{"id":"https://openalex.org/W2803462582","doi":"https://doi.org/10.1186/s13321-018-0279-6","title":"Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database","display_name":"Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database","publication_year":2018,"publication_date":"2018-05-18","ids":{"openalex":"https://openalex.org/W2803462582","doi":"https://doi.org/10.1186/s13321-018-0279-6","mag":"2803462582","pmid":"https://pubmed.ncbi.nlm.nih.gov/29777317"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-018-0279-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0279-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0279-6","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/track/pdf/10.1186/s13321-018-0279-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085426373","display_name":"M. Quir\u00f3s","orcid":"https://orcid.org/0000-0002-1583-4468"},"institutions":[{"id":"https://openalex.org/I173304897","display_name":"Universidad de Granada","ror":"https://ror.org/04njjy449","country_code":"ES","type":"education","lineage":["https://openalex.org/I173304897"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Miguel Quir\u00f3s","raw_affiliation_strings":["Departamento de Qu\u00edmica Inorg\u00e1nica, Universidad de Granada, 18071, Granada, Spain. mquiros@ugr.es","Departamento de Qu\u00edmica Inorg\u00e1nica, Universidad de Granada, 18071, Granada, Spain"],"raw_orcid":"https://orcid.org/0000-0002-1583-4468","affiliations":[{"raw_affiliation_string":"Departamento de Qu\u00edmica Inorg\u00e1nica, Universidad de Granada, 18071, Granada, Spain. mquiros@ugr.es","institution_ids":["https://openalex.org/I173304897"]},{"raw_affiliation_string":"Departamento de Qu\u00edmica Inorg\u00e1nica, Universidad de Granada, 18071, Granada, Spain","institution_ids":["https://openalex.org/I173304897"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055816979","display_name":"S. Gra\u017eulis","orcid":"https://orcid.org/0000-0002-7928-5218"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Saulius Gra\u017eulis","raw_affiliation_strings":["Faculty of Mathematics and Informatics, Vilnius University, Naugarduko st. 24, 03225, Vilnius, Lithuania","Institute of Biotechnology, Vilnius University, Saul\u0117tekio al. 7, 10257, Vilnius, Lithuania"],"raw_orcid":"https://orcid.org/0000-0002-7928-5218","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Informatics, Vilnius University, Naugarduko st. 24, 03225, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]},{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Saul\u0117tekio al. 7, 10257, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015417869","display_name":"Saul\u0117 Girdzijauskait\u0117","orcid":null},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Saul\u0117 Girdzijauskait\u0117","raw_affiliation_strings":["Faculty of Mathematics and Informatics, Vilnius University, Naugarduko st. 24, 03225, Vilnius, Lithuania"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Informatics, Vilnius University, Naugarduko st. 24, 03225, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084681787","display_name":"Andrius Merkys","orcid":"https://orcid.org/0000-0002-7731-6236"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Andrius Merkys","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Saul\u0117tekio al. 7, 10257, Vilnius, Lithuania"],"raw_orcid":"https://orcid.org/0000-0002-7731-6236","affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Saul\u0117tekio al. 7, 10257, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065651218","display_name":"Antanas Vaitkus","orcid":"https://orcid.org/0000-0002-5944-1391"},"institutions":[{"id":"https://openalex.org/I173212132","display_name":"Vilnius University","ror":"https://ror.org/03nadee84","country_code":"LT","type":"education","lineage":["https://openalex.org/I173212132"]}],"countries":["LT"],"is_corresponding":false,"raw_author_name":"Antanas Vaitkus","raw_affiliation_strings":["Institute of Biotechnology, Vilnius University, Saul\u0117tekio al. 7, 10257, Vilnius, Lithuania"],"raw_orcid":"https://orcid.org/0000-0002-5944-1391","affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Vilnius University, Saul\u0117tekio al. 7, 10257, Vilnius, Lithuania","institution_ids":["https://openalex.org/I173212132"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5085426373"],"corresponding_institution_ids":["https://openalex.org/I173304897"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":11.5593,"has_fulltext":true,"cited_by_count":261,"citation_normalized_percentile":{"value":0.98932034,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"10","issue":"1","first_page":"23","last_page":"23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991999864578247,"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":0.9991999864578247,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12748","display_name":"Molecular spectroscopy and chirality","score":0.9824000000953674,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7388203740119934},{"id":"https://openalex.org/keywords/chemical-database","display_name":"Chemical database","score":0.5462063550949097},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5260726809501648},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4904455840587616},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3242255747318268},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2549337148666382}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7388203740119934},{"id":"https://openalex.org/C203394866","wikidata":"https://www.wikidata.org/wiki/Q2881060","display_name":"Chemical database","level":2,"score":0.5462063550949097},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5260726809501648},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4904455840587616},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3242255747318268},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2549337148666382},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-018-0279-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0279-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0279-6","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:29777317","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29777317","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:5959826","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5959826","pdf_url":null,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:digibug.ugr.es:10481/56323","is_oa":true,"landing_page_url":"http://hdl.handle.net/10481/56323","pdf_url":null,"source":{"id":"https://openalex.org/S4306400567","display_name":"Institutional Repository of the University of Granada (University of Granada)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173304897","host_organization_name":"Universidad de Granada","host_organization_lineage":["https://openalex.org/I173304897"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:62a04dbb05084ac9a70da5f579a0a202","is_oa":true,"landing_page_url":"https://doaj.org/article/62a04dbb05084ac9a70da5f579a0a202","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 10, Iss 1, Pp 1-17 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4920191","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5959826","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-018-0279-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0279-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-018-0279-6","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/G900885874","display_name":null,"funder_award_id":"FQM-195","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"}],"funders":[{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2803462582.pdf","grobid_xml":"https://content.openalex.org/works/W2803462582.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1508604947","https://openalex.org/W1975147762","https://openalex.org/W1976892175","https://openalex.org/W1990170643","https://openalex.org/W2034354062","https://openalex.org/W2067294686","https://openalex.org/W2070942956","https://openalex.org/W2091229190","https://openalex.org/W2096729078","https://openalex.org/W2097370873","https://openalex.org/W2102940758","https://openalex.org/W2107790922","https://openalex.org/W2112845989","https://openalex.org/W2120869341","https://openalex.org/W2125904022","https://openalex.org/W2148425900","https://openalex.org/W2153675433","https://openalex.org/W2163363362","https://openalex.org/W2169678694","https://openalex.org/W2170214641","https://openalex.org/W2172216479","https://openalex.org/W2177317049","https://openalex.org/W2319902168","https://openalex.org/W2622236128"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2087762413","https://openalex.org/W2003932708","https://openalex.org/W4308221833","https://openalex.org/W1503231262","https://openalex.org/W2380667145","https://openalex.org/W2097186436"],"abstract_inverted_index":{"Computer":[0],"descriptions":[1],"of":[2,31,47,79,105,124,206,239,247,261],"chemical":[3,10,15,29,53,234,252],"molecular":[4,18],"connectivity":[5,30],"are":[6,90,119,129,185],"necessary":[7],"for":[8,13,52,57,76,92,100],"searching":[9],"databases":[11],"and":[12,236],"predicting":[14],"properties":[16],"from":[17,165,173],"structure.":[19],"In":[20],"this":[21,240,248],"article,":[22],"the":[23,28,35,67,77,86,93,102,106,113,116,125,139,166,174,211,237,245,251,259],"ongoing":[24],"work":[25,249],"to":[26,146,161,215,218,243,250,257],"describe":[27],"entries":[32],"contained":[33],"in":[34,40,115,132,150,194],"Crystallography":[36],"Open":[37,156],"Database":[38],"(COD)":[39],"SMILES":[41,48,103,163],"format":[42],"is":[43,49,66,144,158,242],"reported.":[44],"This":[45],"collection":[46],"publicly":[50],"available":[51],"(substructure)":[54],"search":[55],"or":[56,176],"any":[58],"other":[59],"purpose":[60,238],"on":[61],"an":[62],"open-access":[63],"basis,":[64],"as":[65,254,256],"COD":[68,175],"itself.":[69],"The":[70,98,153,183],"conventions":[71],"that":[72,81,198],"have":[73],"been":[74],"followed":[75],"representation":[78],"compounds":[80],"do":[82],"not":[83,130],"fit":[84],"into":[85],"valence":[87],"bond":[88],"theory":[89],"outlined":[91],"most":[94],"frequently":[95],"found":[96],"cases.":[97,152],"procedure":[99,212],"getting":[101],"out":[104],"CIF":[107,167],"files":[108,168],"starts":[109],"with":[110],"checking":[111],"whether":[112],"atoms":[114],"asymmetric":[117],"unit":[118],"a":[120,133,191,195,203],"chemically":[121],"acceptable":[122],"image":[123,149],"compound.":[126],"When":[127],"they":[128],"(molecule":[131],"symmetry":[134],"element,":[135],"disorder,":[136],"polymeric":[137],"species,etc.),":[138],"previously":[140],"published":[141],"cif_molecule":[142,180],"program":[143,154],"used":[145],"get":[147,162],"such":[148],"many":[151],"package":[155],"Babel":[157],"then":[159,186],"applied":[160],"strings":[164],"(either":[169],"those":[170,177],"directly":[171],"taken":[172],"produced":[178],"by":[179,190],"when":[181],"applicable).":[182],"results":[184],"checked":[187],"and/or":[188],"fixed":[189],"human":[192,207],"editor,":[193],"computer-aided":[196],"task":[197],"at":[199],"present":[200],"still":[201,213],"consumes":[202],"great":[204],"deal":[205],"time.":[208],"Even":[209],"if":[210],"needs":[214],"be":[216],"improved":[217],"make":[219],"it":[220,226],"more":[221,230],"automatic":[222],"(and":[223],"hence":[224],"faster),":[225],"has":[227],"already":[228],"yielded":[229],"than":[231],"160,000":[232],"curated":[233],"structures":[235],"article":[241],"announce":[244],"existence":[246],"community":[253],"well":[255],"spread":[258],"use":[260],"its":[262],"results.":[263]},"counts_by_year":[{"year":2026,"cited_by_count":22},{"year":2025,"cited_by_count":45},{"year":2024,"cited_by_count":50},{"year":2023,"cited_by_count":48},{"year":2022,"cited_by_count":35},{"year":2021,"cited_by_count":36},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}