{"id":"https://openalex.org/W2133413319","doi":"https://doi.org/10.1186/1751-0473-7-12","title":"RMol: a toolset for transforming SD/Molfile structure information into R objects","display_name":"RMol: a toolset for transforming SD/Molfile structure information into R objects","publication_year":2012,"publication_date":"2012-11-14","ids":{"openalex":"https://openalex.org/W2133413319","doi":"https://doi.org/10.1186/1751-0473-7-12","mag":"2133413319","pmid":"https://pubmed.ncbi.nlm.nih.gov/23151338"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-7-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-7-12","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-7-12","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-7-12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000201245","display_name":"Martin Gr\u00e1bner","orcid":"https://orcid.org/0000-0003-1399-094X"},"institutions":[{"id":"https://openalex.org/I4210114246","display_name":"UMIT - Private Universit\u00e4t f\u00fcr Gesundheitswissenschaften, Medizinische Informatik und Technik","ror":"https://ror.org/02d0kps43","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210114246"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Martin Grabner","raw_affiliation_strings":["Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, A-6060, Austria. matthias.dehmer@umit.at","Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, A-6060, Austria. matthias.dehmer@umit.at","institution_ids":["https://openalex.org/I4210114246"]},{"raw_affiliation_string":"Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, Austria","institution_ids":["https://openalex.org/I4210114246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022882863","display_name":"\u041a\u0443\u0440\u0442 \u0412\u0430\u0440\u043c\u0443\u0437\u0430","orcid":"https://orcid.org/0000-0002-3534-4001"},"institutions":[{"id":"https://openalex.org/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Kurt Varmuza","raw_affiliation_strings":["Laboratory for Chemometrics, Institute of Chemical Engineering, Vienna University of Technology, A-1060 Vienna, Getreidemarkt, 9/166, Austria","Laboratory for Chemometrics, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Chemometrics, Institute of Chemical Engineering, Vienna University of Technology, A-1060 Vienna, Getreidemarkt, 9/166, Austria","institution_ids":["https://openalex.org/I145847075"]},{"raw_affiliation_string":"Laboratory for Chemometrics, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt, Austria","institution_ids":["https://openalex.org/I145847075"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044244385","display_name":"Matthias Dehmer","orcid":"https://orcid.org/0000-0001-8454-5857"},"institutions":[{"id":"https://openalex.org/I4210114246","display_name":"UMIT - Private Universit\u00e4t f\u00fcr Gesundheitswissenschaften, Medizinische Informatik und Technik","ror":"https://ror.org/02d0kps43","country_code":"AT","type":"education","lineage":["https://openalex.org/I4210114246"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Matthias Dehmer","raw_affiliation_strings":["Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, A-6060, Austria","Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, A-6060, Austria","institution_ids":["https://openalex.org/I4210114246"]},{"raw_affiliation_string":"Department of Biomedical Sciences and Engineering, Institute for Bioinformatics and Translational Research, University for Health Sciences, Medical Informatics and Technology (UMIT), Eduard Walln\u00f6fer Zentrum 1, Hall in Tyrol, Austria","institution_ids":["https://openalex.org/I4210114246"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000201245"],"corresponding_institution_ids":["https://openalex.org/I4210114246"],"apc_list":null,"apc_paid":null,"fwci":1.0414,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78822353,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"7","issue":"1","first_page":"12","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.32519999146461487,"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":0.32519999146461487,"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":0.22190000116825104,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.03139999881386757,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8659298419952393},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.849666953086853},{"id":"https://openalex.org/keywords/lossless-compression","display_name":"Lossless compression","score":0.6885841488838196},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6573423147201538},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5490123629570007},{"id":"https://openalex.org/keywords/object","display_name":"Object (grammar)","score":0.5461335182189941},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4977684020996094},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.4277685582637787},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.41648975014686584},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40355125069618225},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3938792049884796},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37469127774238586},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18307870626449585},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1000438928604126}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8659298419952393},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.849666953086853},{"id":"https://openalex.org/C81081738","wikidata":"https://www.wikidata.org/wiki/Q55542","display_name":"Lossless compression","level":3,"score":0.6885841488838196},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6573423147201538},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5490123629570007},{"id":"https://openalex.org/C2781238097","wikidata":"https://www.wikidata.org/wiki/Q175026","display_name":"Object (grammar)","level":2,"score":0.5461335182189941},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4977684020996094},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.4277685582637787},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.41648975014686584},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40355125069618225},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3938792049884796},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37469127774238586},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18307870626449585},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1000438928604126},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1751-0473-7-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-7-12","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-7-12","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23151338","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23151338","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:europepmc.org:2598064","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3599689","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:10.1186/1751-0473-7-12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-7-12","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-7-12","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2133413319.pdf"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W106879616","https://openalex.org/W118172891","https://openalex.org/W229097380","https://openalex.org/W623814603","https://openalex.org/W635830827","https://openalex.org/W1520184440","https://openalex.org/W1545231783","https://openalex.org/W1862448690","https://openalex.org/W2019486877","https://openalex.org/W2034468283","https://openalex.org/W2051810242","https://openalex.org/W2099308584","https://openalex.org/W2115088702","https://openalex.org/W2132022337","https://openalex.org/W2148797284","https://openalex.org/W2160697532","https://openalex.org/W2167592961","https://openalex.org/W2471313847","https://openalex.org/W2582743722","https://openalex.org/W4251903194"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W1570419641","https://openalex.org/W4386509167","https://openalex.org/W2889938001","https://openalex.org/W4293771607","https://openalex.org/W3165034028","https://openalex.org/W2296499206","https://openalex.org/W3210319767","https://openalex.org/W132037564","https://openalex.org/W2074440087"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,211],"graph-theoretical":[2],"analysis":[3,46,188],"of":[4,27,54,86,124,158],"molecular":[5,69],"networks":[6],"has":[7],"a":[8,16,82,122,167],"long":[9],"tradition":[10],"in":[11,47,153,200],"chemoinformatics.":[12],"As":[13],"demonstrated":[14],"frequently,":[15],"well":[17],"designed":[18],"format":[19],"to":[20,38,62,98,130,172,181,196],"encode":[21],"chemical":[22],"structures":[23],"and":[24,49,67,133],"structure-related":[25],"information":[26,84,88],"organic":[28],"compounds":[29],"is":[30,166,179,204],"the":[31,55,96,100,119,128,135,208],"Molfile":[32,64,108],"format.":[33],"But":[34],"when":[35],"it":[36],"comes":[37],"use":[39,99],"modern":[40],"programming":[41,176],"languages":[42,59],"for":[43,106,114,144,185],"statistical":[44],"data":[45,65,71,109,137,147,192],"Bio-":[48],"Chemoinformatics,":[50],"R":[51,78,92,112,125,151,168,201],"as":[52,103],"one":[53],"most":[56],"powerful":[57],"free":[58],"lacks":[60],"tools":[61],"process":[63,197],"collections":[66,110],"import":[68],"network":[70,191],"into":[72,91,183],"R.":[73],"RESULTS:":[74],"We":[75],"design":[76],"an":[77,104],"object":[79,102],"which":[80],"allows":[81],"lossless":[83],"mapping":[85],"structural":[87],"from":[89,217],"Molfiles":[90],"objects.":[93],"This":[94],"provides":[95],"basis":[97],"RMol":[101,120,165],"anchor":[105],"connecting":[107],"with":[111,118],"libraries":[113,174],"analyzing":[115],"graphs.":[116],"Associated":[117],"objects,":[121],"set":[123],"functions":[126],"completes":[127],"toolset":[129,169],"organize,":[131],"describe":[132],"manipulate":[134],"converted":[136],"sets.":[138],"Further,":[139],"we":[140],"bypass":[141],"R-typical":[142],"limits":[143],"manipulating":[145],"large":[146],"sets":[148,199],"by":[149,189],"storing":[150],"objects":[152],"bz-compressed":[154],"serialized":[155,186],"files":[156],"instead":[157],"employing":[159],"RData":[160],"files.":[161],"CONCLUSIONS:":[162],"By":[163],"design,":[164],"without":[170],"dependencies":[171],"other":[173],"or":[175],"languages.":[177],"It":[178,203],"useful":[180],"integrate":[182],"pipelines":[184],"batch":[187],"using":[190],"and,":[193],"therefore,":[194],"helps":[195],"sdf-data":[198],"efficiently.":[202],"freely":[205],"available":[206],"under":[207],"BSD":[209],"licence.":[210],"script":[212],"source":[213],"can":[214],"be":[215],"downloaded":[216],"http://sourceforge.net/p/rmol-toolset.":[218]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}