{"id":"https://openalex.org/W2138807684","doi":"https://doi.org/10.1093/database/bar013","title":"Allie: a database and a search service of abbreviations and long forms","display_name":"Allie: a database and a search service of abbreviations and long forms","publication_year":2011,"publication_date":"2011-04-15","ids":{"openalex":"https://openalex.org/W2138807684","doi":"https://doi.org/10.1093/database/bar013","mag":"2138807684","pmid":"https://pubmed.ncbi.nlm.nih.gov/21498548"},"language":"en","primary_location":{"id":"doi:10.1093/database/bar013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bar013","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bar013/1258304/bar013.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bar013/1258304/bar013.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087660235","display_name":"Yoshiharu Yamamoto","orcid":"https://orcid.org/0000-0002-1132-0355"},"institutions":[{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Y. Yamamoto","raw_affiliation_strings":["Database Center for Life Science, Bunkyo-ku, Tokyo, Japan. yy@dbcls.rois.ac.jp","Database Center for Life Science, Bunkyo-ku, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Bunkyo-ku, Tokyo, Japan. yy@dbcls.rois.ac.jp","institution_ids":["https://openalex.org/I4210158934"]},{"raw_affiliation_string":"Database Center for Life Science, Bunkyo-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001958215","display_name":"Atsuko Yamaguchi","orcid":"https://orcid.org/0000-0001-7538-5337"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"A. Yamaguchi","raw_affiliation_strings":["Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","1Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"1Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079934306","display_name":"Hidemasa Bono","orcid":"https://orcid.org/0000-0003-4413-0651"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"H. Bono","raw_affiliation_strings":["Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","1Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"1Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113508251","display_name":"T. Takagi","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"T. Takagi","raw_affiliation_strings":["Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","1Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"1Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.7049,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.84142224,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2011","issue":"0","first_page":"bar013","last_page":"bar013"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9836000204086304,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9746000170707703,"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":0.6611908674240112},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5865089893341064},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5494491457939148},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.5116296410560608},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.5041555166244507},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.347299724817276},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34097278118133545},{"id":"https://openalex.org/keywords/history","display_name":"History","score":0.09177097678184509},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07279849052429199}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6611908674240112},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5865089893341064},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5494491457939148},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.5116296410560608},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.5041555166244507},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.347299724817276},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34097278118133545},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.09177097678184509},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07279849052429199},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000004","descriptor_name":"Abbreviations as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000004","descriptor_name":"Abbreviations as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000004","descriptor_name":"Abbreviations as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000004","descriptor_name":"Abbreviations as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bar013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bar013","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bar013/1258304/bar013.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:21498548","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21498548","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:2087361","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3077826","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/bar013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bar013","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bar013/1258304/bar013.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W13703775","https://openalex.org/W90158706","https://openalex.org/W138612281","https://openalex.org/W1538486977","https://openalex.org/W1573048037","https://openalex.org/W1933390880","https://openalex.org/W2061167720","https://openalex.org/W2077250344","https://openalex.org/W2109252435","https://openalex.org/W2114420708","https://openalex.org/W2118658201","https://openalex.org/W2120609672","https://openalex.org/W2161132397","https://openalex.org/W2169821936","https://openalex.org/W4250877149"],"related_works":["https://openalex.org/W2003932708","https://openalex.org/W1967424056","https://openalex.org/W2284877871","https://openalex.org/W2138102289","https://openalex.org/W868043274","https://openalex.org/W2513523087","https://openalex.org/W1187916458","https://openalex.org/W2373861055","https://openalex.org/W1559716973","https://openalex.org/W3109364360"],"abstract_inverted_index":{"Many":[0],"abbreviations":[1,14,45,58,111,198,214],"are":[2,27,125,172,184,200],"used":[3],"in":[4,8,64,77,116,121,135,191],"the":[5,9,93,122,133,211],"literature":[6],"especially":[7],"life":[10],"sciences,":[11],"and":[12,22,40,46,59,75,102,112,177,215,226],"polysemous":[13],"appear":[15],"frequently,":[16],"making":[17],"it":[18,118],"difficult":[19],"to":[20],"read":[21],"understand":[23],"scientific":[24],"papers":[25],"that":[26,67,152,199],"outside":[28],"of":[29,44,92,213],"a":[30,38,41,65,80,113,148],"reader's":[31],"expertise.":[32],"Thus,":[33],"we":[34,68,146],"have":[35,69],"developed":[36],"Allie,":[37],"database":[39,66,212],"search":[42],"service":[43,233],"their":[47,60,97,165,189,216,220],"long":[48,62,90,144,217],"forms":[49,52,63,91,218],"(a.k.a.":[50],"full":[51],"or":[53,160],"definitions).":[54],"Allie":[55,86,203,232],"searches":[56],"for":[57,107],"corresponding":[61,221],"generated":[70],"based":[71],"on":[72],"all":[73,88],"titles":[74],"abstracts":[76],"MEDLINE.":[78,192],"When":[79],"user":[81],"query":[82,94],"matches":[83],"an":[84,137,205],"abbreviation,":[85],"returns":[87],"potential":[89],"along":[95,163],"with":[96,142,164,196,219],"bibliographic":[98],"data":[99,124],"(i.e.":[100],"title":[101],"publication":[103],"year).":[104],"In":[105,209],"addition,":[106,210],"each":[108],"candidate,":[109],"co-occurring":[110],"research":[114],"field":[115],"which":[117,136],"frequently":[119],"appears":[120],"MEDLINE":[123],"displayed.":[126],"This":[127],"function":[128],"helps":[129],"users":[130],"learn":[131],"about":[132],"context":[134],"abbreviation":[138],"appears.":[139],"To":[140,193],"deal":[141],"synonymous":[143],"forms,":[145],"use":[147],"dictionary":[149],"called":[150],"GENA":[151],"contains":[153],"domain-specific":[154,170],"terms":[155,171],"such":[156],"as":[157,174],"gene,":[158],"protein":[159],"disease":[161],"names":[162],"synonymic":[166],"information.":[167],"Conceptually":[168],"identical":[169,180],"regarded":[173],"one":[175],"term,":[176],"then":[178],"conceptually":[179],"abbreviation-long":[181],"form":[182],"pairs":[183],"grouped":[185],"taking":[186],"into":[187],"account":[188],"appearance":[190],"keep":[194],"up":[195],"new":[197],"continuously":[201],"introduced,":[202],"has":[204],"automatic":[206],"update":[207],"system.":[208],"PubMed":[222],"IDs":[223],"is":[224,234],"constructed":[225],"updated":[227],"weekly.":[228],"Database":[229],"URL:":[230],"The":[231],"available":[235],"at":[236],"http://allie.dbcls.jp/.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}
