{"id":"https://openalex.org/W2981350712","doi":"https://doi.org/10.1093/nar/gkz946","title":"Pathway Commons 2019 Update: integration, analysis and exploration of pathway data","display_name":"Pathway Commons 2019 Update: integration, analysis and exploration of pathway data","publication_year":2019,"publication_date":"2019-10-10","ids":{"openalex":"https://openalex.org/W2981350712","doi":"https://doi.org/10.1093/nar/gkz946","mag":"2981350712","pmid":"https://pubmed.ncbi.nlm.nih.gov/31647099"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz946","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz946","pdf_url":"https://academic.oup.com/nar/article-pdf/48/D1/D489/31697764/gkz946.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/48/D1/D489/31697764/gkz946.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086939772","display_name":"Igor Rodchenkov","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Igor Rodchenkov","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006448195","display_name":"\u00d6zg\u00fcn Babur","orcid":"https://orcid.org/0000-0002-0239-5259"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ozgun Babur","raw_affiliation_strings":["Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA"],"raw_orcid":"https://orcid.org/0000-0002-0239-5259","affiliations":[{"raw_affiliation_string":"Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026945351","display_name":"Augustin Luna","orcid":"https://orcid.org/0000-0001-5709-371X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Augustin Luna","raw_affiliation_strings":["Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA","cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020220136","display_name":"B\u00fclent Arman Aksoy","orcid":"https://orcid.org/0000-0002-0135-2505"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I4210100942","display_name":"Tri-Institutional PhD Program in Chemical Biology","ror":"https://ror.org/016twdg30","country_code":"US","type":"education","lineage":["https://openalex.org/I4210100942"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bulent Arman Aksoy","raw_affiliation_strings":["Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA","institution_ids":["https://openalex.org/I4210100942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012697477","display_name":"Jeffrey V. Wong","orcid":"https://orcid.org/0000-0002-8912-5699"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jeffrey V Wong","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":"https://orcid.org/0000-0002-8912-5699","affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075221471","display_name":"Dylan Fong","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Dylan Fong","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071016289","display_name":"Max Franz","orcid":"https://orcid.org/0000-0003-0169-0480"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Max Franz","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063270370","display_name":"Metin Can Siper","orcid":"https://orcid.org/0000-0002-7556-093X"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Metin Can Siper","raw_affiliation_strings":["Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051108737","display_name":"Manfred Cheung","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Manfred Cheung","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011366758","display_name":"Michael Wrana","orcid":"https://orcid.org/0000-0003-1884-9566"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Michael Wrana","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013367153","display_name":"Harsh Mistry","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Harsh Mistry","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041526222","display_name":"Logan Mosier","orcid":"https://orcid.org/0009-0004-9163-411X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Logan Mosier","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026007076","display_name":"Jonah Dlin","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jonah Dlin","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061975395","display_name":"Qizhi Wen","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Qizhi Wen","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031392991","display_name":"Caitlin O\u2019Callaghan","orcid":"https://orcid.org/0000-0003-3388-6496"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Caitlin O\u2019Callaghan","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101539088","display_name":"Wanxin Li","orcid":"https://orcid.org/0000-0001-7513-7368"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Wanxin Li","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014080106","display_name":"G Domingues Elder","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Geoffrey Elder","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102305957","display_name":"Peter T. Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Peter T Smith","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088531553","display_name":"Christian Dallago","orcid":"https://orcid.org/0000-0003-4650-6181"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Christian Dallago","raw_affiliation_strings":["Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA","Department of Informatics, Technische Universit\u00e4t M\u00fcnchen, 85748 Garching, Germany","Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA"],"raw_orcid":"https://orcid.org/0000-0003-4650-6181","affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Informatics, Technische Universit\u00e4t M\u00fcnchen, 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071787046","display_name":"Ethan Cerami","orcid":"https://orcid.org/0009-0009-2340-4490"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ethan Cerami","raw_affiliation_strings":["Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026873890","display_name":"Benjamin Gro\u00df","orcid":"https://orcid.org/0000-0003-4976-8304"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I4210150208","display_name":"Molecular Oncology (United States)","ror":"https://ror.org/04rtkc841","country_code":"US","type":"company","lineage":["https://openalex.org/I4210150208"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Gross","raw_affiliation_strings":["Marie-Jos\u00e9e and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marie-Jos\u00e9e and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA","institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I4210150208"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006798669","display_name":"U\u011fur Do\u011frus\u00f6z","orcid":"https://orcid.org/0000-0002-7153-0784"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ugur Dogrusoz","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-7153-0784","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037803004","display_name":"Emek Demir","orcid":"https://orcid.org/0000-0002-3663-7113"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emek Demir","raw_affiliation_strings":["Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010789029","display_name":"Gary D. Bader","orcid":"https://orcid.org/0000-0003-0185-8861"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Gary D Bader","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada"],"raw_orcid":"https://orcid.org/0000-0003-0185-8861","affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008166270","display_name":"Chris Sander","orcid":"https://orcid.org/0000-0001-6059-6270"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chris Sander","raw_affiliation_strings":["Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA","cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":25,"corresponding_author_ids":["https://openalex.org/A5008166270","https://openalex.org/A5010789029","https://openalex.org/A5037803004"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I165690674","https://openalex.org/I185261750","https://openalex.org/I4210117453"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":13.934,"has_fulltext":false,"cited_by_count":331,"citation_normalized_percentile":{"value":0.99362916,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"48","issue":"D1","first_page":"D489","last_page":"D497"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962999820709229,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9426000118255615,"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/biology","display_name":"Biology","score":0.9236565828323364},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5425428152084351},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.41312265396118164},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3518074154853821},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32780027389526367},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3217717111110687},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32013991475105286},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.1219465434551239},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.10991591215133667}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9236565828323364},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5425428152084351},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.41312265396118164},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3518074154853821},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32780027389526367},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3217717111110687},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32013991475105286},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.1219465434551239},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.10991591215133667}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":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},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkz946","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz946","pdf_url":"https://academic.oup.com/nar/article-pdf/48/D1/D489/31697764/gkz946.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31647099","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31647099","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7145667","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7145667","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/75706","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/75706","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz946","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz946","pdf_url":"https://academic.oup.com/nar/article-pdf/48/D1/D489/31697764/gkz946.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1432320905","display_name":null,"funder_award_id":"ARO W911NF-14-C-0119","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G3989842470","display_name":null,"funder_award_id":"U41 HG006623","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":91,"referenced_works":["https://openalex.org/W956820549","https://openalex.org/W1490161904","https://openalex.org/W1597403892","https://openalex.org/W1969709265","https://openalex.org/W1973661008","https://openalex.org/W1986365650","https://openalex.org/W1989277387","https://openalex.org/W1997207382","https://openalex.org/W2004919210","https://openalex.org/W2010502047","https://openalex.org/W2038264484","https://openalex.org/W2043274355","https://openalex.org/W2043764521","https://openalex.org/W2052685738","https://openalex.org/W2054035764","https://openalex.org/W2069157810","https://openalex.org/W2095304455","https://openalex.org/W2096589119","https://openalex.org/W2096766502","https://openalex.org/W2097948046","https://openalex.org/W2100980426","https://openalex.org/W2114843025","https://openalex.org/W2114904907","https://openalex.org/W2116944463","https://openalex.org/W2122863289","https://openalex.org/W2123280311","https://openalex.org/W2125904022","https://openalex.org/W2126399647","https://openalex.org/W2128128648","https://openalex.org/W2130410032","https://openalex.org/W2130687290","https://openalex.org/W2132218677","https://openalex.org/W2134185611","https://openalex.org/W2134394193","https://openalex.org/W2139254860","https://openalex.org/W2141811925","https://openalex.org/W2143969914","https://openalex.org/W2148043260","https://openalex.org/W2149441684","https://openalex.org/W2157253968","https://openalex.org/W2158439765","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2163485494","https://openalex.org/W2164298117","https://openalex.org/W2164750538","https://openalex.org/W2171599819","https://openalex.org/W2179127114","https://openalex.org/W2234559012","https://openalex.org/W2273647512","https://openalex.org/W2280966365","https://openalex.org/W2291307173","https://openalex.org/W2344638171","https://openalex.org/W2462053388","https://openalex.org/W2465888413","https://openalex.org/W2514649790","https://openalex.org/W2524227683","https://openalex.org/W2555756186","https://openalex.org/W2558366645","https://openalex.org/W2559466477","https://openalex.org/W2597175664","https://openalex.org/W2767546566","https://openalex.org/W2767683865","https://openalex.org/W2767891136","https://openalex.org/W2786963443","https://openalex.org/W2790682049","https://openalex.org/W2794479004","https://openalex.org/W2804894235","https://openalex.org/W2809129882","https://openalex.org/W2894374770","https://openalex.org/W2897334647","https://openalex.org/W2899078837","https://openalex.org/W2910111050","https://openalex.org/W2915769855","https://openalex.org/W2915806464","https://openalex.org/W2936686072","https://openalex.org/W2944545583","https://openalex.org/W2949176808","https://openalex.org/W2949311246","https://openalex.org/W2950021574","https://openalex.org/W2950427239","https://openalex.org/W2952755768","https://openalex.org/W3136918052","https://openalex.org/W3163501683","https://openalex.org/W4233698560","https://openalex.org/W4239615733","https://openalex.org/W4243979784","https://openalex.org/W4255855797","https://openalex.org/W4294216483","https://openalex.org/W6680606729","https://openalex.org/W6718757135"],"related_works":["https://openalex.org/W1979101951","https://openalex.org/W9371027","https://openalex.org/W2020045149","https://openalex.org/W2232328117","https://openalex.org/W4293712663","https://openalex.org/W2922683035","https://openalex.org/W2355440778","https://openalex.org/W2126703991","https://openalex.org/W2610897791","https://openalex.org/W4366463707"],"abstract_inverted_index":{"Pathway":[0,52,67,138],"Commons":[1,68,139],"(https://www.pathwaycommons.org)":[2],"is":[3,41,129],"an":[4],"integrated":[5,84],"resource":[6,165],"of":[7,18,87,92,127,162],"publicly":[8],"available":[9],"information":[10,105],"about":[11],"biological":[12],"pathways":[13,128],"including":[14,49],"biochemical":[15,150],"reactions,":[16],"assembly":[17],"biomolecular":[19],"complexes,":[20],"transport":[21],"and":[22,25,32,37,56,64,94,113,115,154,170,175,182],"catalysis":[23],"events":[24],"physical":[26],"interactions":[27,93],"involving":[28],"proteins,":[29],"DNA,":[30],"RNA,":[31],"small":[33],"molecules":[34],"(e.g.":[35,90],"metabolites":[36],"drug":[38],"compounds).":[39],"Data":[40],"collected":[42],"from":[43,143],"multiple":[44],"providers":[45],"in":[46,106],"standard":[47],"formats,":[48],"the":[50,57,123,132,160],"Biological":[51,134],"Exchange":[53],"(BioPAX)":[54],"language":[55],"Proteomics":[58],"Standards":[59],"Initiative":[60],"Molecular":[61],"Interactions":[62],"format,":[63],"then":[65],"integrated.":[66],"provides":[69],"biologists":[70],"with":[71,103,146],"(i)":[72],"tools":[73],"to":[74],"search":[75],"this":[76,163],"comprehensive":[77],"resource,":[78],"(ii)":[79],"a":[80,117],"download":[81],"site":[82],"offering":[83],"bulk":[85],"sets":[86],"pathway":[88,104,180],"data":[89,142],"tables":[91],"gene":[95],"sets),":[96],"(iii)":[97],"reusable":[98],"software":[99],"libraries":[100],"for":[101,120,166],"working":[102],"several":[107],"programming":[108],"languages":[109],"(Java,":[110],"R,":[111],"Python":[112],"Javascript)":[114],"(iv)":[116],"web":[118,173],"service":[119],"programmatically":[121],"querying":[122],"entire":[124],"dataset.":[125],"Visualization":[126],"supported":[130],"using":[131],"Systems":[133],"Graphical":[135],"Notation":[136],"(SBGN).":[137],"currently":[140],"contains":[141],"22":[144],"databases":[145],"4794":[147],"detailed":[148],"human":[149],"processes":[151],"(i.e.":[152],"pathways)":[153],"\u223c2.3":[155],"million":[156],"interactions.":[157],"To":[158],"enhance":[159],"usability":[161],"large":[164],"end-users,":[167],"we":[168],"develop":[169],"maintain":[171],"interactive":[172],"applications":[174],"training":[176],"materials":[177],"that":[178],"enable":[179],"exploration":[181],"advanced":[183],"analysis.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":55},{"year":2023,"cited_by_count":61},{"year":2022,"cited_by_count":63},{"year":2021,"cited_by_count":56},{"year":2020,"cited_by_count":41},{"year":2019,"cited_by_count":3}],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2025-10-10T00:00:00"}
