{"id":"https://openalex.org/W105835089","doi":"https://doi.org/10.3233/978-1-61499-052-9-89","title":"Pathogens and Gene Product Normalization in the Biomedical Literature","display_name":"Pathogens and Gene Product Normalization in the Biomedical Literature","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W105835089","doi":"https://doi.org/10.3233/978-1-61499-052-9-89","mag":"105835089","pmid":"https://pubmed.ncbi.nlm.nih.gov/22491118"},"language":"en","primary_location":{"id":"doi:10.3233/978-1-61499-052-9-89","is_oa":false,"landing_page_url":"https://doi.org/10.3233/978-1-61499-052-9-89","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://archive-ouverte.unige.ch/unige:21579","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022872913","display_name":"Dina Vishnyakova","orcid":"https://orcid.org/0000-0001-9101-5993"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Vishnyakova Dina","raw_affiliation_strings":["BiTeM Group. din.vishnyakova@hcuge.ch"],"affiliations":[{"raw_affiliation_string":"BiTeM Group. din.vishnyakova@hcuge.ch","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017034341","display_name":"Emilie Pasche","orcid":"https://orcid.org/0000-0002-9118-5762"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pasche Emilie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042070839","display_name":"Douglas Teodoro","orcid":"https://orcid.org/0000-0001-6238-4503"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Teodoro Douglas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016557721","display_name":"Christian Lovis","orcid":"https://orcid.org/0000-0002-2681-8076"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lovis Christian","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5042384742","display_name":"Patrick Ruch","orcid":"https://orcid.org/0000-0002-3374-2962"},"institutions":[{"id":"https://openalex.org/I4210088449","display_name":"HES-SO Gen\u00e8ve","ror":"https://ror.org/007gfwn20","country_code":"CH","type":"education","lineage":["https://openalex.org/I173439891","https://openalex.org/I4210088449"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Ruch Patrick","raw_affiliation_strings":["Haute \u00e9cole de gestion de Gen\u00e8ve"],"affiliations":[{"raw_affiliation_string":"Haute \u00e9cole de gestion de Gen\u00e8ve","institution_ids":["https://openalex.org/I4210088449"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022872913"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03657529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"174","issue":null,"first_page":"89","last_page":"93"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9908999800682068,"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":0.9876000285148621,"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/normalization","display_name":"Normalization (sociology)","score":0.6220316290855408},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5473943948745728},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4623692035675049},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.45115411281585693},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3671213984489441},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35070037841796875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28248700499534607}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.6220316290855408},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5473943948745728},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4623692035675049},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.45115411281585693},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3671213984489441},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35070037841796875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28248700499534607},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"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":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.3233/978-1-61499-052-9-89","is_oa":false,"landing_page_url":"https://doi.org/10.3233/978-1-61499-052-9-89","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:22491118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22491118","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":"Studies in health technology and informatics","raw_type":null},{"id":"pmh:oai:unige.ch:unige:21579","is_oa":true,"landing_page_url":"https://archive-ouverte.unige.ch/unige:21579","pdf_url":"https://archive-ouverte.unige.ch/unige:21579","source":{"id":"https://openalex.org/S4306402259","display_name":"Archive ouverte UNIGE (University of Geneva)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114457229","host_organization_name":"University of Geneva","host_organization_lineage":["https://openalex.org/I114457229"],"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":"ISSN: 0926-9630","raw_type":"Text"},{"id":"pmh:oai:doc.rero.ch:20130110151925-ZT","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:hesso.tind.io:372","is_oa":false,"landing_page_url":"http://arodes.hes-so.ch/record/372","pdf_url":null,"source":{"id":"https://openalex.org/S4306402432","display_name":"ArODES (HES-SO (https://www.hes-so.ch/))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210088449","host_organization_name":"HES-SO Gen\u00e8ve","host_organization_lineage":["https://openalex.org/I4210088449"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arodes.hes-so.ch/record/372","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:unige.ch:unige:21579","is_oa":true,"landing_page_url":"https://archive-ouverte.unige.ch/unige:21579","pdf_url":"https://archive-ouverte.unige.ch/unige:21579","source":{"id":"https://openalex.org/S4306402259","display_name":"Archive ouverte UNIGE (University of Geneva)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114457229","host_organization_name":"University of Geneva","host_organization_lineage":["https://openalex.org/I114457229"],"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":"ISSN: 0926-9630","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.5699999928474426}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W105835089.pdf","grobid_xml":"https://content.openalex.org/works/W105835089.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W46501758","https://openalex.org/W2114370860","https://openalex.org/W2129113459","https://openalex.org/W2141959870","https://openalex.org/W2172016350"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,71],"new":[3],"approach":[4,19,60],"for":[5,156,160],"pathogens":[6,112,189],"and":[7,47,76,103,113,134,158,170,183,190,218],"gene":[8,49,184,193],"product":[9],"normalization":[10,109,164,216],"in":[11,28,108],"the":[12,32,64,81,85,106,147,152,196,199,209,221],"biomedical":[13],"literature.":[14],"The":[15,116,174],"idea":[16],"of":[17,34,39,66,87,111,124,129,143,154,168,172,176,181,198,208,224],"this":[18],"was":[20,118],"motivated":[21],"by":[22,140,203],"needs":[23],"such":[24],"as":[25],"literature":[26],"curation,":[27],"particular":[29],"applied":[30],"to":[31,101,104,213,219],"field":[33],"infectious":[35],"diseases":[36],"thus,":[37],"variants":[38],"bacterial":[40],"species":[41],"(S.":[42],"aureus,":[43,45],"Staphyloccocus":[44],"...)":[46],"their":[48,114],"products":[50],"(protein":[51],"ArsC,":[52],"Arsenical":[53],"pump":[54],"modifier,":[55],"Arsenate":[56],"reductase,":[57],"...).":[58],"Our":[59],"is":[61,211],"based":[62],"on":[63,120,195],"use":[65,86],"an":[67],"Ontology":[68,73],"Look-up":[69],"Service,":[70],"Gene":[72,77],"Categorizer":[74],"(GOCat)":[75],"Normalization":[78],"methods.":[79],"In":[80],"pathogen":[82,91,182,210],"detection":[83],"task":[84],"OLS":[88],"disambiguates":[89],"found":[90],"names.":[92],"GOCat":[93,177],"results":[94,142,165,180],"are":[95],"incorporated":[96],"into":[97],"overall":[98],"score":[99],"system":[100],"support":[102],"confirm":[105],"decisionmaking":[107],"process":[110],"genomes.":[115],"evaluation":[117],"done":[119],"two":[121],"test":[122],"sets":[123],"BioCreativeIII":[125],"benchmark:":[126],"gold":[127,161],"standard":[128,136],"manual":[130],"curation":[131],"(50":[132],"articles)":[133,138],"silver":[135,157],"(507":[137],"curated":[139],"collective":[141],"BCIII":[144],"participants.":[145],"For":[146],"cross-species":[148],"GN":[149],"we":[150],"achieved":[151],"precision":[153,169],"46%":[155],"27%":[159],"sets.":[162],"Pathogen":[163],"showed":[166],"95%":[167],"93%":[171],"recall.":[173],"impact":[175],"explicitly":[178],"improves":[179],"normalization,":[185],"basically":[186],"confirming":[187],"identified":[188],"boosting":[191],"correct":[192,206],"identifiers":[194],"top":[197],"results'":[200],"list":[201],"ranked":[202],"confidence.":[204],"A":[205],"identification":[207],"able":[212],"improve":[214],"significantly":[215],"effectiveness":[217],"solve":[220],"disambiguation":[222],"problem":[223],"genes.":[225]},"counts_by_year":[],"updated_date":"2026-03-17T17:19:04.345684","created_date":"2025-10-10T00:00:00"}
