22,50,55,75,123,165,168],"better":[23],"understand":[24],"the":[25,65,87,93,172,188,192,200,237],"molecular":[26,238],"mechanisms":[27,239],"of":[28,35,108,139,202,240,251],"bioactivities.":[30],"With":[31],"dramatic":[33],"increase":[34],"rich":[36],"data":[37],"sources":[38],"that":[39],"document":[40],"drugs'":[41],"structural,":[42],"chemical,":[43],"biological":[45],"activities,":[46],"it":[47],"necessary":[49],"develop":[51],"an":[52],"automated":[53],"tool":[54,99,119,177,194,247],"construct":[56,76,129],"drug-target":[58,77,148],"network":[59,132,160,225],"candidate":[61,125],"drugs,":[62,205,208],"thus":[63],"facilitating":[64],"discovery":[67],"process.":[68],"Results":[69],"We":[70,243],"designed":[71],"computational":[73],"workflow":[74],"networks":[78],"from":[79],"different":[80],"knowledge":[81],"bases":[82],"including":[83],"DrugBank,":[84],"PharmGKB,":[85],"PINA":[88],"database.":[89],"To":[90],"automatically":[91],"implement":[92],"workflow,":[94],"we":[95,156],"created":[96],"web-based":[98,121],"called":[100],"DTome":[101,118,131,173,176,193,224],"(Drug-Target":[102],"interactome":[103],"tool),":[104],"which":[105],"comprised":[107],"database":[110],"schema":[111],"user-friendly":[114],"web":[115],"interface.":[116],"The":[117,141,175,222],"utilizes":[120],"queries":[122],"search":[124],"drugs":[126],"then":[128],"by":[133],"extracting":[134],"integrating":[136],"four":[137,142],"types":[138,143],"interactions.":[140,154,257],"are":[144],"adverse":[145,206,256],"interactions,":[147,149],"drug-gene":[150],"associations,":[151],"target-/gene-protein":[153],"Additionally,":[155],"provided":[157],"detailed":[159],"analysis":[161],"visualization":[163],"process":[164],"illustrate":[166],"how":[167],"analyze":[169],"interpret":[171],"network.":[174],"publicly":[179],"available":[180],"at":[181],"http://bioinfo.mc.vanderbilt.edu/DTome":[182],".":[183],"Conclusions":[184],"As":[185],"demonstrated":[186],"with":[187,218,228],"antipsychotic":[189],"clozapine,":[191],"was":[195],"effective":[196],"investigation":[201],"relationships":[203],"among":[204],"interaction":[207],"primary":[210],"targets,":[211],"drug-associated":[212],"genes,":[213],"proteins":[215],"directly":[216],"interacting":[217],"targets":[219,253],"or":[220],"genes.":[221],"resultant":[223],"provides":[226],"researchers":[227],"direct":[229],"insights":[230],"into":[231],"their":[232],"interest":[233],"drug(s),":[234],"such":[235,245],"as":[236],"actions.":[242],"believe":[244],"can":[248],"facilitate":[249],"identification":[250]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
