{"id":"https://openalex.org/W2562598438","doi":"https://doi.org/10.1186/s13321-016-0175-x","title":"ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files","display_name":"ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2562598438","doi":"https://doi.org/10.1186/s13321-016-0175-x","mag":"2562598438"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-016-0175-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0175-x","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0175-x","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0175-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101586963","display_name":"Muthukumarasamy Karthikeyan","orcid":"https://orcid.org/0000-0002-4322-8991"},"institutions":[{"id":"https://openalex.org/I3125981224","display_name":"National Chemical Laboratory","ror":"https://ror.org/057mn3690","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3125981224","https://openalex.org/I4210134808","https://openalex.org/I66760702"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Muthukumarasamy Karthikeyan","raw_affiliation_strings":["Chemical Engineering and Process Development (CEPD), CSIR-National Chemical Laboratory, Pashan Road, Pune, Maharastra 411008, India","Chemical Engineering and Process Development (CEPD), CSIR-National Chemical Laboratory, Pune, India"],"affiliations":[{"raw_affiliation_string":"Chemical Engineering and Process Development (CEPD), CSIR-National Chemical Laboratory, Pashan Road, Pune, Maharastra 411008, India","institution_ids":["https://openalex.org/I3125981224"]},{"raw_affiliation_string":"Chemical Engineering and Process Development (CEPD), CSIR-National Chemical Laboratory, Pune, India","institution_ids":["https://openalex.org/I3125981224"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087772789","display_name":"Renu Vyas","orcid":"https://orcid.org/0000-0001-6530-3238"},"institutions":[{"id":"https://openalex.org/I4210162439","display_name":"MIT Art, Design and Technology University","ror":"https://ror.org/05b69xa56","country_code":"IN","type":"education","lineage":["https://openalex.org/I4210162439"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Renu Vyas","raw_affiliation_strings":["MIT School of Bioengineering Sciences and Research, ADT (Art, Design and Technology) University, Loni Kalbhor, Pune, Maharashtra, 412201, India","MIT School of Bioengineering Sciences and Research, ADT (Art, Design and Technology) University, Pune, India"],"affiliations":[{"raw_affiliation_string":"MIT School of Bioengineering Sciences and Research, ADT (Art, Design and Technology) University, Loni Kalbhor, Pune, Maharashtra, 412201, India","institution_ids":["https://openalex.org/I4210162439"]},{"raw_affiliation_string":"MIT School of Bioengineering Sciences and Research, ADT (Art, Design and Technology) University, Pune, India","institution_ids":["https://openalex.org/I4210162439"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101586963"],"corresponding_institution_ids":["https://openalex.org/I3125981224"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.6827,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.73725838,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"8","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9837999939918518,"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"}},"topics":[{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9837999939918518,"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"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9620000123977661,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9455999732017517,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6193561553955078},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4420269727706909},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3788580298423767},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3443136215209961}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6193561553955078},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4420269727706909},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3788580298423767},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3443136215209961}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/s13321-016-0175-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0175-x","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0175-x","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":"pmh:oai:europepmc.org:4128626","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5195924","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/s13321-016-0175-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0175-x","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0175-x","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":[{"id":"https://metadata.un.org/sdg/9","score":0.5099999904632568,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1197655997","display_name":null,"funder_award_id":"HCP0001","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"},{"id":"https://openalex.org/G238570193","display_name":null,"funder_award_id":"New Delhi","funder_id":"https://openalex.org/F4320320719","funder_display_name":"Department of Science and Technology, Ministry of Science and Technology, India"},{"id":"https://openalex.org/G3383371438","display_name":null,"funder_award_id":"CSC0107","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"},{"id":"https://openalex.org/G3822940170","display_name":null,"funder_award_id":"BSC 0121","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"},{"id":"https://openalex.org/G6658149070","display_name":null,"funder_award_id":"fellowship","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"}],"funders":[{"id":"https://openalex.org/F4320320719","display_name":"Department of Science and Technology, Ministry of Science and Technology, India","ror":"https://ror.org/0101xrq71"},{"id":"https://openalex.org/F4320320721","display_name":"Council of Scientific and Industrial Research, India","ror":"https://ror.org/021wm7p51"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2562598438.pdf","grobid_xml":"https://content.openalex.org/works/W2562598438.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W17045578","https://openalex.org/W1510223697","https://openalex.org/W1562293507","https://openalex.org/W1759440238","https://openalex.org/W1902120158","https://openalex.org/W1965204689","https://openalex.org/W1977287658","https://openalex.org/W1978077854","https://openalex.org/W1996888414","https://openalex.org/W1999145583","https://openalex.org/W2019653144","https://openalex.org/W2049961577","https://openalex.org/W2051985737","https://openalex.org/W2057418400","https://openalex.org/W2069719501","https://openalex.org/W2070713869","https://openalex.org/W2116877707","https://openalex.org/W2119220281","https://openalex.org/W2220435532","https://openalex.org/W2325623133","https://openalex.org/W2334127072","https://openalex.org/W2338943230","https://openalex.org/W2415234544","https://openalex.org/W2485749800"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Digital":[0],"access":[1],"to":[2,45,67,118,219],"chemical":[3],"journals":[4],"resulted":[5],"in":[6,17,22,80,141,176,206],"a":[7,32,37,81,89,119,211],"vast":[8],"array":[9],"of":[10,54,71,121,137,162,199,213],"molecular":[11,28,48,107,164,200,217],"information":[12,53,143,201],"that":[13,58,114,174,191],"is":[14,36,189],"now":[15],"available":[16,61,205,235],"the":[18,51,69,101,149,180,186,192,207],"supplementary":[19,102,142,203],"material":[20],"files":[21,204],"PDF":[23,33,77,208],"format.":[24],"However,":[25],"extracting":[26,72],"this":[27],"information,":[29],"generally":[30],"from":[31,50,62,76,100,202],"document":[34],"format":[35,209],"daunting":[38],"task.":[39],"Here":[40],"we":[41,86],"present":[42],"an":[43,221],"approach":[44],"harvest":[46],"3D":[47],"data":[49,103,109,139,166,183,218],"supporting":[52],"scientific":[55],"research":[56],"articles":[57],"are":[59],"normally":[60],"publisher\u2019s":[63],"resources.":[64],"In":[65],"order":[66],"demonstrate":[68],"feasibility":[70],"truly":[73],"computable":[74],"molecules":[75,156],"file":[78],"formats":[79,136],"fast":[82],"and":[83,104,152,233],"efficient":[84],"manner,":[85],"have":[87],"developed":[88],"Java":[90],"based":[91],"application,":[92],"namely":[93],"ChemEngine.":[94],"This":[95],"program":[96],"recognizes":[97],"textual":[98],"patterns":[99],"generates":[105],"standard":[106],"structure":[108],"(bond":[110],"matrix,":[111],"atomic":[112,150],"coordinates)":[113],"can":[115],"be":[116],"subjected":[117],"multitude":[120],"computational":[122,226],"processes":[123],"automatically.":[124],"The":[125,160],"methodology":[126,193],"has":[127],"been":[128],"demonstrated":[129,168],"via":[130],"several":[131],"case":[132],"studies":[133],"on":[134],"different":[135],"coordinates":[138,151],"stored":[140],"files,":[144],"wherein":[145],"ChemEngine":[146],"selectively":[147],"harvested":[148],"interpreted":[153],"them":[154],"as":[155],"with":[157,179,185,230],"high":[158],"accuracy.":[159],"reusability":[161],"extracted":[163],"coordinate":[165],"was":[167],"by":[169],"computing":[170],"Single":[171],"Point":[172],"Energies":[173],"were":[175],"close":[177],"agreement":[178],"original":[181],"computed":[182],"provided":[184],"articles.":[187],"It":[188],"envisaged":[190],"will":[194],"enable":[195],"large":[196],"scale":[197],"conversion":[198],"into":[210],"collection":[212],"ready-":[214],"to-":[215],"compute":[216],"create":[220],"automated":[222],"workflow":[223],"for":[224],"advanced":[225],"processes.":[227],"Software":[228],"along":[229],"source":[231],"codes":[232],"instructions":[234],"at":[236],"https://sourceforge.net/projects/chemengine/files/?source=navbar":[237],".":[238]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":3}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2017-01-06T00:00:00"}
