{"id":"https://openalex.org/W4404043800","doi":"https://doi.org/10.1093/bib/bbae569","title":"Making PBPK models more reproducible in practice","display_name":"Making PBPK models more reproducible in practice","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404043800","doi":"https://doi.org/10.1093/bib/bbae569","pmid":"https://pubmed.ncbi.nlm.nih.gov/39494970"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae569","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbae569","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067146733","display_name":"Elena Dom\u00ednguez-Romero","orcid":"https://orcid.org/0000-0001-9795-5628"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Elena Dom\u00ednguez-Romero","raw_affiliation_strings":["Department of Bioinformatics\u2014BiGCaT , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","Maastricht University , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","Masaryk University , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","RECETOX , Faculty of Science, , Kotlarska 2, 611 37, Brno ,"],"raw_orcid":"https://orcid.org/0000-0001-9795-5628","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics\u2014BiGCaT , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","institution_ids":[]},{"raw_affiliation_string":"Maastricht University , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","institution_ids":[]},{"raw_affiliation_string":"Masaryk University , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"RECETOX , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042501458","display_name":"Stanislav Mazurenko","orcid":"https://orcid.org/0000-0003-3659-4819"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210102302","display_name":"University Hospital Brno","ror":"https://ror.org/00qq1fp34","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210102302"]},{"id":"https://openalex.org/I4210136987","display_name":"St. Anne's University Hospital Brno","ror":"https://ror.org/049bjee35","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210136987"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Stanislav Mazurenko","raw_affiliation_strings":["International Clinical Research Center, St. Anne\u2019s University Hospital Brno , Peka\u0159sk\u00e1 53, 656 91, Brno ,","Loschmidt Laboratories , Department of Experimental Biology and RECETOX, Faculty of Science, , Kamenice 5, 625 00, Brno ,","Masaryk University , Department of Experimental Biology and RECETOX, Faculty of Science, , Kamenice 5, 625 00, Brno ,"],"raw_orcid":"https://orcid.org/0000-0003-3659-4819","affiliations":[{"raw_affiliation_string":"International Clinical Research Center, St. Anne\u2019s University Hospital Brno , Peka\u0159sk\u00e1 53, 656 91, Brno ,","institution_ids":["https://openalex.org/I4210102302","https://openalex.org/I4210136987"]},{"raw_affiliation_string":"Loschmidt Laboratories , Department of Experimental Biology and RECETOX, Faculty of Science, , Kamenice 5, 625 00, Brno ,","institution_ids":[]},{"raw_affiliation_string":"Masaryk University , Department of Experimental Biology and RECETOX, Faculty of Science, , Kamenice 5, 625 00, Brno ,","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085391651","display_name":"Martin Scheringer","orcid":"https://orcid.org/0000-0002-0809-7826"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Martin Scheringer","raw_affiliation_strings":["Masaryk University , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","RECETOX , Faculty of Science, , Kotlarska 2, 611 37, Brno ,"],"raw_orcid":"https://orcid.org/0000-0002-0809-7826","affiliations":[{"raw_affiliation_string":"Masaryk University , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"RECETOX , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039324414","display_name":"V\u00edtor A. P. Martins dos Santos","orcid":"https://orcid.org/0000-0002-2352-9017"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"V\u00edtor A P Martins dos Santos","raw_affiliation_strings":["Laboratory of Bioprocess Engineering, Wageningen University and Research , Droevendaalsesteeg 1, 6708 PB, Wageningen ,"],"raw_orcid":"https://orcid.org/0000-0002-2352-9017","affiliations":[{"raw_affiliation_string":"Laboratory of Bioprocess Engineering, Wageningen University and Research , Droevendaalsesteeg 1, 6708 PB, Wageningen ,","institution_ids":["https://openalex.org/I913481162"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075750072","display_name":"Chris T. Evelo","orcid":"https://orcid.org/0000-0002-5301-3142"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chris T Evelo","raw_affiliation_strings":["Department of Bioinformatics\u2014BiGCaT , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","Maastricht University , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,"],"raw_orcid":"https://orcid.org/0000-0002-5301-3142","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics\u2014BiGCaT , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","institution_ids":[]},{"raw_affiliation_string":"Maastricht University , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038426035","display_name":"Mihail Anton","orcid":null},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I4210163572","display_name":"Elixir Medical (United States)","ror":"https://ror.org/05hgx8v86","country_code":"US","type":"company","lineage":["https://openalex.org/I4210163572"]},{"id":"https://openalex.org/I4387154792","display_name":"National Bioinformatics Infrastructure Sweden","ror":"https://ror.org/00enajs79","country_code":null,"type":"other","lineage":["https://openalex.org/I123387679","https://openalex.org/I4387153960","https://openalex.org/I4387154792"]},{"id":"https://openalex.org/I66862912","display_name":"Chalmers University of Technology","ror":"https://ror.org/040wg7k59","country_code":"SE","type":"education","lineage":["https://openalex.org/I66862912"]}],"countries":["SE","US"],"is_corresponding":false,"raw_author_name":"Mihail Anton","raw_affiliation_strings":["Chalmers University of Technology , National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, , Kemig\u00e5rden 1, Gothenburg SE-412 96 ,","Department of Life Sciences , National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, , Kemig\u00e5rden 1, Gothenburg SE-412 96 ,","ELIXIR, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD ,"],"raw_orcid":"https://orcid.org/0000-0002-7753-9042","affiliations":[{"raw_affiliation_string":"Chalmers University of Technology , National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, , Kemig\u00e5rden 1, Gothenburg SE-412 96 ,","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I4387154792","https://openalex.org/I66862912"]},{"raw_affiliation_string":"Department of Life Sciences , National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, , Kemig\u00e5rden 1, Gothenburg SE-412 96 ,","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I4387154792"]},{"raw_affiliation_string":"ELIXIR, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD ,","institution_ids":["https://openalex.org/I4210163572"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030731998","display_name":"John M. Hancock","orcid":"https://orcid.org/0000-0003-2991-2217"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"John M Hancock","raw_affiliation_strings":["Institute of Biochemistry and Molecular Genetics , Faculty of Medicine, , Zalo\u0161ka 4, 1000 Ljubljana ,","University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka 4, 1000 Ljubljana ,"],"raw_orcid":"https://orcid.org/0000-0003-2991-2217","affiliations":[{"raw_affiliation_string":"Institute of Biochemistry and Molecular Genetics , Faculty of Medicine, , Zalo\u0161ka 4, 1000 Ljubljana ,","institution_ids":[]},{"raw_affiliation_string":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka 4, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045271558","display_name":"An\u017ee \u017dupani\u010d","orcid":"https://orcid.org/0000-0003-3303-9086"},"institutions":[{"id":"https://openalex.org/I4210140619","display_name":"National Institute of Biology","ror":"https://ror.org/03s5t0r17","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210140619"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"An\u017ee \u017dupani\u010d","raw_affiliation_strings":["Department of Biotechnology and Systems Biology, National Institute of Biology , Ve\u010dna pot 121, 1000 Ljubljana ,"],"raw_orcid":"https://orcid.org/0000-0003-3303-9086","affiliations":[{"raw_affiliation_string":"Department of Biotechnology and Systems Biology, National Institute of Biology , Ve\u010dna pot 121, 1000 Ljubljana ,","institution_ids":["https://openalex.org/I4210140619"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041170743","display_name":"Mar\u00eda Su\u00e1rez\u2010Diez","orcid":"https://orcid.org/0000-0001-5845-146X"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Maria Suarez-Diez","raw_affiliation_strings":["Laboratory of Systems and Synthetic Biology (SSB), Wageningen University and Research, Agrotechnology and Food Sciences , Stippeneng 4, 6708 WE Wageningen ,"],"raw_orcid":"https://orcid.org/0000-0001-5845-146X","affiliations":[{"raw_affiliation_string":"Laboratory of Systems and Synthetic Biology (SSB), Wageningen University and Research, Agrotechnology and Food Sciences , Stippeneng 4, 6708 WE Wageningen ,","institution_ids":["https://openalex.org/I913481162"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.811,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.85597625,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9986000061035156,"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"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9986000061035156,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9922000169754028,"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":0.9836999773979187,"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/physiologically-based-pharmacokinetic-modelling","display_name":"Physiologically based pharmacokinetic modelling","score":0.9618956446647644},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7333821058273315},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6135217547416687},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.5492081046104431},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5109116435050964},{"id":"https://openalex.org/keywords/harmonization","display_name":"Harmonization","score":0.46723252534866333},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.41049179434776306},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38781145215034485},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.3716747760772705},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.17942774295806885},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17380249500274658},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14454036951065063},{"id":"https://openalex.org/keywords/pharmacokinetics","display_name":"Pharmacokinetics","score":0.12090501189231873},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10379746556282043},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10373282432556152}],"concepts":[{"id":"https://openalex.org/C185867374","wikidata":"https://www.wikidata.org/wiki/Q2562769","display_name":"Physiologically based pharmacokinetic modelling","level":3,"score":0.9618956446647644},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7333821058273315},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6135217547416687},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5492081046104431},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5109116435050964},{"id":"https://openalex.org/C2779962950","wikidata":"https://www.wikidata.org/wiki/Q5659376","display_name":"Harmonization","level":2,"score":0.46723252534866333},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.41049179434776306},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38781145215034485},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.3716747760772705},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.17942774295806885},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17380249500274658},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14454036951065063},{"id":"https://openalex.org/C112705442","wikidata":"https://www.wikidata.org/wiki/Q323936","display_name":"Pharmacokinetics","level":2,"score":0.12090501189231873},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10379746556282043},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10373282432556152},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010599","descriptor_name":"Pharmacokinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1093/bib/bbae569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae569","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39494970","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39494970","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:cris.maastrichtuniversity.nl:openaire_cris_publications/2aeaf689-e850-40b1-a490-f7a7a68a83a7","is_oa":true,"landing_page_url":"https://cris.maastrichtuniversity.nl/en/publications/2aeaf689-e850-40b1-a490-f7a7a68a83a7","pdf_url":null,"source":{"id":"https://openalex.org/S4306402616","display_name":"Research Publications (Maastricht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I34352273","host_organization_name":"Maastricht University","host_organization_lineage":["https://openalex.org/I34352273"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Dominguez-Romero, E, Mazurenko, S, Scheringer, M, dos Santos, V A P M, Evelo, C T, Anton, M, Hancock, J M, Zupanic, A & Suarez-Diez, M 2024, 'Making PBPK models more reproducible in practice', Briefings in Bioinformatics, vol. 25, no. 6, bbae569. https://doi.org/10.1093/bib/bbae569","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:repozitorij.uni-lj.si:IzpisGradiva.php?id=182107","is_oa":true,"landing_page_url":"https://repozitorij.uni-lj.si/IzpisGradiva.php?id=182107","pdf_url":null,"source":{"id":"https://openalex.org/S4377196268","display_name":"Repository of the University of Ljubljana (University of Ljubljana)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I153976015","host_organization_name":"University of Ljubljana","host_organization_lineage":["https://openalex.org/I153976015"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ISSN: 1477-4054","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:dirros.openscience.si:IzpisGradiva.php?id=20784","is_oa":true,"landing_page_url":"https://dirros.openscience.si/Dokument.php?id=29336&amp;dn=","pdf_url":"https://dirros.openscience.si/Dokument.php?id=29337&amp;dn=","source":{"id":"https://openalex.org/S4377196363","display_name":"DiRROS repository (University of Maribor)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I37696226","host_organization_name":"University of Maribor","host_organization_lineage":["https://openalex.org/I37696226"],"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":"ISSN: 1477-4054","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:library.wur.nl:wurpubs/637645","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/making-pbpk-models-more-reproducible-in-practice","pdf_url":"https://edepot.wur.nl/679240","source":{"id":"https://openalex.org/S4210201231","display_name":"Socio-Environmental Systems Modeling","issn_l":"2663-3027","issn":["2663-3027"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1467-5463","raw_type":"Article/Letter to editor"},{"id":"pmh:oai:pubmedcentral.nih.gov:11533111","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11533111","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11533111/pdf/bbae569.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":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:research.chalmers.se:543754","is_oa":true,"landing_page_url":"https://research.chalmers.se/en/publication/543754","pdf_url":"https://research.chalmers.se/publication/543754/file/543754_Fulltext.pdf","source":{"id":"https://openalex.org/S4306402469","display_name":"Chalmers Research (Chalmers University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66862912","host_organization_name":"Chalmers University of Technology","host_organization_lineage":["https://openalex.org/I66862912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbae569","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae569","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2313148124","display_name":"European Human Biomonitoring Initiative","funder_award_id":"733032","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2351268093","display_name":"CETOCOEN Excellence","funder_award_id":"857560","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G252385833","display_name":null,"funder_award_id":"LM2023069","funder_id":"https://openalex.org/F4320336687","funder_display_name":"RECETOX P\u0159\u00edrodov\u011bdeck\u00e9 Fakulty Masarykovy Univerzity"},{"id":"https://openalex.org/G3797148788","display_name":null,"funder_award_id":"ESFRI ELIXIR LM2023055","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G4158262239","display_name":null,"funder_award_id":"ELIXIR LM2023055","funder_id":"https://openalex.org/F4320336687","funder_display_name":"RECETOX P\u0159\u00edrodov\u011bdeck\u00e9 Fakulty Masarykovy Univerzity"},{"id":"https://openalex.org/G7353528434","display_name":null,"funder_award_id":"ESFRI RECETOX RI LM2023069","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G7994376114","display_name":null,"funder_award_id":"NWA-ORC 1292.19.272","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G8459432851","display_name":null,"funder_award_id":"1292.19.272","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G8844530579","display_name":null,"funder_award_id":"RI LM2023069","funder_id":"https://openalex.org/F4320336687","funder_display_name":"RECETOX P\u0159\u00edrodov\u011bdeck\u00e9 Fakulty Masarykovy Univerzity"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320321016","display_name":"Universiteit Maastricht","ror":"https://ror.org/02jz4aj89"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320336687","display_name":"RECETOX P\u0159\u00edrodov\u011bdeck\u00e9 Fakulty Masarykovy Univerzity","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1509358020","https://openalex.org/W1968593485","https://openalex.org/W1978486653","https://openalex.org/W1979264461","https://openalex.org/W1991419980","https://openalex.org/W2010604119","https://openalex.org/W2020561965","https://openalex.org/W2028696793","https://openalex.org/W2031639867","https://openalex.org/W2033609748","https://openalex.org/W2047856391","https://openalex.org/W2070320306","https://openalex.org/W2113777491","https://openalex.org/W2127676159","https://openalex.org/W2147462150","https://openalex.org/W2260313294","https://openalex.org/W2302501749","https://openalex.org/W2413797628","https://openalex.org/W2414283705","https://openalex.org/W2507987915","https://openalex.org/W2526123986","https://openalex.org/W2788254992","https://openalex.org/W2789816182","https://openalex.org/W2901130774","https://openalex.org/W2980029690","https://openalex.org/W2988361147","https://openalex.org/W2988998130","https://openalex.org/W3001949973","https://openalex.org/W3032761836","https://openalex.org/W3049040472","https://openalex.org/W3132502413","https://openalex.org/W3170186615","https://openalex.org/W3216585077","https://openalex.org/W4255768676","https://openalex.org/W4281655261","https://openalex.org/W4294599666","https://openalex.org/W4308410747","https://openalex.org/W4322505936","https://openalex.org/W4362722444","https://openalex.org/W4385295938","https://openalex.org/W4386894015","https://openalex.org/W4399203480","https://openalex.org/W4399494145"],"related_works":["https://openalex.org/W2909814037","https://openalex.org/W325264682","https://openalex.org/W4384070006","https://openalex.org/W2620300421","https://openalex.org/W3188839759","https://openalex.org/W2596073864","https://openalex.org/W2351741005","https://openalex.org/W4225086330","https://openalex.org/W4324157342","https://openalex.org/W3205500694"],"abstract_inverted_index":{"Systems":[0,173],"biology":[1,211,231,251],"aims":[2],"to":[3,19,30,75,132,143,172,187,213],"understand":[4],"living":[5],"organisms":[6],"through":[7],"mathematically":[8],"modeling":[9,246],"their":[10],"behaviors":[11],"at":[12],"different":[13,71,193,249],"organizational":[14],"levels,":[15],"ranging":[16],"from":[17,25,192],"molecules":[18],"populations.":[20],"Modeling":[21],"involves":[22],"several":[23],"steps,":[24],"determining":[26],"the":[27,32,39,45,60,65,105,201,221,228],"model":[28,48,77,120,126,134,161],"purpose":[29],"developing":[31],"mathematical":[33],"model,":[34],"implementing":[35],"it":[36],"computationally,":[37],"simulating":[38],"model's":[40],"behavior,":[41],"evaluating,":[42],"and":[43,128,136,158,242],"refining":[44],"model.":[46],"Importantly,":[47],"simulation":[49],"results":[50,62],"must":[51],"be":[52],"reproducible,":[53],"ensuring":[54],"that":[55,122],"other":[56,209],"researchers":[57],"can":[58],"obtain":[59],"same":[61],"after":[63],"writing":[64],"code":[66,162,170],"de":[67],"novo":[68],"and/or":[69],"using":[70,178],"software":[72,194],"tools.":[73],"Guidelines":[74],"increase":[76,200],"reproducibility":[78,83,135],"have":[79],"been":[80],"published.":[81],"However,":[82],"remains":[84],"a":[85,140],"major":[86],"challenge":[87,97],"in":[88,111,130,147,163,248],"this":[89,92,96,237],"field.":[90],"In":[91],"paper,":[93],"we":[94,154],"tackle":[95],"for":[98,118,182],"physiologically-based":[99],"pharmacokinetic":[100],"(PBPK)":[101],"models,":[102],"which":[103],"represent":[104],"pharmacokinetics":[106],"of":[107,168,203,208,223,244],"chemicals":[108],"following":[109],"exposure":[110],"humans":[112],"or":[113],"animals.":[114],"We":[115,138],"summarize":[116],"recommendations":[117],"PBPK":[119,148,160,190,214],"reporting":[121],"should":[123],"apply":[124],"during":[125],"development":[127],"implementation,":[129],"order":[131],"ensure":[133],"comprehensibility.":[137],"make":[139],"proposal":[141],"aiming":[142],"harmonize":[144],"abbreviations":[145],"used":[146],"models.":[149,205],"To":[150],"illustrate":[151],"these":[152,204],"recommendations,":[153],"present":[155],"an":[156,166,224],"original":[157],"reproducible":[159],"MATLAB,":[164],"alongside":[165],"example":[167],"MATLAB":[169],"converted":[171],"Biology":[174],"Markup":[175],"Language":[176],"format":[177],"MOCCASIN.":[179],"As":[180],"directions":[181],"future":[183],"improvement,":[184],"more":[185],"tools":[186],"convert":[188],"computational":[189],"models":[191,215],"platforms":[195],"into":[196],"standard":[197],"formats":[198],"would":[199,238],"interoperability":[202],"The":[206],"application":[207,243],"systems":[210,230,250],"standards":[212],"is":[216,220],"encouraged.":[217],"This":[218],"work":[219],"result":[222],"interdisciplinary":[225,234],"collaboration":[226],"involving":[227],"ELIXIR":[229],"community.":[232],"More":[233],"collaborations":[235],"like":[236],"facilitate":[239],"further":[240],"harmonization":[241],"good":[245],"practices":[247],"fields.":[252]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
