{"id":"https://openalex.org/W2319614057","doi":"https://doi.org/10.1093/bioinformatics/btw096","title":"Reaction Decoder Tool (RDT): extracting features from chemical reactions","display_name":"Reaction Decoder Tool (RDT): extracting features from chemical reactions","publication_year":2016,"publication_date":"2016-02-22","ids":{"openalex":"https://openalex.org/W2319614057","doi":"https://doi.org/10.1093/bioinformatics/btw096","mag":"2319614057"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw096","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2065/49019364/bioinformatics_32_13_2065.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2065/49019364/bioinformatics_32_13_2065.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012394374","display_name":"Syed Asad Rahman","orcid":"https://orcid.org/0000-0002-7602-6675"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Syed Asad Rahman","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","2 Congenica Ltd, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"2 Congenica Ltd, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016516266","display_name":"Gilliean Torrance","orcid":null},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Gilliean Torrance","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013550205","display_name":"Lorenzo Baldacci","orcid":"https://orcid.org/0000-0002-1638-4972"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB","IT"],"is_corresponding":false,"raw_author_name":"Lorenzo Baldacci","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","3 DISI, University of Bologna, V.Le Risorgimento 2, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"3 DISI, University of Bologna, V.Le Risorgimento 2, Bologna, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001196104","display_name":"Sergio Mart\u00ednez Cuesta","orcid":"https://orcid.org/0000-0001-9806-2805"},"institutions":[{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sergio Mart\u00ednez Cuesta","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","4 Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"4 Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK","institution_ids":["https://openalex.org/I2801316944","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049585784","display_name":"Franz Fenninger","orcid":"https://orcid.org/0000-0002-3859-6626"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA","GB"],"is_corresponding":false,"raw_author_name":"Franz Fenninger","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","5 Michael Smith Laboratories, the University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada,"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"5 Michael Smith Laboratories, the University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada,","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063873421","display_name":"Nimish Gopal","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nimish Gopal","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079824465","display_name":"Saket Choudhary","orcid":"https://orcid.org/0000-0001-5202-7633"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Saket Choudhary","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005209468","display_name":"John W. May","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John W. May","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","6 Innovation Centre (Unit 23), Cambridge Science Park, NextMove Software Ltd, Cambridge CB4 0EY, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"6 Innovation Centre (Unit 23), Cambridge Science Park, NextMove Software Ltd, Cambridge CB4 0EY, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087551864","display_name":"Gemma L. Holliday","orcid":"https://orcid.org/0000-0002-6731-6398"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Gemma L. Holliday","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","7 Bioengineering, UCSF School of Pharmacy, San Francisco, CA 94158, USA"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"7 Bioengineering, UCSF School of Pharmacy, San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040194803","display_name":"Christoph Steinbeck","orcid":"https://orcid.org/0000-0001-6966-0814"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christoph Steinbeck","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068874280","display_name":"Janet M. Thornton","orcid":"https://orcid.org/0000-0003-0824-4096"},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Janet M. Thornton","raw_affiliation_strings":["1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"1 European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5012394374"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.5931,"has_fulltext":true,"cited_by_count":105,"citation_normalized_percentile":{"value":0.96344679,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"13","first_page":"2065","last_page":"2066"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9993000030517578,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9993000030517578,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9939000010490417,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.992900013923645,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8050874471664429},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5851636528968811},{"id":"https://openalex.org/keywords/chemical-reaction","display_name":"Chemical reaction","score":0.5562797784805298},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5449768900871277},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4429696798324585},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2875075340270996},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23843327164649963},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08603644371032715}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8050874471664429},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5851636528968811},{"id":"https://openalex.org/C177801218","wikidata":"https://www.wikidata.org/wiki/Q36534","display_name":"Chemical reaction","level":2,"score":0.5562797784805298},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5449768900871277},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4429696798324585},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2875075340270996},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23843327164649963},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08603644371032715},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw096","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2065/49019364/bioinformatics_32_13_2065.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:3885728","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4920114","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"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/13/2065","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/13/2065","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw096","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/13/2065/49019364/bioinformatics_32_13_2065.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2319614057.pdf","grobid_xml":"https://content.openalex.org/works/W2319614057.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W560846839","https://openalex.org/W1849399280","https://openalex.org/W1964189732","https://openalex.org/W1982631789","https://openalex.org/W1996830618","https://openalex.org/W2024038403","https://openalex.org/W2040103915","https://openalex.org/W2098889731","https://openalex.org/W2101536914","https://openalex.org/W2108723491","https://openalex.org/W2131848047","https://openalex.org/W2143000571","https://openalex.org/W2144322446","https://openalex.org/W2145661853","https://openalex.org/W2177003373","https://openalex.org/W2498752956"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"Extracting":[2],"chemical":[3,22,45,78],"features":[4],"like":[5],"Atom\u2013Atom":[6],"Mapping":[7],"(AAM),":[8],"Bond":[9],"Changes":[10],"(BCs)":[11],"and":[12,55,70,85,97,100],"Reaction":[13,27],"Centres":[14],"from":[15],"biochemical":[16],"reactions":[17,79],"helps":[18],"us":[19],"understand":[20],"the":[21,59,65,71],"composition":[23],"of":[24,58,67,77],"enzymatic":[25],"reactions.":[26],"Decoder":[28],"is":[29,89],"a":[30],"robust":[31],"command":[32],"line":[33],"tool,":[34],"which":[35],"performs":[36],"this":[37],"task":[38],"with":[39],"high":[40],"accuracy.":[41],"It":[42],"supports":[43],"standard":[44],"input/output":[46],"exchange":[47],"formats":[48],"i.e.":[49],"RXN/SMILES,":[50],"computes":[51],"AAM,":[52],"highlights":[53],"BCs":[54],"creates":[56],"images":[57],"mapped":[60],"reaction.":[61],"This":[62,87],"aids":[63],"in":[64,91],"analysis":[66],"metabolic":[68],"pathways":[69],"ability":[72],"to":[73],"perform":[74],"comparative":[75],"studies":[76],"based":[80],"on":[81,94],"these":[82],"features.":[83],"Availability":[84],"implementation:":[86],"software":[88],"implemented":[90],"Java,":[92],"supported":[93],"Windows,":[95],"Linux":[96],"Mac":[98],"OSX,":[99],"freely":[101],"available":[102],"at":[103],"https://github.com/asad/ReactionDecoder":[104],"Contact:":[105],"asad@ebi.ac.uk":[106],"or":[107],"s9asad@gmail.com":[108]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
