{"id":"https://openalex.org/W4400375519","doi":"https://doi.org/10.48550/arxiv.2407.02626","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":"2024-07-02","ids":{"openalex":"https://openalex.org/W4400375519","doi":"https://doi.org/10.48550/arxiv.2407.02626"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2407.02626","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.02626","pdf_url":"https://arxiv.org/pdf/2407.02626","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2407.02626","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111250633","display_name":"Rafael S. Gon\u00e7alves","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Gon\u00e7alves, Rafael S.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110992292","display_name":"Jason Payne","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Payne, Jason","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Tan, Amelia","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tan, Amelia","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032065113","display_name":"Carmen Ben\u0131\u0301tez","orcid":"https://orcid.org/0000-0002-5407-8335"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Benitez, Carmen","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048004087","display_name":"Jamie Haddock","orcid":"https://orcid.org/0000-0002-1449-2574"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Haddock, Jamie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5039040940","display_name":"Robert Gentleman","orcid":"https://orcid.org/0000-0003-4505-9893"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gentleman, Robert","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5111250633"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"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":0.9922999739646912,"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":0.9922999739646912,"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":0.9851999878883362,"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/computer-science","display_name":"Computer science","score":0.536566436290741},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4823950529098511},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3527614176273346}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.536566436290741},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4823950529098511},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3527614176273346}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2407.02626","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.02626","pdf_url":"https://arxiv.org/pdf/2407.02626","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2407.02626","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2407.02626","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2407.02626","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.02626","pdf_url":"https://arxiv.org/pdf/2407.02626","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},"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/W4400375519.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"There":[0],"is":[1,140,160],"an":[2,121],"ongoing":[3],"need":[4],"for":[5,107],"scalable":[6],"tools":[7],"to":[8,52,58,67,73,109,133,152],"aid":[9],"researchers":[10],"in":[11,34,100,103,115,136,147],"both":[12],"retrospective":[13,81],"and":[14,54,83,143,155,164],"prospective":[15],"standardization":[16,82],"of":[17,85,91,95,112,130,198],"discrete":[18],"entity":[19],"types":[20,27],"--":[21,30,78,98,117,158],"such":[22],"as":[23,169],"disease":[24],"names,":[25],"cell":[26],"or":[28,45,61,102,182,192],"chemicals":[29],"that":[31,126,150],"are":[32,42,50,55],"used":[33,146,167,177],"metadata":[35,41,97],"associated":[36,48],"with":[37,63],"biomedical":[38,113,131],"data.":[39],"When":[40],"not":[43],"well-structured":[44],"precise,":[46],"the":[47,68,75,86,89,93],"data":[49,76],"harder":[51],"find":[53],"often":[56],"burdensome":[57],"reuse,":[59],"analyze":[60],"integrate":[62],"other":[64],"datasets":[65],"due":[66],"upfront":[69],"curation":[70],"effort":[71],"required":[72],"make":[74],"usable":[77],"typically":[79],"through":[80],"cleaning":[84],"(meta)data.":[87],"With":[88],"goal":[90],"facilitating":[92],"task":[94],"standardizing":[96],"either":[99],"bulk":[101],"a":[104,179,195],"one-by-one":[105],"fashion;":[106],"example,":[108],"support":[110],"auto-completion":[111],"entities":[114,132],"forms":[116],"we":[118],"have":[119],"developed":[120],"open-source":[122],"tool":[123,139],"called":[124],"text2term":[125],"maps":[127],"free-text":[128],"descriptions":[129],"controlled":[134],"terms":[135],"ontologies.":[137],"The":[138],"highly":[141],"configurable":[142],"can":[144,165,174],"be":[145,166,176],"multiple":[148],"ways":[149],"cater":[151],"different":[153],"users":[154],"expertise":[156],"levels":[157],"it":[159,173],"available":[161],"on":[162],"PyPI":[163],"programmatically":[168],"any":[170],"Python":[171],"package;":[172],"also":[175],"via":[178,183],"command-line":[180],"interface;":[181],"our":[184,199],"hosted,":[185],"graphical":[186],"user":[187],"interface-based":[188],"Web":[189],"application":[190,201],"(https://text2term.hms.harvard.edu);":[191],"by":[193],"deploying":[194],"local":[196],"instance":[197],"interactive":[200],"using":[202],"Docker.":[203]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2024-07-06T00:00:00"}
