{"id":"https://openalex.org/W2123931667","doi":"https://doi.org/10.1007/978-3-642-34123-6_11","title":"An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction","display_name":"An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2123931667","doi":"https://doi.org/10.1007/978-3-642-34123-6_11","mag":"2123931667"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-642-34123-6_11","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-34123-6_11","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1822/23782","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076738885","display_name":"Jo\u00e3o Cardoso","orcid":"https://orcid.org/0000-0001-8173-2673"},"institutions":[{"id":"https://openalex.org/I4210114428","display_name":"SilicoLife (Portugal)","ror":"https://ror.org/029gksr15","country_code":"PT","type":"company","lineage":["https://openalex.org/I4210114428"]},{"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 Cardoso","raw_affiliation_strings":["CCTC, School of Engineering, University of Minho, Portugal","SilicoLife Lda., Spinpark, Avepark, Apart. 4152, 4806-909, Guimar\u00e3es, Portugal"],"affiliations":[{"raw_affiliation_string":"CCTC, School of Engineering, University of Minho, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"SilicoLife Lda., Spinpark, Avepark, Apart. 4152, 4806-909, Guimar\u00e3es, Portugal","institution_ids":["https://openalex.org/I4210114428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085847301","display_name":"Paulo Vila\u00e7a","orcid":"https://orcid.org/0000-0002-1098-5849"},"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"]},{"id":"https://openalex.org/I4210114428","display_name":"SilicoLife (Portugal)","ror":"https://ror.org/029gksr15","country_code":"PT","type":"company","lineage":["https://openalex.org/I4210114428"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Paulo Vila\u00e7a","raw_affiliation_strings":["CCTC, School of Engineering, University of Minho, Portugal","SilicoLife Lda., Spinpark, Avepark, Apart. 4152, 4806-909, Guimar\u00e3es, Portugal"],"affiliations":[{"raw_affiliation_string":"CCTC, School of Engineering, University of Minho, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"SilicoLife Lda., Spinpark, Avepark, Apart. 4152, 4806-909, Guimar\u00e3es, Portugal","institution_ids":["https://openalex.org/I4210114428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002874757","display_name":"Sim\u00e3o Soares","orcid":"https://orcid.org/0000-0002-8811-8403"},"institutions":[{"id":"https://openalex.org/I4210114428","display_name":"SilicoLife (Portugal)","ror":"https://ror.org/029gksr15","country_code":"PT","type":"company","lineage":["https://openalex.org/I4210114428"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Sim\u00e3o Soares","raw_affiliation_strings":["SilicoLife Lda., Spinpark, Avepark, Apart. 4152, 4806-909, Guimar\u00e3es, Portugal"],"affiliations":[{"raw_affiliation_string":"SilicoLife Lda., Spinpark, Avepark, Apart. 4152, 4806-909, Guimar\u00e3es, Portugal","institution_ids":["https://openalex.org/I4210114428"]}]},{"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":["CCTC, School of Engineering, University of Minho, Portugal"],"affiliations":[{"raw_affiliation_string":"CCTC, School of Engineering, University of Minho, Portugal","institution_ids":["https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076738885"],"corresponding_institution_ids":["https://openalex.org/I4210114428","https://openalex.org/I99682543"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.12663365,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"118","last_page":"128"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9909999966621399,"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/uniprot","display_name":"UniProt","score":0.8413647413253784},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6589059233665466},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6021538972854614},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5621530413627625},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5604305267333984},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5027358531951904},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.441213995218277},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4176931381225586},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3947930335998535},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32949793338775635},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29917240142822266},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2004433274269104},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1837320327758789},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14368295669555664},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12984517216682434}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.8413647413253784},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6589059233665466},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6021538972854614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5621530413627625},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5604305267333984},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5027358531951904},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.441213995218277},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4176931381225586},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3947930335998535},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32949793338775635},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29917240142822266},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2004433274269104},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1837320327758789},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14368295669555664},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12984517216682434},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-642-34123-6_11","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-34123-6_11","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/23782","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/23782","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:repositorium.uminho.pt:1822/23782","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/23782","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference paper"}],"best_oa_location":{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/23782","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/23782","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1604281503","https://openalex.org/W1771437493","https://openalex.org/W2030776070","https://openalex.org/W2040102554","https://openalex.org/W2067469807","https://openalex.org/W2072743957","https://openalex.org/W2083011190","https://openalex.org/W2085993965","https://openalex.org/W2096245011","https://openalex.org/W2100084634","https://openalex.org/W2125377494","https://openalex.org/W2126175129","https://openalex.org/W2130253098","https://openalex.org/W2170427655","https://openalex.org/W4233744131","https://openalex.org/W4247892585","https://openalex.org/W6822430352"],"related_works":["https://openalex.org/W24553703","https://openalex.org/W4211000692","https://openalex.org/W4212920271","https://openalex.org/W2102027645","https://openalex.org/W2107785922","https://openalex.org/W2035528219","https://openalex.org/W2402478170","https://openalex.org/W2946410450","https://openalex.org/W2999847357","https://openalex.org/W2901823680"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
