{"id":"https://openalex.org/W4408640258","doi":"https://doi.org/10.1515/jib-2024-0050","title":"Predicting precursors of plant specialized metabolites using DeepMol automated machine learning","display_name":"Predicting precursors of plant specialized metabolites using DeepMol automated machine learning","publication_year":2025,"publication_date":"2025-03-19","ids":{"openalex":"https://openalex.org/W4408640258","doi":"https://doi.org/10.1515/jib-2024-0050","pmid":"https://pubmed.ncbi.nlm.nih.gov/40103340"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2024-0050","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0050","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0050/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0050/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056807631","display_name":"Jo\u00e3o Capela","orcid":"https://orcid.org/0000-0002-1235-2922"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Jo\u00e3o Capela","raw_affiliation_strings":["Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116710415","display_name":"Jo\u00e3o Cheixo","orcid":null},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o Cheixo","raw_affiliation_strings":["Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080533789","display_name":"Dick de Ridder","orcid":"https://orcid.org/0000-0002-4944-4310"},"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":"Dick de Ridder","raw_affiliation_strings":["Bioinformatics Group, Department of Plant Sciences , Wageningen University and Research , Wageningen , The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Plant Sciences , Wageningen University and Research , Wageningen , The Netherlands","institution_ids":["https://openalex.org/I913481162"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044535959","display_name":"\u00d3scar Dias","orcid":"https://orcid.org/0000-0002-1765-7178"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Oscar Dias","raw_affiliation_strings":["Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal","LABBELS \u2013 Associate Laboratory , Braga/Guimar\u00e3es , Portugal"],"raw_orcid":"https://orcid.org/0000-0002-1765-7178","affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"LABBELS \u2013 Associate Laboratory , Braga/Guimar\u00e3es , Portugal","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal","LABBELS \u2013 Associate Laboratory , Braga/Guimar\u00e3es , Portugal"],"raw_orcid":"https://orcid.org/0000-0001-8439-8172","affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering , University of Minho , 4710-057 , Braga , Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"LABBELS \u2013 Associate Laboratory , Braga/Guimar\u00e3es , Portugal","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5056807631"],"corresponding_institution_ids":["https://openalex.org/I99682543"],"apc_list":null,"apc_paid":null,"fwci":1.3019,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.78134314,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"22","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9998000264167786,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9998000264167786,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11237","display_name":"Plant Gene Expression Analysis","score":0.9959999918937683,"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/pipeline","display_name":"Pipeline (software)","score":0.7390663623809814},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6469852924346924},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5845813155174255},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5343626737594604},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5197243690490723},{"id":"https://openalex.org/keywords/abiotic-component","display_name":"Abiotic component","score":0.4620401859283447},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3894481062889099},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3238932490348816},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2014155089855194},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12696972489356995},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11914452910423279},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10409244894981384}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7390663623809814},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6469852924346924},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5845813155174255},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5343626737594604},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5197243690490723},{"id":"https://openalex.org/C132215390","wikidata":"https://www.wikidata.org/wiki/Q461335","display_name":"Abiotic component","level":2,"score":0.4620401859283447},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3894481062889099},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3238932490348816},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2014155089855194},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12696972489356995},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11914452910423279},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10409244894981384},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","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}],"locations_count":6,"locations":[{"id":"doi:10.1515/jib-2024-0050","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0050","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0050/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40103340","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40103340","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 integrative bioinformatics","raw_type":null},{"id":"pmh:oai:library.wur.nl:wurpubs/646187","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/predicting-precursors-of-plant-specialized-metabolites-using-deep","pdf_url":"https://edepot.wur.nl/693912","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: 1613-4516","raw_type":"Article/Letter to editor"},{"id":"pmh:oai:repositorium.uminho.pt:1822/98178","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/98178","pdf_url":"https://repositorium.uminho.pt/bitstreams/9ae0521f-a212-481c-ba8c-c55068cceb6f/download","source":{"id":"https://openalex.org/S4306400624","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:97a4352427ae4d80bf88eb1d40cb172a","is_oa":true,"landing_page_url":"https://doaj.org/article/97a4352427ae4d80bf88eb1d40cb172a","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 Integrative Bioinformatics, Vol 22, Iss 2, Pp 2294-316 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11375572","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12569576","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:10.1515/jib-2024-0050","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0050","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0050/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7448862362","display_name":null,"funder_award_id":"10.54499/CEECIND/03425/2018/CP1581/CT0020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8562927013","display_name":null,"funder_award_id":"DFA/BD/08789/2021","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408640258.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W30455059","https://openalex.org/W108684213","https://openalex.org/W1992581858","https://openalex.org/W2042599561","https://openalex.org/W2057747651","https://openalex.org/W2071342447","https://openalex.org/W2109385242","https://openalex.org/W2141631378","https://openalex.org/W2156264591","https://openalex.org/W2292607645","https://openalex.org/W2474525766","https://openalex.org/W2495332999","https://openalex.org/W2570528167","https://openalex.org/W2885171375","https://openalex.org/W2905012389","https://openalex.org/W2914601428","https://openalex.org/W2920175649","https://openalex.org/W2927127949","https://openalex.org/W2950056962","https://openalex.org/W2956914893","https://openalex.org/W3007987127","https://openalex.org/W3128005059","https://openalex.org/W3130585455","https://openalex.org/W3141855080","https://openalex.org/W3206742358","https://openalex.org/W3216174003","https://openalex.org/W4211254291","https://openalex.org/W4220918794","https://openalex.org/W4281697264","https://openalex.org/W4390751159","https://openalex.org/W4393152099","https://openalex.org/W4401192719","https://openalex.org/W4405074077","https://openalex.org/W6723200264"],"related_works":["https://openalex.org/W792574362","https://openalex.org/W3035909062","https://openalex.org/W4205930591","https://openalex.org/W4387854787","https://openalex.org/W4313345548","https://openalex.org/W4247064867","https://openalex.org/W3033694412","https://openalex.org/W3099785777","https://openalex.org/W2090240224","https://openalex.org/W4225263967"],"abstract_inverted_index":{"Plants":[0],"produce":[1],"specialized":[2],"metabolites,":[3],"which":[4],"play":[5],"critical":[6],"roles":[7],"in":[8,29],"defending":[9],"against":[10],"biotic":[11],"and":[12,20,32,78,96],"abiotic":[13],"stresses.":[14],"Due":[15],"to":[16],"their":[17,36,51,92],"chemical":[18,89],"diversity":[19],"bioactivity,":[21],"these":[22,42],"compounds":[23],"have":[24],"significant":[25],"economic":[26],"implications,":[27],"particularly":[28],"the":[30,38,48,101],"pharmaceutical":[31],"agrotechnology":[33],"sectors.":[34],"Despite":[35],"importance,":[37],"biosynthetic":[39],"pathways":[40],"of":[41,50],"metabolites":[43],"remain":[44],"largely":[45],"unresolved.":[46],"Automating":[47],"prediction":[49],"precursors,":[52],"derived":[53],"from":[54],"primary":[55],"metabolism,":[56],"is":[57],"essential":[58],"for":[59,81],"accelerating":[60],"pathway":[61],"discovery.":[62],"Using":[63],"DeepMol's":[64],"automated":[65],"machine":[66],"learning":[67],"engine,":[68],"we":[69],"found":[70],"that":[71],"regularized":[72],"linear":[73],"classifiers":[74],"offer":[75],"optimal,":[76],"accurate,":[77],"interpretable":[79],"models":[80,86,97],"this":[82],"task,":[83],"outperforming":[84],"state-of-the-art":[85],"while":[87],"providing":[88],"insights":[90],"into":[91],"predictions.":[93],"The":[94],"pipeline":[95],"are":[98],"available":[99],"at":[100],"repository:":[102],"https://github.com/jcapels/SMPrecursorPredictor.":[103]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-15T08:27:34.491423","created_date":"2025-03-20T00:00:00"}
