{"id":"https://openalex.org/W4392817267","doi":"https://doi.org/10.1186/s13321-024-00826-z","title":"A new workflow for the effective curation of membrane permeability data from open ADME information","display_name":"A new workflow for the effective curation of membrane permeability data from open ADME information","publication_year":2024,"publication_date":"2024-03-14","ids":{"openalex":"https://openalex.org/W4392817267","doi":"https://doi.org/10.1186/s13321-024-00826-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/38481269"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-024-00826-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00826-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00826-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00826-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018312648","display_name":"Tsuyoshi Esaki","orcid":"https://orcid.org/0000-0001-8780-6346"},"institutions":[{"id":"https://openalex.org/I133984924","display_name":"Doshisha University","ror":"https://ror.org/01fxdkm29","country_code":"JP","type":"education","lineage":["https://openalex.org/I133984924"]},{"id":"https://openalex.org/I171494771","display_name":"Shiga University","ror":"https://ror.org/01vvhy971","country_code":"JP","type":"education","lineage":["https://openalex.org/I171494771"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Tsuyoshi Esaki","raw_affiliation_strings":["Faculty of Culture and Information Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan. tsuyoshi-esaki@biwako.shiga-u.ac.jp","Faculty of Data Science, Shiga University, 1-1-1 Banba, Hikone, Shiga, 522-8522, Japan. tsuyoshi-esaki@biwako.shiga-u.ac.jp","Faculty of Data Science, Shiga University, 1-1-1 Banba, Hikone, Shiga, 522-8522, Japan","Faculty of Culture and Information Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Culture and Information Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan. tsuyoshi-esaki@biwako.shiga-u.ac.jp","institution_ids":["https://openalex.org/I133984924"]},{"raw_affiliation_string":"Faculty of Data Science, Shiga University, 1-1-1 Banba, Hikone, Shiga, 522-8522, Japan. tsuyoshi-esaki@biwako.shiga-u.ac.jp","institution_ids":["https://openalex.org/I171494771"]},{"raw_affiliation_string":"Faculty of Data Science, Shiga University, 1-1-1 Banba, Hikone, Shiga, 522-8522, Japan","institution_ids":["https://openalex.org/I171494771"]},{"raw_affiliation_string":"Faculty of Culture and Information Science, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan","institution_ids":["https://openalex.org/I133984924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001878736","display_name":"Tomoki Yonezawa","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tomoki Yonezawa","raw_affiliation_strings":["Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038763185","display_name":"Kazuyoshi Ikeda","orcid":"https://orcid.org/0000-0002-8433-8206"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]},{"id":"https://openalex.org/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazuyoshi Ikeda","raw_affiliation_strings":["Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan","HPC-and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 4230-0045, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"HPC-and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 4230-0045, Japan","institution_ids":["https://openalex.org/I4210150921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5018312648"],"corresponding_institution_ids":["https://openalex.org/I133984924","https://openalex.org/I171494771"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":4.1487,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.94524316,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"16","issue":"1","first_page":"30","last_page":"30"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9972000122070312,"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/T10570","display_name":"Drug Transport and Resistance Mechanisms","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chembl","display_name":"chEMBL","score":0.890596866607666},{"id":"https://openalex.org/keywords/adme","display_name":"ADME","score":0.8125247359275818},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8077661991119385},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7127863764762878},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.6299964785575867},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5852120518684387},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.4264165163040161},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34541940689086914},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31642580032348633},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.30771851539611816},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.28021132946014404},{"id":"https://openalex.org/keywords/in-vitro","display_name":"In vitro","score":0.20549964904785156},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08384251594543457}],"concepts":[{"id":"https://openalex.org/C63222358","wikidata":"https://www.wikidata.org/wiki/Q6120337","display_name":"chEMBL","level":3,"score":0.890596866607666},{"id":"https://openalex.org/C69366308","wikidata":"https://www.wikidata.org/wiki/Q2272286","display_name":"ADME","level":3,"score":0.8125247359275818},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8077661991119385},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7127863764762878},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.6299964785575867},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5852120518684387},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.4264165163040161},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34541940689086914},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31642580032348633},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.30771851539611816},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.28021132946014404},{"id":"https://openalex.org/C202751555","wikidata":"https://www.wikidata.org/wiki/Q221681","display_name":"In vitro","level":2,"score":0.20549964904785156},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08384251594543457},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-024-00826-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00826-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00826-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:38481269","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38481269","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10938840","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10938840","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10938840/pdf/13321_2024_Article_826.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:2bcbc21b9dbd471cbd991451510adb17","is_oa":true,"landing_page_url":"https://doaj.org/article/2bcbc21b9dbd471cbd991451510adb17","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 16, Iss 1, Pp 1-11 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-024-00826-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00826-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00826-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3447499788","display_name":null,"funder_award_id":"JP23K14382","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320327566","display_name":"Mitsubishi Tanabe Pharma Corporation","ror":"https://ror.org/038ehsm73"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392817267.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1486751963","https://openalex.org/W1516634954","https://openalex.org/W1835740130","https://openalex.org/W1904678284","https://openalex.org/W1964426728","https://openalex.org/W1972650279","https://openalex.org/W1982292082","https://openalex.org/W1987652341","https://openalex.org/W1988137261","https://openalex.org/W2016003728","https://openalex.org/W2046827775","https://openalex.org/W2073347694","https://openalex.org/W2084375116","https://openalex.org/W2091940856","https://openalex.org/W2096541451","https://openalex.org/W2128245586","https://openalex.org/W2148083369","https://openalex.org/W2170484170","https://openalex.org/W2170711396","https://openalex.org/W2305293558","https://openalex.org/W2509990821","https://openalex.org/W2533151130","https://openalex.org/W2535436227","https://openalex.org/W2603033062","https://openalex.org/W2902000771","https://openalex.org/W2903800243","https://openalex.org/W2963832292","https://openalex.org/W2972497960","https://openalex.org/W3009999522","https://openalex.org/W3014476516","https://openalex.org/W3023983310","https://openalex.org/W3047697246","https://openalex.org/W3082081167","https://openalex.org/W3108856375","https://openalex.org/W3174653015","https://openalex.org/W3194368700","https://openalex.org/W4232529163","https://openalex.org/W4310102410","https://openalex.org/W4315778078","https://openalex.org/W4320558475","https://openalex.org/W4366090395","https://openalex.org/W4388455891"],"related_works":["https://openalex.org/W3005441379","https://openalex.org/W4207063555","https://openalex.org/W2604173773","https://openalex.org/W2997728144","https://openalex.org/W4210747027","https://openalex.org/W2000985969","https://openalex.org/W2770765812","https://openalex.org/W2405266681","https://openalex.org/W3117153716","https://openalex.org/W2791678506"],"abstract_inverted_index":{"Membrane":[0],"permeability":[1,11],"is":[2,17,141,176,238,330],"an":[3],"in":[4,26,74,93,121,138,192,264,313,332],"vitro":[5,94],"parameter":[6,25],"that":[7,184],"represents":[8],"the":[9,30,35,48,81,116,125,132,164,173,193,221,260,287,296,322,333],"apparent":[10],"(Papp)":[12],"of":[13,92,103,118,134,166,172,188,208,226,262,275,289,319,324],"a":[14,18,107,181,251],"compound,":[15],"and":[16,23,57,84,128,160,196,217,244,258,298,304],"key":[19],"absorption,":[20],"distribution,":[21],"metabolism,":[22],"excretion":[24],"drug":[27,269],"development.":[28],"Although":[29],"Caco-2":[31],"cell":[32,38,44,63,86,198],"lines":[33,39,87,199],"are":[34],"most":[36],"used":[37,68,151],"to":[40,69,152,155,219,308],"measure":[41],"Papp,":[42],"other":[43,317],"lines,":[45,64],"such":[46,328],"as":[47],"Madin-Darby":[49],"Canine":[50,60],"Kidney":[51,54,61],"(MDCK),":[52],"LLC-Pig":[53],"1":[55],"(LLC-PK1),":[56],"Ralph":[58],"Russ":[59],"(RRCK)":[62],"can":[65,241,281],"also":[66],"be":[67,242,282],"estimate":[70],"Papp.":[71],"Therefore,":[72],"constructing":[73,311],"silico":[75,139,265,314],"models":[76,140,154,266,280,315],"for":[77,136,254,267,301,316],"Papp":[78,95,189],"estimation":[79],"using":[80,203],"MDCK,":[82,194],"LLC-PK1,":[83,195],"RRCK":[85,197],"requires":[88],"collecting":[89],"extensive":[90,101],"amounts":[91],"data.":[96,292],"An":[97],"open":[98,122],"database":[99],"offers":[100],"measurements":[102],"various":[104,157],"compounds":[105],"covering":[106],"vast":[108],"chemical":[109],"space;":[110],"however,":[111],"concerns":[112],"were":[113,213,230],"reported":[114],"on":[115,310],"use":[117],"data":[119,161,175,190,255,302],"published":[120],"databases":[123],"without":[124],"appropriate":[126],"accuracy":[127],"quality":[129,133,162,256],"checks.":[130],"Ensuring":[131],"datasets":[135],"training":[137],"critical":[142],"because":[143],"artificial":[144],"intelligence":[145],"(AI,":[146],"including":[147],"deep":[148],"learning)":[149],"was":[150],"develop":[153],"predict":[156],"pharmacokinetic":[158],"properties,":[159],"affects":[163],"performance":[165],"these":[167],"models.":[168],"Hence,":[169],"careful":[170],"curation":[171,187],"collected":[174,200],"imperative.":[177],"Herein,":[178],"we":[179],"developed":[180],"new":[182],"workflow":[183,206,237],"supports":[185],"automatic":[186],"measured":[191],"from":[201,215],"ChEMBL":[202,216],"KNIME.":[204],"The":[205,236,273],"consisted":[207],"four":[209],"main":[210],"phases.":[211],"Data":[212],"extracted":[214],"filtered":[218],"identify":[220],"target":[222],"protocols.":[223],"A":[224],"total":[225],"1661":[227],"high-quality":[228],"entries":[229],"retained":[231],"after":[232],"checking":[233],"436":[234],"articles.":[235],"freely":[239],"available,":[240],"updated,":[243],"has":[245],"high":[246],"reusability.":[247],"Our":[248,293],"study":[249],"provides":[250],"novel":[252],"approach":[253],"analysis":[257],"accelerates":[259],"development":[261],"helpful":[263],"effective":[268],"discovery.":[270],"Scientific":[271],"Contribution:":[272],"cost":[274],"building":[276],"highly":[277],"accurate":[278],"predictive":[279],"significantly":[283],"reduced":[284],"by":[285],"automating":[286],"collection":[288,303],"reliable":[290],"measurement":[291],"tool":[294,329],"reduces":[295],"time":[297],"effort":[299],"required":[300],"will":[305],"enable":[306],"researchers":[307],"focus":[309],"high-performance":[312],"types":[318],"analysis.":[320],"To":[321],"best":[323],"our":[325],"knowledge,":[326],"no":[327],"available":[331],"literature.":[334]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-13T07:54:00.901334","created_date":"2025-10-10T00:00:00"}