{"id":"https://openalex.org/W2135411671","doi":"https://doi.org/10.1186/1471-2105-13-s11-s3","title":"BioNLP Shared Task - The Bacteria Track","display_name":"BioNLP Shared Task - The Bacteria Track","publication_year":2012,"publication_date":"2012-06-01","ids":{"openalex":"https://openalex.org/W2135411671","doi":"https://doi.org/10.1186/1471-2105-13-s11-s3","mag":"2135411671","pmid":"https://pubmed.ncbi.nlm.nih.gov/22759457"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s11-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s11-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S11-S3","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/10.1186/1471-2105-13-S11-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083008473","display_name":"Robert Bossy","orcid":"https://orcid.org/0000-0001-6652-9319"},"institutions":[{"id":"https://openalex.org/I1314251682","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/05y503v71","country_code":"MA","type":"facility","lineage":["https://openalex.org/I1314251682"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR","MA"],"is_corresponding":true,"raw_author_name":"Robert Bossy","raw_affiliation_strings":["Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352 Jouy-en-Josas, France","Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352 Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I1314251682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025365568","display_name":"Julien Jourde","orcid":null},"institutions":[{"id":"https://openalex.org/I1314251682","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/05y503v71","country_code":"MA","type":"facility","lineage":["https://openalex.org/I1314251682"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR","MA"],"is_corresponding":false,"raw_author_name":"Julien Jourde","raw_affiliation_strings":["Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I1314251682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110938616","display_name":"Alain-Pierre Manine","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114331","display_name":"Predict (France)","ror":"https://ror.org/02h0hx086","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210114331"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alain-Pierre Manine","raw_affiliation_strings":["PredictiveDB - 16, rue Alexandre Parodi, F75010, Paris, France","PredictiveDB - 16, rue Alexandre Parodi, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PredictiveDB - 16, rue Alexandre Parodi, F75010, Paris, France","institution_ids":["https://openalex.org/I4210114331"]},{"raw_affiliation_string":"PredictiveDB - 16, rue Alexandre Parodi, Paris, France","institution_ids":["https://openalex.org/I4210114331"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112813196","display_name":"Philippe Veber","orcid":"https://orcid.org/0000-0003-0328-0143"},"institutions":[{"id":"https://openalex.org/I1314251682","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/05y503v71","country_code":"MA","type":"facility","lineage":["https://openalex.org/I1314251682"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR","MA"],"is_corresponding":false,"raw_author_name":"Philippe Veber","raw_affiliation_strings":["Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I1314251682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056249331","display_name":"\u00c9rick Alphonse","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114331","display_name":"Predict (France)","ror":"https://ror.org/02h0hx086","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210114331"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Erick Alphonse","raw_affiliation_strings":["PredictiveDB - 16, rue Alexandre Parodi, F75010, Paris, France","PredictiveDB - 16, rue Alexandre Parodi, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PredictiveDB - 16, rue Alexandre Parodi, F75010, Paris, France","institution_ids":["https://openalex.org/I4210114331"]},{"raw_affiliation_string":"PredictiveDB - 16, rue Alexandre Parodi, Paris, France","institution_ids":["https://openalex.org/I4210114331"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102841266","display_name":"Maarten van de Guchte","orcid":null},"institutions":[{"id":"https://openalex.org/I3017594750","display_name":"Microbiologie de l\u2019alimentation au service de la sant\u00e9","ror":"https://ror.org/0471cyx86","country_code":"FR","type":"facility","lineage":["https://openalex.org/I22248866","https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I3017594750","https://openalex.org/I4210088668","https://openalex.org/I4210099460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Maarten van de Guchte","raw_affiliation_strings":["MICALIS, Institut National de la Recherche Agronomique, UMR1319 - F78352, Jouy-en-Josas, France","MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MICALIS, Institut National de la Recherche Agronomique, UMR1319 - F78352, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I3017594750"]},{"raw_affiliation_string":"MICALIS, Institut National de la Recherche Agronomique, Jouy en Josas, France","institution_ids":["https://openalex.org/I3017594750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068002461","display_name":"Philippe Bessi\u00e8res","orcid":null},"institutions":[{"id":"https://openalex.org/I1314251682","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/05y503v71","country_code":"MA","type":"facility","lineage":["https://openalex.org/I1314251682"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR","MA"],"is_corresponding":false,"raw_author_name":"Philippe Bessi\u00e8res","raw_affiliation_strings":["Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I1314251682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063577222","display_name":"Claire N\u00e9dellec","orcid":"https://orcid.org/0000-0002-0577-0595"},"institutions":[{"id":"https://openalex.org/I1314251682","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/05y503v71","country_code":"MA","type":"facility","lineage":["https://openalex.org/I1314251682"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR","MA"],"is_corresponding":false,"raw_author_name":"Claire N\u00e9dellec","raw_affiliation_strings":["Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Math\u00e9matique Informatique et G\u00e9nome, Institut National de la Recherche Agronomique, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I1314251682"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5083008473"],"corresponding_institution_ids":["https://openalex.org/I1314251682","https://openalex.org/I4210159481"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.3586,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.93178822,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"S11","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9915000200271606,"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":0.9915000200271606,"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":0.0015999999595806003,"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"}},{"id":"https://openalex.org/T13083","display_name":"Advanced Text Analysis Techniques","score":0.0010000000474974513,"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/computer-science","display_name":"Computer science","score":0.7246825098991394},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.7032788395881653},{"id":"https://openalex.org/keywords/coreference","display_name":"Coreference","score":0.677020788192749},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4585106670856476},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.44369786977767944},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.43746837973594666},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38969600200653076},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3889242112636566},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.28135931491851807},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.11577221751213074}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7246825098991394},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.7032788395881653},{"id":"https://openalex.org/C28076734","wikidata":"https://www.wikidata.org/wiki/Q63087","display_name":"Coreference","level":3,"score":0.677020788192749},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4585106670856476},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.44369786977767944},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.43746837973594666},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38969600200653076},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3889242112636566},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.28135931491851807},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.11577221751213074},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-13-s11-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s11-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S11-S3","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:22759457","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22759457","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:HAL:hal-01190775v1","is_oa":true,"landing_page_url":"https://hal.science/hal-01190775","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"BMC Bioinformatics, 2012, 13, &#x27E8;10.1186/1471-2105-13-S11-S3&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:2388902","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3384254","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:10.1186/1471-2105-13-s11-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s11-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S11-S3","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":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.5400000214576721}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320323910","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/01x3gbx83"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135411671.pdf","grobid_xml":"https://content.openalex.org/works/W2135411671.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W5557833","https://openalex.org/W1490137556","https://openalex.org/W1525521077","https://openalex.org/W1864960538","https://openalex.org/W1987902506","https://openalex.org/W2031647041","https://openalex.org/W2032566933","https://openalex.org/W2046620928","https://openalex.org/W2064030835","https://openalex.org/W2098562307","https://openalex.org/W2100276951","https://openalex.org/W2108791029","https://openalex.org/W2110946298","https://openalex.org/W2112388284","https://openalex.org/W2122496795","https://openalex.org/W2127304021","https://openalex.org/W2130956021","https://openalex.org/W2149803936","https://openalex.org/W2159657801","https://openalex.org/W2171567870","https://openalex.org/W2252226131","https://openalex.org/W2914431807"],"related_works":["https://openalex.org/W2139373276","https://openalex.org/W2227889443","https://openalex.org/W2152228269","https://openalex.org/W2916147465","https://openalex.org/W1757434866","https://openalex.org/W2016071726","https://openalex.org/W2339319059","https://openalex.org/W2803693270","https://openalex.org/W2098562307","https://openalex.org/W2251431888"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,100,241],"present":[2],"the":[3,10,80,84,90,102,107,119,124,132,137,146,151,163,177,185,194,198,203,216,246,250,260,263,268,283],"BioNLP":[4],"2011":[5],"Shared":[6],"Task":[7],"Bacteria":[8,31,50,85,133,147,178,217,264],"Track,":[9],"first":[11],"Information":[12,231],"Extraction":[13],"challenge":[14],"entirely":[15],"dedicated":[16],"to":[17,122,131,171,176,223],"bacteria.":[18],"It":[19],"includes":[20],"three":[21,108,213],"tasks":[22,214],"that":[23],"cover":[24],"different":[25,69,183],"levels":[26],"of":[27,76,94,104,143,160,191,197,207,215,228,253,262,270],"biological":[28],"knowledge.":[29],"The":[30,49,62,212],"Gene":[32,51,134,148],"Renaming":[33,135],"supporting":[34],"task":[35,58,87,180,266],"is":[36,53],"aimed":[37],"at":[38,79],"extracting":[39],"gene":[40,43],"renaming":[41],"and":[42,92,113,205,238,256,274],"name":[44],"synonymy":[45],"in":[46,97,230,245],"PubMed":[47],"abstracts.":[48],"Interaction":[52,149],"a":[54,73,157,221,225],"gene/protein":[55],"interaction":[56],"extraction":[57],"from":[59,168],"individual":[60],"sentences.":[61],"interactions":[63],"have":[64],"been":[65],"categorized":[66],"into":[67],"ten":[68],"sub-types,":[70],"thus":[71],"giving":[72],"detailed":[74,195],"account":[75],"genetic":[77],"regulations":[78],"molecular":[81],"level.":[82],"Finally,":[83],"Biotopes":[86,179,265],"focuses":[88],"on":[89],"localization":[91],"environment":[93],"bacteria":[95],"mentioned":[96],"textbook":[98],"articles.":[99],"describe":[101],"process":[103],"creation":[105],"for":[106],"corpora,":[109],"including":[110,233],"document":[111],"acquisition":[112],"manual":[114],"annotation,":[115],"as":[116,118,277],"well":[117],"metrics":[120],"used":[121],"evaluate":[123],"participants'":[125],"submissions.":[126],"RESULTS:":[127],"Three":[128,173],"teams":[129,174],"submitted":[130,175],"task;":[136],"best":[138,186],"team":[139,187],"achieved":[140,188],"an":[141,189],"F-score":[142,159,190],"87%.":[144],"For":[145],"task,":[150],"only":[152],"participant's":[153],"score":[154],"had":[155],"reached":[156],"global":[158],"77%,":[161],"although":[162],"system":[164],"efficiency":[165,201],"varies":[166],"significantly":[167],"one":[169],"sub-type":[170],"another.":[172],"with":[181],"very":[182],"approaches;":[184],"45%.":[192],"However,":[193],"study":[196],"participating":[199,209],"systems":[200],"reveals":[202],"strengths":[204],"weaknesses":[206],"each":[208],"system.":[210],"CONCLUSIONS:":[211],"Track":[218],"offer":[219],"participants":[220],"chance":[222],"address":[224],"wide":[226],"range":[227],"issues":[229],"Extraction,":[232],"entity":[234],"recognition,":[235],"semantic":[236],"typing":[237],"coreference":[239],"resolution.":[240],"found":[242],"common":[243],"trends":[244],"most":[247],"efficient":[248],"systems:":[249],"systematic":[251],"use":[252,269],"syntactic":[254],"dependencies":[255],"machine":[257],"learning.":[258],"Nevertheless,":[259],"originality":[261],"encouraged":[267],"interesting":[271],"novel":[272],"methods":[273],"techniques,":[275],"such":[276],"term":[278],"compositionality,":[279],"scopes":[280],"wider":[281],"than":[282],"sentence.":[284]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
