{"id":"https://openalex.org/W2171691447","doi":"https://doi.org/10.1093/bioinformatics/btr358","title":"Integration of gene normalization stages and co-reference resolution using a Markov logic network","display_name":"Integration of gene normalization stages and co-reference resolution using a Markov logic network","publication_year":2011,"publication_date":"2011-06-17","ids":{"openalex":"https://openalex.org/W2171691447","doi":"https://doi.org/10.1093/bioinformatics/btr358","mag":"2171691447","pmid":"https://pubmed.ncbi.nlm.nih.gov/21685052"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr358","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr358","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/18/2586/48866996/bioinformatics_27_18_2586.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/18/2586/48866996/bioinformatics_27_18_2586.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037362113","display_name":"Hong-Jie Dai","orcid":"https://orcid.org/0000-0002-1516-7255"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Hong-Jie Dai","raw_affiliation_strings":["1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100901071","display_name":"Yen\u2212Ching Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yen\u2212Ching Chang","raw_affiliation_strings":["1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030771512","display_name":"Richard Tzong\u2010Han Tsai","orcid":"https://orcid.org/0000-0003-0513-107X"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Richard Tzong-Han Tsai","raw_affiliation_strings":["1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5119558606","display_name":"Wen\u2212Lian Hsu","orcid":"https://orcid.org/0000-0001-7061-3513"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]},{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Wen\u2212Lian Hsu","raw_affiliation_strings":["1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, National Tsing\u2212Hua University, Hsinchu, 2Intelligent Agent Systems Lab., Institute of Information Science, Academia Sinica, 3Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan, R.O.C","institution_ids":["https://openalex.org/I25846049","https://openalex.org/I148366613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5037362113"],"corresponding_institution_ids":["https://openalex.org/I148366613","https://openalex.org/I25846049"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1726,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.78091005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"27","issue":"18","first_page":"2586","last_page":"2594"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9980000257492065,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9970999956130981,"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/computer-science","display_name":"Computer science","score":0.7814615964889526},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.7808293104171753},{"id":"https://openalex.org/keywords/salience","display_name":"Salience (neuroscience)","score":0.4669310450553894},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.4643006920814514},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.45946359634399414},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45412981510162354},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44784632325172424},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37849903106689453},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3343289792537689}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7814615964889526},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7808293104171753},{"id":"https://openalex.org/C108154423","wikidata":"https://www.wikidata.org/wiki/Q1469792","display_name":"Salience (neuroscience)","level":2,"score":0.4669310450553894},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.4643006920814514},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.45946359634399414},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45412981510162354},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44784632325172424},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37849903106689453},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3343289792537689},{"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":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr358","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr358","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/18/2586/48866996/bioinformatics_27_18_2586.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21685052","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21685052","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/18/2586","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/18/2586","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr358","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr358","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/18/2586/48866996/bioinformatics_27_18_2586.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"},{"id":"https://openalex.org/F4320321041","display_name":"Academia Sinica","ror":"https://ror.org/05bxb3784"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171691447.pdf","grobid_xml":"https://content.openalex.org/works/W2171691447.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W603809537","https://openalex.org/W1519235666","https://openalex.org/W1538211826","https://openalex.org/W1559923427","https://openalex.org/W1747861911","https://openalex.org/W1977970897","https://openalex.org/W1992967856","https://openalex.org/W2016085990","https://openalex.org/W2044602212","https://openalex.org/W2055494382","https://openalex.org/W2074640468","https://openalex.org/W2085577304","https://openalex.org/W2097678794","https://openalex.org/W2101265630","https://openalex.org/W2103316358","https://openalex.org/W2104619957","https://openalex.org/W2105114854","https://openalex.org/W2122410182","https://openalex.org/W2123566741","https://openalex.org/W2124176947","https://openalex.org/W2124741472","https://openalex.org/W2129113459","https://openalex.org/W2129267433","https://openalex.org/W2133627190","https://openalex.org/W2135912801","https://openalex.org/W2146954401","https://openalex.org/W2150131767","https://openalex.org/W2154142897","https://openalex.org/W2164455818","https://openalex.org/W2169423212","https://openalex.org/W2623293810","https://openalex.org/W2792932412","https://openalex.org/W2914181088","https://openalex.org/W3137298232","https://openalex.org/W4285719527","https://openalex.org/W6632066347","https://openalex.org/W6633702045","https://openalex.org/W6648414650","https://openalex.org/W6664667411","https://openalex.org/W6676155074","https://openalex.org/W6678290171","https://openalex.org/W6682120076","https://openalex.org/W6684549341","https://openalex.org/W6999244237"],"related_works":["https://openalex.org/W1557094818","https://openalex.org/W2591697403","https://openalex.org/W2953716828","https://openalex.org/W2904857019","https://openalex.org/W2944728705","https://openalex.org/W3011538607","https://openalex.org/W2904022177","https://openalex.org/W4321441197","https://openalex.org/W2359348847","https://openalex.org/W2183246718"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}