{"id":"https://openalex.org/W4247745385","doi":"https://doi.org/10.1093/database/bax029","title":"Strategies towards digital and semi-automated curation in RegulonDB","display_name":"Strategies towards digital and semi-automated curation in RegulonDB","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W4247745385","doi":"https://doi.org/10.1093/database/bax029"},"language":"en","primary_location":{"id":"doi:10.1093/database/bax029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax029","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax012/19231098/bax012.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":"erratum","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax012/19231098/bax012.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","MX"],"is_corresponding":true,"raw_author_name":"Fabio 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","Swiss Institute of Bioinformatics and Institute of Computational Linguistics, University of Zurich, Andreasstrasse 15, Zurich 8050, Switzerland"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics and Institute of Computational Linguistics, University of Zurich, Andreasstrasse 15, Zurich 8050, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004896711","display_name":"Oscar Lithgow","orcid":null},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]},{"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":"Oscar Lithgow","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"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033098879","display_name":"Socorro Gama\u2010Castro","orcid":"https://orcid.org/0000-0001-7708-5143"},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]},{"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":"Socorro 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"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086619875","display_name":"Hilda Solano","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"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Hilda Solano","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"],"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","institution_ids":["https://openalex.org/I884181516","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"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Alejandra L\u00f3pez-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"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069565054","display_name":"Luis Jos\u00e9 Mu\u00f1iz Rascado","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"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Luis Jos\u00e9 Mu\u00f1iz Rascado","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"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089360167","display_name":"Cecilia Ishida-Guti\u00e9rrez","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"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Cecilia Ishida-Guti\u00e9rrez","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"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086154618","display_name":"Carlos-Francisco M\u00e9ndez-Cruz","orcid":"https://orcid.org/0000-0002-2549-1614"},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]},{"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":"Carlos-Francisco M\u00e9ndez-Cruz","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"],"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","institution_ids":["https://openalex.org/I884181516","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"]},{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Julio 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"],"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","institution_ids":["https://openalex.org/I884181516","https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5025307528","https://openalex.org/A5004896711"],"corresponding_institution_ids":["https://openalex.org/I8961855","https://openalex.org/I884181516","https://openalex.org/I202697423","https://openalex.org/I12708293"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.40849622,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2017","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9853000044822693,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9646999835968018,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.7245331406593323},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6617529392242432},{"id":"https://openalex.org/keywords/digital-curation","display_name":"Digital curation","score":0.6517963409423828},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5105489492416382},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3795315623283386},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32092833518981934}],"concepts":[{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.7245331406593323},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6617529392242432},{"id":"https://openalex.org/C2775953033","wikidata":"https://www.wikidata.org/wiki/Q5276060","display_name":"Digital curation","level":2,"score":0.6517963409423828},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5105489492416382},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3795315623283386},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32092833518981934}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/database/bax029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax029","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax012/19231098/bax012.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"}],"best_oa_location":{"id":"doi:10.1093/database/bax029","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bax029","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bax012/19231098/bax012.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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4247745385.pdf","grobid_xml":"https://content.openalex.org/works/W4247745385.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3114344106","https://openalex.org/W4221164369","https://openalex.org/W2016408706","https://openalex.org/W947447849","https://openalex.org/W3059364583","https://openalex.org/W2007447178","https://openalex.org/W1522326043","https://openalex.org/W3200541379","https://openalex.org/W2736466919","https://openalex.org/W1984363735"],"abstract_inverted_index":{"Experimentally":[0],"generated":[1],"biological":[2],"information":[3,22],"needs":[4,149],"to":[5,12,31,50,55,102,106,125,130,150,169,199],"be":[6,151,170],"organized":[7],"and":[8,42,82,188],"structured":[9],"in":[10,74,175],"order":[11],"become":[13],"meaningful":[14],"knowledge.":[15],"However,":[16],"the":[17,58,68,75,79,85,89,92,117,126,144,164,176,180,207],"rate":[18],"at":[19],"which":[20,112],"new":[21,34],"is":[23,100,172],"being":[24,173],"published":[25],"makes":[26],"manual":[27,211],"curation":[28,35,76,118,204],"increasingly":[29],"unable":[30],"cope.":[32],"Devising":[33],"strategies":[36],"that":[37,148],"leverage":[38],"upon":[39],"data":[40],"mining":[41,72],"text":[43,71,147],"analysis":[44],"is,":[45],"therefore,":[46],"a":[47,95,107,131,154,201],"promising":[48],"avenue":[49],"help":[51],"life":[52],"science":[53],"databases":[54],"cope":[56],"with":[57,206],"deluge":[59],"of":[60,70,78,91,109,140,146,157,167,185],"novel":[61],"information.":[62],"In":[63],"this":[64],"article,":[65],"we":[66],"describe":[67],"integration":[69],"technologies":[73],"pipeline":[77],"RegulonDB":[80],"database,":[81],"discuss":[83],"how":[84],"process":[86,205],"can":[87,134],"enhance":[88],"productivity":[90],"curators.":[93],"Specifically,":[94],"named":[96],"entity":[97],"recognition":[98],"approach":[99],"used":[101],"pre-annotate":[103],"terms":[104],"referring":[105],"set":[108],"domain":[110,190],"entities":[111],"are":[113,123,195],"potentially":[114],"relevant":[115],"for":[116],"process.":[119],"The":[120],"annotated":[121],"documents":[122],"presented":[124],"curator,":[127],"who,":[128],"thanks":[129],"custom-designed":[132],"interface,":[133],"select":[135],"sentences":[136,162],"containing":[137],"specific":[138],"types":[139],"entities,":[141],"thus":[142],"restricting":[143],"amount":[145],"inspected.":[152],"Additionally,":[153],"module":[155,181],"capable":[156],"computing":[158],"semantic":[159],"similarity":[160],"between":[161],"across":[163],"entire":[165],"collection":[166],"articles":[168,187],"curated":[171],"integrated":[174],"system.":[177],"We":[178],"tested":[179],"using":[182],"three":[183],"sets":[184],"scientific":[186],"six":[189],"experts.":[191],"All":[192],"these":[193],"improvements":[194],"gradually":[196],"enabling":[197],"us":[198],"obtain":[200],"high":[202],"throughput":[203],"same":[208],"quality":[209],"as":[210],"curation.":[212]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
