{"id":"https://openalex.org/W2983315135","doi":"https://doi.org/10.18653/v1/d19-5719","title":"Bacteria Biotope at BioNLP Open Shared Tasks 2019","display_name":"Bacteria Biotope at BioNLP Open Shared Tasks 2019","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2983315135","doi":"https://doi.org/10.18653/v1/d19-5719","mag":"2983315135"},"language":"en","primary_location":{"id":"doi:10.18653/v1/d19-5719","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5719","pdf_url":"https://www.aclweb.org/anthology/D19-5719.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/D19-5719.pdf","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/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"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/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Robert Bossy","raw_affiliation_strings":["MaIAGE, INRA, Universit Paris-Saclay, 78350 Jouy-en-Josas, France","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MaIAGE, INRA, Universit Paris-Saclay, 78350 Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059209944","display_name":"Louise Del\u00e9ger","orcid":"https://orcid.org/0000-0003-1399-4828"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"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/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Louise Del\u00e9ger","raw_affiliation_strings":["MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]},{"raw_affiliation_string":"Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)","institution_ids":["https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018451398","display_name":"Estelle Chaix","orcid":"https://orcid.org/0000-0003-0975-7854"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"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/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Estelle Chaix","raw_affiliation_strings":["MaIAGE, INRA, Universit Paris-Saclay, 78350 Jouy-en-Josas, France","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MaIAGE, INRA, Universit Paris-Saclay, 78350 Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009068115","display_name":"Mouhamadou Ba","orcid":"https://orcid.org/0000-0001-7233-7831"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"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/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mouhamadou Ba","raw_affiliation_strings":["MaIAGE, INRA, Universit Paris-Saclay, 78350 Jouy-en-Josas, France","Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MaIAGE, INRA, Universit Paris-Saclay, 78350 Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481","https://openalex.org/I277688954"]},{"raw_affiliation_string":"Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]}]},{"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/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"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/I4210099460","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Claire N\u00e9dellec","raw_affiliation_strings":["Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)","MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Saclay (COmUE) (Espace Technologique, B\u00e2t. Discovery - RD 128 - 2\u00e8 \u00e9t\u00e9tage, 91190 Saint-Aubin - France)","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MaIAGE - Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement [Jouy-En-Josas] (B\u00e2t. 233, Domaine de Vilvert - 78352 Jouy-en-Josas Cedex - France)","institution_ids":["https://openalex.org/I4210159481"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083008473"],"corresponding_institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210159481"],"apc_list":null,"apc_paid":null,"fwci":2.7354,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.91348013,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"121","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991000294685364,"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":0.9991000294685364,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9932000041007996,"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/biomedical-text-mining","display_name":"Biomedical text mining","score":0.8069802522659302},{"id":"https://openalex.org/keywords/biotope","display_name":"Biotope","score":0.8040170073509216},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7811490297317505},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.7019246220588684},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5758535861968994},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.5527985692024231},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5397347807884216},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3529166579246521},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.343761146068573},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3268003463745117},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14653298258781433},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.12131845951080322},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11133599281311035},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.06912964582443237}],"concepts":[{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.8069802522659302},{"id":"https://openalex.org/C112149622","wikidata":"https://www.wikidata.org/wiki/Q175208","display_name":"Biotope","level":3,"score":0.8040170073509216},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7811490297317505},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.7019246220588684},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5758535861968994},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.5527985692024231},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5397347807884216},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3529166579246521},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.343761146068573},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3268003463745117},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14653298258781433},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.12131845951080322},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11133599281311035},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.06912964582443237},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C185933670","wikidata":"https://www.wikidata.org/wiki/Q52105","display_name":"Habitat","level":2,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.18653/v1/d19-5719","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5719","pdf_url":"https://www.aclweb.org/anthology/D19-5719.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},{"id":"pmh:oai:HAL:hal-02437609v1","is_oa":true,"landing_page_url":"https://hal.science/hal-02437609","pdf_url":"https://hal.science/hal-02437609v1/file/D19-5719.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://www.aclweb.org/anthology/D19-57.pdf","raw_type":"Conference papers"}],"best_oa_location":{"id":"doi:10.18653/v1/d19-5719","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5719","pdf_url":"https://www.aclweb.org/anthology/D19-5719.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324529","display_name":"Agence Nationale de S\u00e9curit\u00e9 Sanitaire de l\u2019Alimentation, de l\u2019Environnement et du Travail","ror":"https://ror.org/0471kz689"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2983315135.pdf","grobid_xml":"https://content.openalex.org/works/W2983315135.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W192665053","https://openalex.org/W1614298861","https://openalex.org/W2096765155","https://openalex.org/W2123442489","https://openalex.org/W2135411671","https://openalex.org/W2142678031","https://openalex.org/W2252145363","https://openalex.org/W2518463060","https://openalex.org/W2527896214","https://openalex.org/W2532039214","https://openalex.org/W2759280239","https://openalex.org/W2791976577","https://openalex.org/W2799862684","https://openalex.org/W2802711901","https://openalex.org/W2950577311","https://openalex.org/W2963341956","https://openalex.org/W2970597249","https://openalex.org/W2982940135","https://openalex.org/W2984624504","https://openalex.org/W2985461273","https://openalex.org/W2987255980","https://openalex.org/W2988294541","https://openalex.org/W4300963242"],"related_works":["https://openalex.org/W2427798806","https://openalex.org/W1965419689","https://openalex.org/W311807596","https://openalex.org/W2383221697","https://openalex.org/W3116059436","https://openalex.org/W2916147465","https://openalex.org/W1757434866","https://openalex.org/W2250232417","https://openalex.org/W2251431888","https://openalex.org/W2107530479"],"abstract_inverted_index":{"This":[0],"paper":[1,72],"presents":[2],"the":[3,7,21,24,37,57,60,74,78,82,91,98,101,104],"fourth":[4],"edition":[5,106],"of":[6,23,28,39,59,90,100],"Bacteria":[8],"Biotope":[9],"task":[10,18,53],"at":[11],"BioNLP":[12],"Open":[13],"Shared":[14],"Tasks":[15],"2019.":[16],"The":[17,52,71],"focuses":[19],"on":[20,62],"extraction":[22],"locations":[25],"and":[26,33,36,67,81,96],"phenotypes":[27],"microorganisms":[29],"from":[30],"PubMed":[31],"abstracts":[32],"fulltext":[34],"excerpts,":[35],"characterization":[38],"these":[40],"entities":[41],"with":[42],"respect":[43],"to":[44],"reference":[45],"knowledge":[46,61],"sources":[47],"(NCBI":[48],"taxonomy,":[49],"OntoBiotope":[50],"ontology).":[51],"is":[54],"motivated":[55],"by":[56,94],"importance":[58],"biodiversity":[63],"for":[64],"fundamental":[65],"research":[66],"applications":[68],"in":[69,107],"microbiology.":[70],"describes":[73],"different":[75],"proposed":[76],"subtasks,":[77],"corpus":[79],"characteristics,":[80],"challenge":[83],"organization.":[84],"We":[85],"also":[86],"provide":[87],"an":[88],"analysis":[89],"results":[92,102],"obtained":[93],"participants,":[95],"inspect":[97],"evolution":[99],"since":[103],"last":[105],"2016.":[108]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
