{"id":"https://openalex.org/W2129522786","doi":"https://doi.org/10.1093/database/bau049","title":"Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12","display_name":"Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12","publication_year":2014,"publication_date":"2014-06-04","ids":{"openalex":"https://openalex.org/W2129522786","doi":"https://doi.org/10.1093/database/bau049","mag":"2129522786","pmid":"https://pubmed.ncbi.nlm.nih.gov/24903516"},"language":"en","primary_location":{"id":"doi:10.1093/database/bau049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau049","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau049/8246027/bau049.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/bau049/8246027/bau049.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033098879","display_name":"Socorro Gama\u2010Castro","orcid":"https://orcid.org/0000-0001-7708-5143"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"S. Gama-Castro","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025307528","display_name":"Fabio Rinaldi","orcid":"https://orcid.org/0000-0001-5718-5462"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"F. Rinaldi","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland collado@ccg.unam.mx","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland collado@ccg.unam.mx","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110712788","display_name":"Alejandra L\u00f3pez-Fuentes","orcid":null},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"A. Lopez-Fuentes","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019583077","display_name":"Yalbi Itzel Balderas-Mart\u00ednez","orcid":"https://orcid.org/0000-0001-6400-0526"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Y. I. Balderas-Martinez","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073027507","display_name":"Simon Clematide","orcid":"https://orcid.org/0000-0003-1365-0662"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"S. Clematide","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069674228","display_name":"Tilia Ellendorff","orcid":"https://orcid.org/0000-0002-8543-4902"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"T. R. Ellendorff","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026565466","display_name":"Alberto Santos-Zavaleta","orcid":"https://orcid.org/0000-0002-2178-4006"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"A. Santos-Zavaleta","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5097642591","display_name":"H. Marques-Madeira","orcid":null},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"H. Marques-Madeira","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079232768","display_name":"Julio Collado\u2010Vides","orcid":"https://orcid.org/0000-0001-8780-7664"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"J. Collado-Vides","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland collado@ccg.unam.mx","Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, A.P. 565-A, Cuernavaca, Morelos 62100 and Institute of Computational Linguistics, University of Zurich, Binzmuhlestrasse 14, Zurich 8050, Switzerland collado@ccg.unam.mx","institution_ids":[]},{"raw_affiliation_string":"Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City, Mexico","institution_ids":["https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5033098879"],"corresponding_institution_ids":["https://openalex.org/I8961855"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.5687,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.82985681,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2014","issue":"0","first_page":"bau049","last_page":"bau049"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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":0.996999979019165,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.991100013256073,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7059679627418518},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5999935865402222},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.43142277002334595},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.429299920797348},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.42828407883644104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33788105845451355},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2112615406513214}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7059679627418518},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5999935865402222},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43142277002334595},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.429299920797348},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.42828407883644104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33788105845451355},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2112615406513214},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","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":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bau049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau049","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau049/8246027/bau049.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:24903516","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24903516","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:europepmc.org:3177568","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4207228","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bau049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau049","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau049/8246027/bau049.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/G1565274940","display_name":"Estimation des d\u00e9bits d'\u00e9tiage sur des cours d'eau sans mesures directes","funder_award_id":"10531","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G250864464","display_name":"Intelligent computational control for complex structures","funder_award_id":"105315","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G3426842625","display_name":"Regionale Einkommensinzidenz der Bundesbauten","funder_award_id":"10435","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G533832786","display_name":"Semi-automated semantic enrichment of biomedical literature","funder_award_id":"130558","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321739","display_name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","ror":"https://ror.org/059ex5q34"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129522786.pdf","grobid_xml":"https://content.openalex.org/works/W2129522786.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1487254759","https://openalex.org/W1535380218","https://openalex.org/W1646462907","https://openalex.org/W1844489234","https://openalex.org/W1990406293","https://openalex.org/W2002144817","https://openalex.org/W2056224444","https://openalex.org/W2064000861","https://openalex.org/W2069024774","https://openalex.org/W2074431736","https://openalex.org/W2078208374","https://openalex.org/W2094812249","https://openalex.org/W2098008966","https://openalex.org/W2111504670","https://openalex.org/W2112271889","https://openalex.org/W2115378879","https://openalex.org/W2118640842","https://openalex.org/W2121365413","https://openalex.org/W2127014487","https://openalex.org/W2134701031","https://openalex.org/W2146598476","https://openalex.org/W2147641929","https://openalex.org/W2153646016","https://openalex.org/W2159827502","https://openalex.org/W2166256097","https://openalex.org/W2169346653","https://openalex.org/W2170587483","https://openalex.org/W2170806980"],"related_works":["https://openalex.org/W1657880117","https://openalex.org/W2082860237","https://openalex.org/W2595172197","https://openalex.org/W2119695867","https://openalex.org/W2127970246","https://openalex.org/W2084856301","https://openalex.org/W1001352512","https://openalex.org/W2130076355","https://openalex.org/W4382618745","https://openalex.org/W2885125400"],"abstract_inverted_index":{"Given":[0],"the":[1,11,19,38,64,74,98,128,136,177,180,205,210,216,228,231],"current":[2],"explosion":[3],"of":[4,13,21,41,67,112,127,162,179,190,196,209,212,218,230,234],"data":[5],"within":[6],"original":[7,39,191],"publications":[8],"generated":[9],"in":[10,37,70,89,133,199,215,227],"field":[12],"genomics,":[14],"a":[15,60,90,110,160,165,187,224],"recognized":[16],"bottleneck":[17],"is":[18,51],"transfer":[20],"such":[22],"knowledge":[23,32,213],"into":[24,45],"comprehensive":[25],"databases.":[26],"We":[27],"have":[28],"for":[29,164,186],"years":[30],"organized":[31],"on":[33,94,109,142],"transcriptional":[34],"regulation":[35,195],"reported":[36],"literature":[40,192,217],"Escherichia":[42],"coli":[43],"K-12":[44],"RegulonDB":[46,237],"(http://regulondb.ccg.unam.mx),":[47],"our":[48],"database":[49],"that":[50,96],"currently":[52],"supported":[53],"by":[54,119],">5000":[55],"papers.":[56,107],"Here,":[57],"we":[58,79,121,152],"report":[59],"first":[61],"step":[62],"towards":[63],"automatic":[65],"biocuration":[66],"growth":[68,87,155],"conditions":[69,88],"this":[71],"corpus.":[72],"Using":[73],"OntoGene":[75,241],"text-mining":[76],"system":[77],"(http://www.ontogene.org),":[78],"extracted":[80],"and":[81,86,139,168,172,207,221],"manually":[82],"validated":[83],"regulatory":[84,130,232],"interactions":[85,131],"new":[91],"approach":[92],"based":[93],"filters":[95],"enable":[97],"curator":[99],"to":[100,124,149,175,183,223],"select":[101],"informative":[102],"sentences":[103],"from":[104],"preprocessed":[105],"full":[106],"Based":[108],"set":[111],"48":[113],"papers":[114],"dealing":[115,193],"with":[116,194],"oxidative":[117],"stress":[118],"OxyR,":[120],"were":[122],"able":[123],"retrieve":[125],"100%":[126],"OxyR":[129],"present":[132,214],"RegulonDB,":[134],"including":[135],"transcription":[137],"factors":[138],"their":[140,154],"effect":[141],"target":[143],"genes.":[144],"Our":[145],"strategy":[146,178],"was":[147],"designed":[148],"extract,":[150],"as":[151],"did,":[153],"conditions.":[156],"This":[157,201],"result":[158],"provides":[159],"proof":[161],"concept":[163],"more":[166],"direct":[167],"efficient":[169],"curation":[170,189,211],"process,":[171],"enables":[173],"us":[174],"define":[176],"subsequent":[181],"steps":[182],"be":[184],"implemented":[185],"semi-automatic":[188],"gene":[197,219],"expression":[198],"bacteria.":[200],"project":[202],"will":[203],"enhance":[204],"efficiency":[206],"quality":[208],"regulation,":[220],"contribute":[222],"significant":[225],"increase":[226],"encoding":[229],"network":[233],"E.":[235],"coli.":[236],"Database":[238],"URL:":[239,242],"http://regulondb.ccg.unam.mx":[240],"http://www.ontogene.org.":[243]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
