{"id":"https://openalex.org/W1990928629","doi":"https://doi.org/10.1186/1471-2105-8-293","title":"Automatic reconstruction of a bacterial regulatory network using Natural Language Processing","display_name":"Automatic reconstruction of a bacterial regulatory network using Natural Language Processing","publication_year":2007,"publication_date":"2007-08-07","ids":{"openalex":"https://openalex.org/W1990928629","doi":"https://doi.org/10.1186/1471-2105-8-293","mag":"1990928629","pmid":"https://pubmed.ncbi.nlm.nih.gov/17683642"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-293","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-293","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-293","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-293","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044768193","display_name":"Carlos Gerardo Rodriguez-Penagos","orcid":"https://orcid.org/0000-0001-8744-0380"},"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":"Carlos Rodr\u00edguez-Penagos","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico. crodrigp@ccg.unam.mx","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico. crodrigp@ccg.unam.mx","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091338305","display_name":"Heladia Salgado","orcid":"https://orcid.org/0000-0002-3166-5801"},"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":"Heladia Salgado","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083901001","display_name":"Irma Mart\u00ednez\u2010Flores","orcid":"https://orcid.org/0000-0001-9350-8978"},"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":"Irma Mart\u00ednez-Flores","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, 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":"Julio Collado-Vides","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Postal 565-A, Avenida Universidad, Cuernavaca, Morelos, 62100, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Apdo, Cuernavaca, Mexico","institution_ids":["https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044768193"],"corresponding_institution_ids":["https://openalex.org/I8961855"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.263,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.87612584,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"8","issue":"1","first_page":"293","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9416999816894531,"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":0.9416999816894531,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.004800000227987766,"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/T10028","display_name":"Topic Modeling","score":0.004699999932199717,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/markup-language","display_name":"Markup language","score":0.8074542880058289},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.8023732304573059},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7979225516319275},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.681774377822876},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6544641852378845},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.6121280789375305},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.5537551045417786},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.47096091508865356},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4427482783794403},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37579840421676636},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3349749445915222},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.31993359327316284},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.30155646800994873},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24356916546821594},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1678883135318756},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14949488639831543}],"concepts":[{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.8074542880058289},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.8023732304573059},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7979225516319275},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.681774377822876},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6544641852378845},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.6121280789375305},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.5537551045417786},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.47096091508865356},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4427482783794403},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37579840421676636},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3349749445915222},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.31993359327316284},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.30155646800994873},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24356916546821594},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1678883135318756},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14949488639831543},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000043","descriptor_name":"Abstracting and Indexing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-293","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-293","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-293","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17683642","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17683642","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:ddf7e18e4969453293257d2759dc0aa4","is_oa":false,"landing_page_url":"https://doaj.org/article/ddf7e18e4969453293257d2759dc0aa4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Bioinformatics, Vol 8, Iss 1, p 293 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1964768","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1964768","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-293","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-293","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-293","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G7353960246","display_name":null,"funder_award_id":"R01 GM071962","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8894682088","display_name":null,"funder_award_id":"5R01 GM071962 02","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1990928629.pdf","grobid_xml":"https://content.openalex.org/works/W1990928629.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1541931954","https://openalex.org/W1582187731","https://openalex.org/W1917508089","https://openalex.org/W2009433284","https://openalex.org/W2035967403","https://openalex.org/W2044514479","https://openalex.org/W2068882115","https://openalex.org/W2079672926","https://openalex.org/W2100525485","https://openalex.org/W2108078368","https://openalex.org/W2113024448","https://openalex.org/W2118806902","https://openalex.org/W2122904379","https://openalex.org/W2126276057","https://openalex.org/W2132773777","https://openalex.org/W2146856779","https://openalex.org/W2158505321","https://openalex.org/W2158896284","https://openalex.org/W2168905447","https://openalex.org/W2753765968","https://openalex.org/W3022037017","https://openalex.org/W4242156070"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W1546010648","https://openalex.org/W2890725831"],"abstract_inverted_index":{"BACKGROUND:":[0],"Manual":[1,171],"curation":[2,63,172,220],"of":[3,25,36,43,64,78,106,142,163,173,176,179,191,199],"biological":[4,65],"databases,":[5],"an":[6],"expensive":[7],"and":[8,45,140,167,209],"labor-intensive":[9],"process,":[10],"is":[11,51,90,181],"essential":[12],"for":[13,99,159,165,195,206],"high":[14],"quality":[15],"integrated":[16],"data.":[17],"In":[18],"this":[19],"paper":[20],"we":[21,108,118],"report":[22],"the":[23,93,102,137,143,174,192,197,217],"implementation":[24],"a":[26,69,149,182,187],"state-of-the-art":[27],"Natural":[28],"Language":[29,154],"Processing":[30],"system":[31,71],"that":[32,133,211],"creates":[33],"computer-readable":[34],"networks":[35,74],"regulatory":[37],"interactions":[38,126],"directly":[39],"from":[40,75,127],"different":[41,76],"collections":[42],"abstracts":[44],"full-text":[46],"papers.":[47],"Our":[48],"major":[49],"aim":[50],"to":[52,72,111,122,185],"understand":[53],"how":[54],"automatic":[55,177],"annotation":[56],"using":[57],"Text-Mining":[58],"techniques":[59],"can":[60],"complement":[61,186],"manual":[62,138],"databases.":[66],"We":[67,145],"implemented":[68],"rule-based":[70],"generate":[73],"sets":[77],"documents":[79],"dealing":[80],"with":[81],"regulation":[82,97],"in":[83,136],"Escherichia":[84],"coli":[85],"K-12.":[86],"RESULTS:":[87],"Performance":[88],"evaluation":[89],"based":[91],"on":[92],"most":[94],"comprehensive":[95],"transcriptional":[96],"database":[98],"any":[100],"organism,":[101],"manually-curated":[103],"RegulonDB,":[104],"45%":[105],"which":[107],"were":[109,119,134],"able":[110,121],"recreate":[112],"automatically.":[113],"From":[114],"our":[115],"automated":[116],"analysis":[117],"also":[120,146],"find":[123],"some":[124],"new":[125],"papers":[128],"not":[129],"already":[130,203],"curated,":[131],"or":[132,205,219],"missed":[135],"filtering":[139],"review":[141,190],"literature.":[144],"put":[147],"forward":[148],"novel":[150],"Regulatory":[151],"Interaction":[152],"Markup":[153],"better":[155],"suited":[156],"than":[157],"SBML":[158],"simultaneously":[160],"representing":[161],"data":[162],"interest":[164],"biologists":[166],"text":[168,180],"miners.":[169],"CONCLUSION:":[170],"output":[175],"processing":[178],"good":[183],"way":[184],"more":[188],"detailed":[189],"literature,":[193],"either":[194],"validating":[196],"results":[198],"what":[200],"has":[201],"been":[202,214],"annotated,":[204],"discovering":[207],"facts":[208],"information":[210],"might":[212],"have":[213],"overlooked":[215],"at":[216],"triage":[218],"stages.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}