{"id":"https://openalex.org/W2514630101","doi":"https://doi.org/10.1093/database/baw126","title":"Modeling biochemical pathways in the gene ontology","display_name":"Modeling biochemical pathways in the gene ontology","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2514630101","doi":"https://doi.org/10.1093/database/baw126","mag":"2514630101","pmid":"https://pubmed.ncbi.nlm.nih.gov/27589964"},"language":"en","primary_location":{"id":"doi:10.1093/database/baw126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw126","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw126/17474522/baw126.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","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/database/article-pdf/doi/10.1093/database/baw126/17474522/baw126.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029292423","display_name":"David P. Hill","orcid":"https://orcid.org/0000-0001-7476-6306"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David P. Hill","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME 04609, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME 04609, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074201106","display_name":"Peter D\u2019Eustachio","orcid":"https://orcid.org/0000-0002-5494-626X"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter D\u2019Eustachio","raw_affiliation_strings":["Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062305384","display_name":"Tanya Berardini","orcid":"https://orcid.org/0000-0002-3837-8864"},"institutions":[{"id":"https://openalex.org/I4210087078","display_name":"Phoenix Bioinformatics","ror":"https://ror.org/0018yg518","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210087078"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tanya Z. Berardini","raw_affiliation_strings":["Arabidopsis Information Resource, Phoenix Bioinformatics, Redwood City, CA 94063, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Arabidopsis Information Resource, Phoenix Bioinformatics, Redwood City, CA 94063, USA","institution_ids":["https://openalex.org/I4210087078"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002223413","display_name":"Chris Mungall","orcid":"https://orcid.org/0000-0002-6601-2165"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher J. Mungall","raw_affiliation_strings":["Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000636287","display_name":"Nikolai Renedo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikolai Renedo","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME 04609, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME 04609, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016349593","display_name":"Judith A. Blake","orcid":"https://orcid.org/0000-0001-8522-334X"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Judith A. Blake","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME 04609, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME 04609, USA","institution_ids":["https://openalex.org/I4210115256"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5074201106"],"corresponding_institution_ids":["https://openalex.org/I57206974"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.0446,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.78860418,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2016","issue":null,"first_page":"baw126","last_page":"baw126"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9921000003814697,"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/ontology","display_name":"Ontology","score":0.7434283494949341},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6660756468772888},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5894327163696289},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.46272721886634827},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4583868384361267},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.4391983449459076},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.41784900426864624},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.41373342275619507},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.332369863986969},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.323138952255249},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2463797926902771},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23727068305015564},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20504486560821533},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08778831362724304}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7434283494949341},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6660756468772888},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5894327163696289},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.46272721886634827},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4583868384361267},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.4391983449459076},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.41784900426864624},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.41373342275619507},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.332369863986969},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.323138952255249},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2463797926902771},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23727068305015564},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20504486560821533},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08778831362724304},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1093/database/baw126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw126","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw126/17474522/baw126.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:27589964","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27589964","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:osti.gov:1377445","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1377445","pdf_url":"https://www.osti.gov/servlets/purl/1377445","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":null,"raw_type":null},{"id":"pmh:ark:/13030/qt71r6w4wv","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt71r6w4wv","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/71r6w4wv","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database : the journal of biological databases and curation, vol 2016","raw_type":"article"},{"id":"pmh:oai:mouseion.jax.org:stfb2016-1174","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfb2016/178","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2016","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:databa:2016/0/baw126","is_oa":false,"landing_page_url":"http://database.oxfordjournals.org/cgi/content/short/2016/0/baw126","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:5009323","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5009323","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":"Database (Oxford)","raw_type":"Text"},{"id":"pmh:qt71r6w4wv","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/71r6w4wv","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Hill, DP; D'Eustachio, P; Berardini, TZ; Mungall, CJ; Renedo, N; &amp; Blake, JA. (2016). Modeling biochemical pathways in the gene ontology. Database : the journal of biological databases and curation, 2016, baw126 - baw126. doi: 10.1093/database/baw126. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/71r6w4wv","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/database/baw126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baw126","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baw126/17474522/baw126.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1286251239","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"},{"id":"https://openalex.org/G1831838341","display_name":null,"funder_award_id":"U41 HG 003751","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2776628454","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5123489780","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7538560101","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8431251193","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320337480","funder_display_name":"Basic Energy Sciences"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337480","display_name":"Basic Energy Sciences","ror":"https://ror.org/05mg91w61"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W55962619","https://openalex.org/W638789088","https://openalex.org/W1236321187","https://openalex.org/W1490161904","https://openalex.org/W1501546233","https://openalex.org/W1545791390","https://openalex.org/W1563676191","https://openalex.org/W1659163511","https://openalex.org/W1965091013","https://openalex.org/W1981021538","https://openalex.org/W1989277387","https://openalex.org/W1992466559","https://openalex.org/W2022451103","https://openalex.org/W2044257395","https://openalex.org/W2073814577","https://openalex.org/W2096704019","https://openalex.org/W2103017472","https://openalex.org/W2103260426","https://openalex.org/W2109899437","https://openalex.org/W2113142309","https://openalex.org/W2120793040","https://openalex.org/W2120828434","https://openalex.org/W2128601422","https://openalex.org/W2130096579","https://openalex.org/W2134245322","https://openalex.org/W2140299962","https://openalex.org/W2140611297","https://openalex.org/W2151712814","https://openalex.org/W2162385209","https://openalex.org/W2172196250","https://openalex.org/W2192374892","https://openalex.org/W3102771275","https://openalex.org/W4230770774"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2045726866","https://openalex.org/W2354320020","https://openalex.org/W2057110953","https://openalex.org/W1998044538","https://openalex.org/W2418415513","https://openalex.org/W3127907745","https://openalex.org/W2551839783","https://openalex.org/W2134380650","https://openalex.org/W75900285"],"abstract_inverted_index":{"The":[0,66],"concept":[1],"of":[2,9,24,28,37,81,109,143],"a":[3,21,58,91,132,148],"biological":[4,82],"pathway,":[5],"an":[6],"ordered":[7],"sequence":[8],"molecular":[10,18,55],"transformations,":[11],"is":[12],"used":[13,155],"to":[14,62],"collect":[15],"and":[16,46,75,95,106,125,159],"represent":[17],"knowledge":[19,39,112],"for":[20,93,102,156],"broad":[22],"span":[23],"organismal":[25],"biology.":[26],"Representations":[27],"biomedical":[29,44],"pathways":[30,83,130],"typically":[31],"are":[32,50],"rich":[33],"but":[34],"idiosyncratic":[35],"presentations":[36],"organized":[38],"about":[40],"individual":[41],"pathways.":[42],"Meanwhile,":[43],"ontologies":[45],"associated":[47],"annotation":[48],"files":[49],"powerful":[51],"tools":[52],"that":[53,152],"organize":[54],"information":[56],"in":[57,99,114,121],"logically":[59],"rigorous":[60],"form":[61],"support":[63],"computational":[64],"analysis.":[65,160],"Gene":[67],"Ontology":[68],"(GO),":[69],"representing":[70],"Molecular":[71],"Functions,":[72],"Biological":[73],"Processes":[74],"Cellular":[76],"Components,":[77],"incorporates":[78],"many":[79],"aspects":[80],"within":[84],"its":[85],"ontological":[86,150],"representations.":[87],"Here":[88],"we":[89,135],"present":[90],"methodology":[92],"extending":[94],"refining":[96],"the":[97,100,122,141],"classes":[98,146],"GO":[101],"more":[103],"comprehensive,":[104],"consistent":[105],"integrated":[107],"representation":[108,139],"pathways,":[110],"leveraging":[111],"embedded":[113],"current":[115],"pathway":[116,145],"representations":[117],"such":[118],"as":[119,131],"those":[120],"Reactome":[123],"Knowledgebase":[124],"MetaCyc.":[126],"With":[127],"carbohydrate":[128],"metabolic":[129],"use":[133],"case,":[134],"discuss":[136],"how":[137],"our":[138],"supports":[140],"integration":[142],"variant":[144],"into":[147],"unified":[149],"structure":[151],"can":[153],"be":[154],"data":[157],"comparison":[158]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-04T09:04:59.091469","created_date":"2025-10-10T00:00:00"}
