{"id":"https://openalex.org/W3036529033","doi":"https://doi.org/10.1186/s12859-020-03583-6","title":"pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms","display_name":"pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms","publication_year":2020,"publication_date":"2020-06-18","ids":{"openalex":"https://openalex.org/W3036529033","doi":"https://doi.org/10.1186/s12859-020-03583-6","mag":"3036529033","pmid":"https://pubmed.ncbi.nlm.nih.gov/32552728"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03583-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03583-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03583-6","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/track/pdf/10.1186/s12859-020-03583-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102026195","display_name":"Zhi-Hui Luo","orcid":"https://orcid.org/0000-0001-7282-4744"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhi-Hui Luo","raw_affiliation_strings":["College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China"],"affiliations":[{"raw_affiliation_string":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080456464","display_name":"Mengwei Shi","orcid":"https://orcid.org/0000-0001-6027-9742"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng-Wei Shi","raw_affiliation_strings":["College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China"],"affiliations":[{"raw_affiliation_string":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101331473","display_name":"Zhuang Yang","orcid":"https://orcid.org/0009-0001-5563-3003"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuang Yang","raw_affiliation_strings":["College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China"],"affiliations":[{"raw_affiliation_string":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100412608","display_name":"Hongyu Zhang","orcid":"https://orcid.org/0000-0002-8078-4401"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong-Yu Zhang","raw_affiliation_strings":["Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. zhy630@mail.hzau.edu.cn","Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. zhy630@mail.hzau.edu.cn","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057184656","display_name":"Zhen\u2010Xia Chen","orcid":"https://orcid.org/0000-0003-0474-902X"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen-Xia Chen","raw_affiliation_strings":["College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. zhen-xia.chen@mail.hzau.edu.cn","Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. zhen-xia.chen@mail.hzau.edu.cn","Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China"],"affiliations":[{"raw_affiliation_string":"College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. zhen-xia.chen@mail.hzau.edu.cn","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China. zhen-xia.chen@mail.hzau.edu.cn","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China","institution_ids":["https://openalex.org/I204823248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5102026195"],"corresponding_institution_ids":["https://openalex.org/I204823248"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.8359,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.7134767,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"252","last_page":"252"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9957000017166138,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9886999726295471,"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/python","display_name":"Python (programming language)","score":0.845181941986084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6844852566719055},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.6566354632377625},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5277650356292725},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3622548580169678},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.28426796197891235}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.845181941986084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6844852566719055},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.6566354632377625},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5277650356292725},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3622548580169678},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.28426796197891235},{"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":"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-03583-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03583-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03583-6","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:32552728","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32552728","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:07bf2a498036484faeda77607ab03d9b","is_oa":true,"landing_page_url":"https://doaj.org/article/07bf2a498036484faeda77607ab03d9b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-14 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7301509","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7301509","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03583-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03583-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03583-6","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":[{"id":"https://metadata.un.org/sdg/4","score":0.7200000286102295,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2056693751","display_name":null,"funder_award_id":"31871305","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G306659448","display_name":null,"funder_award_id":"2662017PY115","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5003822677","display_name":null,"funder_award_id":"2662019PY003","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G764653187","display_name":null,"funder_award_id":"2016RC011","funder_id":"https://openalex.org/F4320324775","funder_display_name":"Huazhong Agricultural University"},{"id":"https://openalex.org/G794431671","display_name":null,"funder_award_id":"2018PY02","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8146947647","display_name":null,"funder_award_id":"31701259","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8919483995","display_name":null,"funder_award_id":"2662018PY021","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324775","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3036529033.pdf","grobid_xml":"https://content.openalex.org/works/W3036529033.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W74342042","https://openalex.org/W90362830","https://openalex.org/W186091728","https://openalex.org/W342077646","https://openalex.org/W1527927437","https://openalex.org/W1952031141","https://openalex.org/W1976502930","https://openalex.org/W2034537627","https://openalex.org/W2041249853","https://openalex.org/W2048296798","https://openalex.org/W2059313072","https://openalex.org/W2070741095","https://openalex.org/W2115871101","https://openalex.org/W2117805756","https://openalex.org/W2118822739","https://openalex.org/W2121343862","https://openalex.org/W2122402213","https://openalex.org/W2128049108","https://openalex.org/W2140099276","https://openalex.org/W2142016317","https://openalex.org/W2156235098","https://openalex.org/W2159092541","https://openalex.org/W2159583324","https://openalex.org/W2160171761","https://openalex.org/W2162151166","https://openalex.org/W2170146596","https://openalex.org/W2172024938","https://openalex.org/W2414378847","https://openalex.org/W2537679995","https://openalex.org/W2734608416","https://openalex.org/W2765372324","https://openalex.org/W2803526872","https://openalex.org/W2953332543","https://openalex.org/W2977393556","https://openalex.org/W6683709678"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4401016539","https://openalex.org/W4400651710","https://openalex.org/W4405093211","https://openalex.org/W4403672447"],"abstract_inverted_index":{"The":[0],"integrative":[1],"MeSH":[2,8],"tool":[3],"pyMeSHSim":[4],"embedded":[5],"with":[6],"the":[7,13],"MHs":[9],"and":[10,17],"SCRs":[11],"realized":[12],"bio-NE":[14],"recognition,":[15],"normalization,":[16],"comparison":[18],"in":[19],"biomedical":[20],"text-mining.":[21]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
