{"id":"https://openalex.org/W4353075579","doi":"https://doi.org/10.1186/s12859-023-05149-8","title":"Pickaxe: a Python library for the prediction of novel metabolic reactions","display_name":"Pickaxe: a Python library for the prediction of novel metabolic reactions","publication_year":2023,"publication_date":"2023-03-22","ids":{"openalex":"https://openalex.org/W4353075579","doi":"https://doi.org/10.1186/s12859-023-05149-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/36949401"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05149-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05149-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05149-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05149-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067028539","display_name":"Kevin M. Shebek","orcid":null},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kevin M. Shebek","raw_affiliation_strings":["Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA","Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA","Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA"],"affiliations":[{"raw_affiliation_string":"Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043770622","display_name":"Jonathan Strutz","orcid":"https://orcid.org/0000-0003-0934-4283"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Strutz","raw_affiliation_strings":["Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA","Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA","Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA"],"affiliations":[{"raw_affiliation_string":"Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054861635","display_name":"Linda J. Broadbelt","orcid":"https://orcid.org/0000-0003-4253-592X"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linda J. Broadbelt","raw_affiliation_strings":["Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA","Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA"],"affiliations":[{"raw_affiliation_string":"Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049701357","display_name":"Keith E. J. Tyo","orcid":"https://orcid.org/0000-0002-2342-0687"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith E. J. Tyo","raw_affiliation_strings":["Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA. k-tyo@northwestern.edu","Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. k-tyo@northwestern.edu","Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. k-tyo@northwestern.edu","Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA"],"affiliations":[{"raw_affiliation_string":"Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA. k-tyo@northwestern.edu","institution_ids":[]},{"raw_affiliation_string":"Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. k-tyo@northwestern.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. k-tyo@northwestern.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5067028539"],"corresponding_institution_ids":["https://openalex.org/I111979921"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.3682,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.88441989,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"106","last_page":"106"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9988999962806702,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9976999759674072,"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/computer-science","display_name":"Computer science","score":0.730982780456543},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.593586266040802},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5809423327445984},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5624351501464844},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.49597176909446716},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.47899195551872253},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4588909447193146},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.45014527440071106},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4394790530204773},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3039296865463257},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2537195682525635},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18179070949554443},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.13324075937271118},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1215730607509613},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.1158246099948883}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.730982780456543},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.593586266040802},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5809423327445984},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5624351501464844},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.49597176909446716},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.47899195551872253},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4588909447193146},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.45014527440071106},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4394790530204773},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3039296865463257},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2537195682525635},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18179070949554443},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.13324075937271118},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1215730607509613},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.1158246099948883},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-023-05149-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05149-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05149-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36949401","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36949401","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10031857","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10031857","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10031857/pdf/12859_2023_Article_5149.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:3877277a2d7e4695981d756edad3fe92","is_oa":true,"landing_page_url":"https://doaj.org/article/3877277a2d7e4695981d756edad3fe92","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"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":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-15 (2023)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1962934","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1962934","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:osti.gov:2420742","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2420742","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05149-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05149-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05149-8","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5286455319","display_name":null,"funder_award_id":"DE-SC0018249","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"}],"funders":[{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4353075579.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1934481644","https://openalex.org/W1983478747","https://openalex.org/W1990088060","https://openalex.org/W2022374283","https://openalex.org/W2030555543","https://openalex.org/W2128312954","https://openalex.org/W2201696856","https://openalex.org/W2466795701","https://openalex.org/W2555587815","https://openalex.org/W2558428302","https://openalex.org/W2559588208","https://openalex.org/W2566364344","https://openalex.org/W2605253412","https://openalex.org/W2782584560","https://openalex.org/W2803153322","https://openalex.org/W2889436607","https://openalex.org/W2901812771","https://openalex.org/W2907470641","https://openalex.org/W2915462167","https://openalex.org/W2916475656","https://openalex.org/W2938072319","https://openalex.org/W2949078105","https://openalex.org/W2971956741","https://openalex.org/W2981670263","https://openalex.org/W3012335944","https://openalex.org/W3016452877","https://openalex.org/W3019108305","https://openalex.org/W3103373754","https://openalex.org/W3116115510","https://openalex.org/W3120686965","https://openalex.org/W3134564396","https://openalex.org/W3135416650","https://openalex.org/W3137348624","https://openalex.org/W3138458927","https://openalex.org/W3155723246","https://openalex.org/W3185730212","https://openalex.org/W3216494066","https://openalex.org/W4247393540","https://openalex.org/W4281257426"],"related_works":["https://openalex.org/W1495449059","https://openalex.org/W2374260038","https://openalex.org/W2216418212","https://openalex.org/W1990404960","https://openalex.org/W2020641517","https://openalex.org/W2072874942","https://openalex.org/W2075919068","https://openalex.org/W1974325331","https://openalex.org/W2045478141","https://openalex.org/W2119961194"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
