{"id":"https://openalex.org/W4404793875","doi":"https://doi.org/10.1093/database/baae119","title":"The text2term tool to map free-text descriptions of biomedical terms to ontologies","display_name":"The text2term tool to map free-text descriptions of biomedical terms to ontologies","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4404793875","doi":"https://doi.org/10.1093/database/baae119","pmid":"https://pubmed.ncbi.nlm.nih.gov/39607847"},"language":"en","primary_location":{"id":"doi:10.1093/database/baae119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae119","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baae119/60896180/baae119.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/baae119/60896180/baae119.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049424768","display_name":"Rafael S. Gon\u00e7alves","orcid":"https://orcid.org/0000-0003-1255-0125"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rafael S Gon\u00e7alves","raw_affiliation_strings":["Stanford Center for Biomedical Informatics Research, Stanford University , 3180 Porter Dr, Palo Alto, CA 94304,"],"raw_orcid":"https://orcid.org/0000-0003-1255-0125","affiliations":[{"raw_affiliation_string":"Stanford Center for Biomedical Informatics Research, Stanford University , 3180 Porter Dr, Palo Alto, CA 94304,","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110992292","display_name":"Jason Payne","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Payne","raw_affiliation_strings":["Center for Computational Biomedicine, Harvard Medical School , 10 Shattuck St, Boston, MA 02115,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biomedicine, Harvard Medical School , 10 Shattuck St, Boston, MA 02115,","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026995526","display_name":"Amelia L.M. Tan","orcid":"https://orcid.org/0000-0003-0623-6623"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I2801543288","display_name":"Lemuel Shattuck Hospital","ror":"https://ror.org/01wpqwr25","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801543288"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amelia Tan","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , 10 Shattuck St, Boston, MA 02115,"],"raw_orcid":"https://orcid.org/0000-0003-0623-6623","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , 10 Shattuck St, Boston, MA 02115,","institution_ids":["https://openalex.org/I2801543288","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032065113","display_name":"Carmen Ben\u0131\u0301tez","orcid":"https://orcid.org/0000-0002-5407-8335"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carmen Benitez","raw_affiliation_strings":["Department of Mathematics, Harvey Mudd College , 301 Platt Blvd, Claremont, CA 91711,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Harvey Mudd College , 301 Platt Blvd, Claremont, CA 91711,","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048004087","display_name":"Jamie Haddock","orcid":"https://orcid.org/0000-0002-1449-2574"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jamie Haddock","raw_affiliation_strings":["Department of Mathematics, Harvey Mudd College , 301 Platt Blvd, Claremont, CA 91711,"],"raw_orcid":"https://orcid.org/0000-0002-1449-2574","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Harvey Mudd College , 301 Platt Blvd, Claremont, CA 91711,","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039040940","display_name":"Robert Gentleman","orcid":"https://orcid.org/0000-0003-4505-9893"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Gentleman","raw_affiliation_strings":["Center for Computational Biomedicine, Harvard Medical School , 10 Shattuck St, Boston, MA 02115,"],"raw_orcid":"https://orcid.org/0000-0003-4505-9893","affiliations":[{"raw_affiliation_string":"Center for Computational Biomedicine, Harvard Medical School , 10 Shattuck St, Boston, MA 02115,","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"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":0.8165,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.73196361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"2024","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9962000250816345,"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/T10350","display_name":"Electronic Health Records Systems","score":0.9060999751091003,"subfield":{"id":"https://openalex.org/subfields/3605","display_name":"Health Information Management"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7350718379020691},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.7076618075370789},{"id":"https://openalex.org/keywords/text-messaging","display_name":"Text messaging","score":0.5187721252441406},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39462944865226746},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3911837935447693}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7350718379020691},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.7076618075370789},{"id":"https://openalex.org/C3018949938","wikidata":"https://www.wikidata.org/wiki/Q17166101","display_name":"Text messaging","level":2,"score":0.5187721252441406},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39462944865226746},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3911837935447693}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","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":"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":"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":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baae119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae119","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baae119/60896180/baae119.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:39607847","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39607847","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:pubmedcentral.nih.gov:11604108","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11604108","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11604108/pdf/baae119.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baae119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae119","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baae119/60896180/baae119.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":[{"id":"https://openalex.org/F4320309332","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404793875.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W102787101","https://openalex.org/W1957272438","https://openalex.org/W2036288429","https://openalex.org/W2049625541","https://openalex.org/W2122402213","https://openalex.org/W2131660156","https://openalex.org/W2146089916","https://openalex.org/W2147018385","https://openalex.org/W2159583324","https://openalex.org/W2244501064","https://openalex.org/W2278812662","https://openalex.org/W2302501749","https://openalex.org/W2559028527","https://openalex.org/W2749087070","https://openalex.org/W2763682064","https://openalex.org/W2950750198","https://openalex.org/W3048245060","https://openalex.org/W3097081481","https://openalex.org/W3100689701","https://openalex.org/W3106143834","https://openalex.org/W4224037213","https://openalex.org/W4281661209","https://openalex.org/W4324130003","https://openalex.org/W4381594492","https://openalex.org/W4403458599","https://openalex.org/W6604181502"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2336574202","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890"],"abstract_inverted_index":{"There":[0],"is":[1,129,147],"an":[2,110],"ongoing":[3],"need":[4],"for":[5],"scalable":[6],"tools":[7],"to":[8,48,54,63,69,100,122,141],"aid":[9],"researchers":[10],"in":[11,30,92,95,106,125,136],"both":[12],"retrospective":[13,75],"and":[14,50,77,132,144,153],"prospective":[15],"standardization":[16,76],"of":[17,79,85,89,103,119,186],"discrete":[18],"entity":[19],"types-such":[20],"as":[21,158],"disease":[22],"names,":[23],"cell":[24],"types,":[25],"or":[26,41,57,94,171,180],"chemicals-that":[27],"are":[28,38,46,51],"used":[29,135,156,166],"metadata":[31,37],"associated":[32,44],"with":[33,59],"biomedical":[34,104,120],"data.":[35],"When":[36],"not":[39],"well-structured":[40],"precise,":[42],"the":[43,64,71,80,83,87],"data":[45,72],"harder":[47],"find":[49],"often":[52],"burdensome":[53],"reuse,":[55],"analyze,":[56],"integrate":[58],"other":[60],"datasets":[61],"due":[62],"upfront":[65],"curation":[66],"effort":[67],"required":[68],"make":[70],"usable-typically":[73],"through":[74],"cleaning":[78],"(meta)data.":[81],"With":[82],"goal":[84],"facilitating":[86],"task":[88],"standardizing":[90],"metadata-either":[91],"bulk":[93],"a":[96,168,183],"one-by-one":[97],"fashion,":[98],"e.g.":[99],"support":[101],"autocompletion":[102],"entities":[105,121],"forms-we":[107],"have":[108],"developed":[109],"open-source":[111],"tool":[112,128],"called":[113],"text2term":[114],"that":[115,139],"maps":[116],"free-text":[117],"descriptions":[118],"controlled":[123],"terms":[124],"ontologies.":[126],"The":[127],"highly":[130],"configurable":[131],"can":[133,154,163],"be":[134,155,165],"multiple":[137],"ways":[138],"cater":[140],"different":[142],"users":[143],"expertise":[145],"levels-it":[146],"available":[148],"on":[149],"Python":[150,160],"Package":[151],"Index":[152],"programmatically":[157],"any":[159],"package;":[161],"it":[162],"also":[164],"via":[167,172],"command-line":[169],"interface":[170],"our":[173,187],"hosted,":[174],"graphical":[175],"user":[176],"interface-based":[177],"web":[178],"application":[179,189],"by":[181],"deploying":[182],"local":[184],"instance":[185],"interactive":[188],"using":[190],"Docker.":[191],"Database":[192],"URL:":[193],"https://pypi.org/project/text2term.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
