{"id":"https://openalex.org/W2131522736","doi":"https://doi.org/10.1142/s0219720014420013","title":"PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list","display_name":"PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list","publication_year":2014,"publication_date":"2014-10-08","ids":{"openalex":"https://openalex.org/W2131522736","doi":"https://doi.org/10.1142/s0219720014420013","mag":"2131522736","pmid":"https://pubmed.ncbi.nlm.nih.gov/25385078"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720014420013","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720014420013","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058370326","display_name":"Masaaki Kotera","orcid":"https://orcid.org/0000-0001-8188-3623"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Masaaki Kotera","raw_affiliation_strings":["Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063092960","display_name":"Yosuke Nishimura","orcid":"https://orcid.org/0000-0002-8028-3228"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yosuke Nishimura","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036120625","display_name":"Zenichi Nakagawa","orcid":null},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Zen-Ichi Nakagawa","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016024055","display_name":"Ai Muto","orcid":null},"institutions":[{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ai Muto","raw_affiliation_strings":["Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan","institution_ids":["https://openalex.org/I75917431"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036198187","display_name":"Yuki Moriya","orcid":"https://orcid.org/0000-0001-8195-5893"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuki Moriya","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109529988","display_name":"Shinobu Okamoto","orcid":null},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shinobu Okamoto","raw_affiliation_strings":["Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039336067","display_name":"Shuichi Kawashima","orcid":"https://orcid.org/0000-0001-7883-3756"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shuichi Kawashima","raw_affiliation_strings":["Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031153467","display_name":"Toshiaki Katayama","orcid":"https://orcid.org/0000-0003-2391-0384"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toshiaki Katayama","raw_affiliation_strings":["Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042132185","display_name":"Toshiaki Tokimatsu","orcid":"https://orcid.org/0009-0006-0834-2461"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toshiaki Tokimatsu","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"raw_affiliation_string":"Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058022821","display_name":"Minoru Kanehisa","orcid":"https://orcid.org/0000-0001-6123-540X"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Minoru Kanehisa","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102872908","display_name":"Susumu Goto","orcid":"https://orcid.org/0000-0003-2989-8486"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Susumu Goto","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5058370326"],"corresponding_institution_ids":["https://openalex.org/I114531698"],"apc_list":null,"apc_paid":null,"fwci":0.4183,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.63876168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"12","issue":"06","first_page":"1442001","last_page":"1442001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9944000244140625,"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":0.742903470993042},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.6755819320678711},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.6054466366767883},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5862473845481873},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5799940824508667},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47833892703056335},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.43671587109565735},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4051149785518646},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33818021416664124},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.28479039669036865},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27677643299102783},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09488362073898315}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.742903470993042},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.6755819320678711},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.6054466366767883},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5862473845481873},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5799940824508667},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47833892703056335},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.43671587109565735},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4051149785518646},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33818021416664124},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.28479039669036865},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27677643299102783},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09488362073898315},{"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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720014420013","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720014420013","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:25385078","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25385078","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1555486317","https://openalex.org/W1969404643","https://openalex.org/W1976308333","https://openalex.org/W1999894606","https://openalex.org/W2005292246","https://openalex.org/W2030342799","https://openalex.org/W2032936332","https://openalex.org/W2059770489","https://openalex.org/W2062926086","https://openalex.org/W2096435725","https://openalex.org/W2103017472","https://openalex.org/W2112687514","https://openalex.org/W2120908187","https://openalex.org/W2131660156","https://openalex.org/W2131848047","https://openalex.org/W2140611297","https://openalex.org/W2152099248","https://openalex.org/W2157414955","https://openalex.org/W2160926845","https://openalex.org/W2408398755"],"related_works":["https://openalex.org/W2350593162","https://openalex.org/W2390350206","https://openalex.org/W1969477129","https://openalex.org/W2921208823","https://openalex.org/W2131808775","https://openalex.org/W2353483812","https://openalex.org/W2360756181","https://openalex.org/W2374093222","https://openalex.org/W3154008094","https://openalex.org/W2359533638"],"abstract_inverted_index":{"Genomics":[0],"is":[1,23],"faced":[2,24],"with":[3,25],"the":[4,26,55,61,64,78,83,86,89,96,102,108,136,144,165,185,199,205,212,217,222],"issue":[5,27],"of":[6,28,42,63,77,85,99,111,187,195,201,211,224],"many":[7,29],"partially":[8],"annotated":[9],"putative":[10,30],"enzyme-encoding":[11],"genes":[12,197],"for":[13,33,129],"which":[14,34],"activities":[15],"have":[16,37],"not":[17,38,68],"yet":[18],"been":[19,39,45,51,69],"verified,":[20],"while":[21],"metabolomics":[22],"enzyme":[31],"reactions":[32,112,140,155],"full":[35],"equations":[36],"verified.":[40],"Knowledge":[41],"enzymes":[43,203],"has":[44,50,67],"collected":[46],"by":[47,72,116],"IUBMB,":[48],"and":[49,105,147,156,181,198,226],"made":[52],"public":[53],"as":[54,133],"Enzyme":[56,65,90,103,145,218],"List.":[57],"To":[58],"date,":[59],"however,":[60],"terminology":[62,100,137],"List":[66,219],"assessed":[70],"comprehensively":[71],"bioinformatics":[73,79],"studies.":[74],"Instead,":[75],"most":[76],"studies":[80],"simply":[81,117],"use":[82],"identifiers":[84],"enzymes,":[87],"i.e.":[88],"Commission":[91],"(EC)":[92],"numbers.":[93,120],"We":[94],"investigated":[95],"actual":[97,166],"usage":[98],"throughout":[101],"List,":[104,146],"demonstrated":[106],"that":[107],"partial":[109,189],"characteristics":[110,191],"cannot":[113],"be":[114],"retrieved":[115,142],"using":[118],"EC":[119,182],"Thus,":[121],"we":[122],"developed":[123],"a":[124],"novel":[125],"ontology,":[126],"named":[127],"PIERO,":[128],"annotating":[130],"biochemical":[131,157],"transformations":[132,167],"follows.":[134],"First,":[135],"describing":[138],"enzymatic":[139,170],"was":[141,148,175],"from":[143,169,192,204],"grouped":[149],"into":[150],"those":[151],"related":[152],"to":[153,177,220],"overall":[154],"transformations.":[158,207],"Consequently,":[159],"these":[160],"terms":[161],"were":[162],"mapped":[163],"onto":[164],"taken":[168],"reaction":[171,190],"equations.":[172],"This":[173],"ontology":[174,214],"linked":[176],"Gene":[178],"Ontology":[179],"(GO)":[180],"numbers,":[183],"allowing":[184],"extraction":[186],"common":[188],"given":[193,206],"sets":[194],"orthologous":[196],"elucidation":[200],"possible":[202],"Further":[208],"future":[209],"development":[210],"PIERO":[213],"should":[215],"enhance":[216],"promote":[221],"integration":[223],"genomics":[225],"metabolomics.":[227]},"counts_by_year":[{"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":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
