{"id":"https://openalex.org/W2136615148","doi":"https://doi.org/10.1186/1471-2105-12-460","title":"Semantic annotation of biological concepts interplaying microbial cellular responses","display_name":"Semantic annotation of biological concepts interplaying microbial cellular responses","publication_year":2011,"publication_date":"2011-11-28","ids":{"openalex":"https://openalex.org/W2136615148","doi":"https://doi.org/10.1186/1471-2105-12-460","mag":"2136615148","pmid":"https://pubmed.ncbi.nlm.nih.gov/22122862"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-460","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-460","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-460","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/10.1186/1471-2105-12-460","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052144488","display_name":"Rafael Carreira","orcid":"https://orcid.org/0000-0003-4102-4204"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rafael Carreira","raw_affiliation_strings":["Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","Department of Informatics/CCTC, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]},{"raw_affiliation_string":"Department of Informatics/CCTC, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054642116","display_name":"S\u00f3nia Carneiro","orcid":"https://orcid.org/0000-0001-8037-937X"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"S\u00f3nia Carneiro","raw_affiliation_strings":["IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059204565","display_name":"Rui Pereira","orcid":"https://orcid.org/0000-0002-0572-875X"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rui Pereira","raw_affiliation_strings":["IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","Department of Informatics/CCTC, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"Department of Informatics/CCTC, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Isabel Rocha","raw_affiliation_strings":["IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064824604","display_name":"Eug\u00e9nio C. Ferreira","orcid":"https://orcid.org/0000-0002-5400-3333"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Eug\u00e9nio C Ferreira","raw_affiliation_strings":["IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033016354","display_name":"An\u00e1lia Louren\u00e7o","orcid":"https://orcid.org/0000-0001-8401-5362"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"An\u00e1lia Louren\u00e7o","raw_affiliation_strings":["IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, PORTUGAL","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5033016354"],"corresponding_institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6653,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.69504402,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"12","issue":"1","first_page":"460","last_page":"460"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.939300000667572,"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":0.939300000667572,"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":0.01640000008046627,"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":0.0142000000923872,"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/annotation","display_name":"Annotation","score":0.712146520614624},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.64124995470047},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6347235441207886},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5382691621780396},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.48598966002464294},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.44590815901756287},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4259111285209656},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.41368579864501953},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4130045175552368},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4088602662086487},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4086509943008423},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35032176971435547},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34032291173934937},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3271394968032837},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31547480821609497},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20188990235328674},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1281661093235016},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.1067715585231781}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.712146520614624},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.64124995470047},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6347235441207886},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5382691621780396},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.48598966002464294},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.44590815901756287},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4259111285209656},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.41368579864501953},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4130045175552368},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4088602662086487},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4086509943008423},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35032176971435547},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34032291173934937},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3271394968032837},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31547480821609497},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20188990235328674},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1281661093235016},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.1067715585231781},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-12-460","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-460","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-460","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:22122862","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22122862","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:b49ae5e48c9f4132910e291e4ffdf875","is_oa":true,"landing_page_url":"https://doaj.org/article/b49ae5e48c9f4132910e291e4ffdf875","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 460 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2267033","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3259143","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"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/16826","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/16826","pdf_url":null,"source":{"id":"https://openalex.org/S4306400354","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-460","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-460","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-460","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":[],"awards":[{"id":"https://openalex.org/G7799952005","display_name":null,"funder_award_id":"SFRH/BD/51111/2010","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2136615148.pdf","grobid_xml":"https://content.openalex.org/works/W2136615148.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W42742550","https://openalex.org/W189514963","https://openalex.org/W192665053","https://openalex.org/W203063536","https://openalex.org/W616284349","https://openalex.org/W1850865022","https://openalex.org/W1974805744","https://openalex.org/W1990928629","https://openalex.org/W2002635898","https://openalex.org/W2022888213","https://openalex.org/W2027943492","https://openalex.org/W2032566933","https://openalex.org/W2035105875","https://openalex.org/W2040223842","https://openalex.org/W2048140075","https://openalex.org/W2049240985","https://openalex.org/W2057830264","https://openalex.org/W2065807795","https://openalex.org/W2075322787","https://openalex.org/W2086948271","https://openalex.org/W2100627415","https://openalex.org/W2100751507","https://openalex.org/W2101819947","https://openalex.org/W2103897355","https://openalex.org/W2107005506","https://openalex.org/W2111164126","https://openalex.org/W2111925240","https://openalex.org/W2113613985","https://openalex.org/W2115977657","https://openalex.org/W2121844933","https://openalex.org/W2123273303","https://openalex.org/W2133775496","https://openalex.org/W2134756663","https://openalex.org/W2135401299","https://openalex.org/W2139915240","https://openalex.org/W2145447349","https://openalex.org/W2147585745","https://openalex.org/W2149803936","https://openalex.org/W2157641143","https://openalex.org/W2158022644","https://openalex.org/W2159053585","https://openalex.org/W2163107094","https://openalex.org/W2167321696","https://openalex.org/W2167713778","https://openalex.org/W2167747827","https://openalex.org/W2169918010","https://openalex.org/W2257914311","https://openalex.org/W2483571705","https://openalex.org/W2917056928","https://openalex.org/W4300762454","https://openalex.org/W6600020421","https://openalex.org/W6629418870"],"related_works":["https://openalex.org/W24843447","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W94193318","https://openalex.org/W2358755282","https://openalex.org/W2073808674","https://openalex.org/W2173289516"],"abstract_inverted_index":{"BACKGROUND:":[0],"Automated":[1],"extraction":[2],"systems":[3],"have":[4],"become":[5],"a":[6,42,61,80,91,133,185,190,215,258],"time":[7],"saving":[8],"necessity":[9],"in":[10,54,72,83,94],"Systems":[11],"Biology.":[12],"Considerable":[13],"human":[14],"effort":[15],"is":[16,36,79,237],"needed":[17],"to":[18,31,40,52,69,200],"model,":[19],"analyse":[20],"and":[21,97,108,116,122,154,231,251],"simulate":[22],"biological":[23,46,194],"networks.":[24],"Thus,":[25],"one":[26],"of":[27,38,45,128,135,151,174,182,193,211,214,243,260],"the":[28,65,73,143,175,180,201,212,224,229,240,248,252],"challenges":[29],"posed":[30],"Biomedical":[32],"Text":[33],"Mining":[34],"tools":[35],"that":[37,84,89,187],"learning":[39],"recognise":[41],"wide":[43,191],"variety":[44],"concepts":[47,88,164,195],"with":[48,132,220],"different":[49,140],"functional":[50,92],"roles":[51],"assist":[53],"these":[55],"processes.":[56],"RESULTS:":[57],"Here,":[58],"we":[59,256],"present":[60],"novel":[62],"corpus":[63,78,126,186,259],"concerning":[64],"integrated":[66],"cellular":[67,163],"responses":[68],"nutrient":[70],"starvation":[71],"model-organism":[74],"Escherichia":[75],"coli.":[76],"Our":[77],"unique":[81,152],"resource":[82],"it":[85,100],"annotates":[86],"biomedical":[87,141],"play":[90],"role":[93],"expression,":[95],"regulation":[96],"metabolism.":[98],"Namely,":[99],"includes":[101],"annotations":[102,137],"for":[103,138,169,234,239],"genetic":[104],"information":[105],"carriers":[106],"(genes":[107],"DNA,":[109],"RNA":[110],"molecules),":[111],"proteins":[112,167],"(transcription":[113],"factors,":[114],"enzymes":[115],"transporters),":[117],"small":[118],"metabolites,":[119],"physiological":[120],"states":[121],"laboratory":[123],"techniques.":[124],"The":[125,205],"consists":[127],"130":[129,244],"full-text":[130,241],"papers":[131],"total":[134],"59043":[136],"3649":[139],"concepts;":[142],"two":[144],"dominant":[145],"classes":[146],"are":[147],"genes":[148],"(highest":[149],"number":[150],"concepts)":[153],"compounds":[155],"(most":[156],"frequently":[157],"annotated":[158,176],"concepts),":[159],"whereas":[160],"other":[161],"important":[162],"such":[165,189,221],"as":[166],"account":[168],"no":[170],"more":[171],"than":[172],"10%":[173],"concepts.":[177],"CONCLUSIONS:":[178],"To":[179],"best":[181],"our":[183],"knowledge,":[184],"details":[188],"range":[192],"has":[196],"never":[197],"been":[198],"presented":[199],"text":[202],"mining":[203],"community.":[204],"inter-annotator":[206],"agreement":[207],"statistics":[208],"provide":[209],"evidence":[210],"importance":[213],"consolidated":[216],"background":[217],"when":[218],"dealing":[219],"complex":[222],"descriptions,":[223],"ambiguities":[225],"naturally":[226],"arising":[227],"from":[228],"terminology":[230],"their":[232],"impact":[233],"modelling":[235],"purposes.Availability":[236],"granted":[238],"corpora":[242],"freely":[245],"accessible":[246],"documents,":[247],"annotation":[249,253],"scheme":[250],"guidelines.":[254],"Also,":[255],"include":[257],"340":[261],"abstracts.":[262]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-21T07:57:09.225873","created_date":"2025-10-10T00:00:00"}
