{"id":"https://openalex.org/W2149018312","doi":"https://doi.org/10.1109/cibcb.2008.4675775","title":"Improving feature representation of natural language gene functional annotations using automatic term expansion","display_name":"Improving feature representation of natural language gene functional annotations using automatic term expansion","publication_year":2008,"publication_date":"2008-09-01","ids":{"openalex":"https://openalex.org/W2149018312","doi":"https://doi.org/10.1109/cibcb.2008.4675775","mag":"2149018312"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2008.4675775","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2008.4675775","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055383192","display_name":"Ji He","orcid":"https://orcid.org/0000-0002-9556-652X"},"institutions":[{"id":"https://openalex.org/I4210126540","display_name":"Noble Research Institute","ror":"https://ror.org/02zta5505","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210126540"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ji He","raw_affiliation_strings":["Bioinformatics Core Facility, Samuel Roberts Noble Foundation, Ardmore, OK, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Core Facility, Samuel Roberts Noble Foundation, Ardmore, OK, USA","institution_ids":["https://openalex.org/I4210126540"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5055383192"],"corresponding_institution_ids":["https://openalex.org/I4210126540"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":null,"first_page":"173","last_page":"179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9969000220298767,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9969000220298767,"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":0.9966999888420105,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9966999888420105,"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":0.7741237878799438},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.6229822635650635},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.5911614298820496},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5669633150100708},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5264811515808105},{"id":"https://openalex.org/keywords/vector-space-model","display_name":"Vector space model","score":0.472125381231308},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.468882292509079},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4659233093261719},{"id":"https://openalex.org/keywords/query-expansion","display_name":"Query expansion","score":0.44890281558036804},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.44725045561790466},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.432658851146698},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3933336138725281},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3652459383010864},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3510848879814148},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21478936076164246}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7741237878799438},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.6229822635650635},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.5911614298820496},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5669633150100708},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5264811515808105},{"id":"https://openalex.org/C89686163","wikidata":"https://www.wikidata.org/wiki/Q1187982","display_name":"Vector space model","level":2,"score":0.472125381231308},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.468882292509079},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4659233093261719},{"id":"https://openalex.org/C99016210","wikidata":"https://www.wikidata.org/wiki/Q5488129","display_name":"Query expansion","level":2,"score":0.44890281558036804},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.44725045561790466},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.432658851146698},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3933336138725281},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3652459383010864},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3510848879814148},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21478936076164246},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/cibcb.2008.4675775","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2008.4675775","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.142.2149","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.142.2149","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.jihe.net/downloads/papers/he08cibcb.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8299999833106995,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W62662976","https://openalex.org/W1533946607","https://openalex.org/W1924689489","https://openalex.org/W1966690718","https://openalex.org/W1974881328","https://openalex.org/W1979046459","https://openalex.org/W1980053379","https://openalex.org/W1999817920","https://openalex.org/W2005422315","https://openalex.org/W2011986160","https://openalex.org/W2012611887","https://openalex.org/W2024932032","https://openalex.org/W2038721957","https://openalex.org/W2055043387","https://openalex.org/W2060907774","https://openalex.org/W2096082161","https://openalex.org/W2098162425","https://openalex.org/W2098290609","https://openalex.org/W2103017472","https://openalex.org/W2105106534","https://openalex.org/W2117805756","https://openalex.org/W2126225210","https://openalex.org/W2159482845","https://openalex.org/W2169896388","https://openalex.org/W2435251607","https://openalex.org/W2950225692","https://openalex.org/W4235505822","https://openalex.org/W4236236547","https://openalex.org/W4285719527","https://openalex.org/W4301756919","https://openalex.org/W6602593179","https://openalex.org/W6632118081","https://openalex.org/W6640261747","https://openalex.org/W6677712588","https://openalex.org/W6717827561","https://openalex.org/W7000527806"],"related_works":["https://openalex.org/W2364053392","https://openalex.org/W2379136362","https://openalex.org/W2063335787","https://openalex.org/W1492957152","https://openalex.org/W4366988866","https://openalex.org/W2107087903","https://openalex.org/W3217693661","https://openalex.org/W1990330161","https://openalex.org/W2026715611","https://openalex.org/W1569439377"],"abstract_inverted_index":{"Despite":[0],"increasing":[1],"work":[2],"for":[3,57],"describing":[4],"gene":[5,13,123,144],"functions":[6],"using":[7],"controlled":[8],"vocabulary,":[9],"natural":[10],"language":[11],"style":[12],"functional":[14,81,124],"annotations":[15],"are":[16,21],"most":[17,22],"easily":[18],"available":[19],"and":[20,76,150],"widely":[23,55],"used":[24],"by":[25],"biologists.":[26],"And":[27],"intelligent":[28],"analysis":[29],"of":[30,37,79,109,119,122,159],"these":[31,68],"data":[32,148],"in":[33,40,102,134],"large":[34],"scale":[35],"is":[36,54,132],"great":[38],"importance":[39],"the":[41,45,73,80,117,152,160],"post-genome":[42],"era.":[43],"While":[44],"vector":[46],"space":[47],"model":[48],"(VSM)":[49],"based":[50,97],"TF*IDF":[51,85],"feature":[52,86],"representation":[53],"adopted":[56],"text":[58],"document":[59],"analysis,":[60],"it":[61],"has":[62,151],"significant":[63],"limitations":[64],"when":[65],"applied":[66],"to":[67,72,116,140,154,165],"data,":[69],"primarily":[70],"due":[71],"high":[74,77],"conciseness":[75],"noisiness":[78],"annotations.":[82,125],"To":[83],"improve":[84],"representation,":[87],"this":[88,146],"paper":[89],"proposes":[90],"two":[91],"automatic":[92],"term":[93],"expansion":[94,100],"(ATE)":[95],"methods":[96],"on":[98,145],"query":[99,143],"(QE)":[101],"information":[103],"retrieval":[104],"(IR)":[105],"theory.":[106],"The":[107],"effectiveness":[108],"ATE":[110,131],"was":[111],"examined":[112],"through":[113],"its":[114],"application":[115],"measurement":[118,158],"pattern":[120,161],"proximity":[121],"Our":[126],"comparative":[127],"results":[128],"show":[129],"that":[130],"effective":[133],"retrieving":[135],"functionally":[136],"correlated":[137],"genes":[138],"corresponding":[139],"a":[141],"random":[142],"particular":[147],"type,":[149],"capability":[153],"produce":[155],"more":[156],"accurate":[157],"similarity,":[162],"with":[163],"reference":[164],"genes\u2019":[166],"biological":[167],"functions.":[168]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
