{"id":"https://openalex.org/W2132099158","doi":"https://doi.org/10.1186/1756-0381-5-13","title":"An automated framework for hypotheses generation using literature","display_name":"An automated framework for hypotheses generation using literature","publication_year":2012,"publication_date":"2012-08-29","ids":{"openalex":"https://openalex.org/W2132099158","doi":"https://doi.org/10.1186/1756-0381-5-13","mag":"2132099158","pmid":"https://pubmed.ncbi.nlm.nih.gov/22931688"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-5-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-5-13","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-13","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-13","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057855237","display_name":"Vida Abedi","orcid":"https://orcid.org/0000-0001-7689-933X"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vida Abedi","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA. myeasin@memphis.edu","Department of Electrical and Computer Engineering, Memphis University, Memphis, USA","College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA. myeasin@memphis.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Memphis University, Memphis, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002765080","display_name":"Ramin Zand","orcid":"https://orcid.org/0000-0002-9477-0094"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramin Zand","raw_affiliation_strings":["Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA","Department of Neurology, University of Tennessee Health Science Center, Memphis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA","institution_ids":["https://openalex.org/I160606119"]},{"raw_affiliation_string":"Department of Neurology, University of Tennessee Health Science Center, Memphis, USA","institution_ids":["https://openalex.org/I160606119"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069645522","display_name":"Mohammed Yeasin","orcid":"https://orcid.org/0000-0003-0579-3030"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammed Yeasin","raw_affiliation_strings":["College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, TN, 38152, USA","Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA","Department of Electrical and Computer Engineering, Memphis University, Memphis, USA","College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Memphis University, Memphis, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079582559","display_name":"Fazle E. Faisal","orcid":"https://orcid.org/0000-0003-1517-0531"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]},{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fazle Elahi Faisal","raw_affiliation_strings":["College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, TN, 38152, USA","Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA","College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, USA","Department of Electrical and Computer Engineering, Memphis University, Memphis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Memphis University, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"College of Arts and Sciences, Bioinformatics Program, Memphis University, Memphis, USA","institution_ids":["https://openalex.org/I103163165"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Memphis University, Memphis, USA","institution_ids":["https://openalex.org/I94658018"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057855237"],"corresponding_institution_ids":["https://openalex.org/I103163165","https://openalex.org/I94658018"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3437,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.801511,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9696000218391418,"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":0.9696000218391418,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.007400000002235174,"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":0.002300000051036477,"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":0.6798549294471741},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.601886510848999},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5142931342124939},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.4384703040122986},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.42662879824638367},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.18932941555976868},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.10042151808738708}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6798549294471741},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.601886510848999},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5142931342124939},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4384703040122986},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.42662879824638367},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.18932941555976868},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.10042151808738708},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1756-0381-5-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-5-13","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-13","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:22931688","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22931688","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:e9b19ab0724246419329cd4591853d0b","is_oa":true,"landing_page_url":"https://doaj.org/article/e9b19ab0724246419329cd4591853d0b","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 5, Iss 1, p 13 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2500004","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3497588","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1756-0381-5-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-5-13","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-5-13","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8826789616","display_name":"CAREER: Co-analysis of Signal and Sense for Understanding Non-verbal Communications and their Applications","funder_award_id":"0746790","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320312842","display_name":"University of Memphis","ror":null},{"id":"https://openalex.org/F4320332511","display_name":"Health Science Center, University of Tennessee","ror":"https://ror.org/0011qv509"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2132099158.pdf","grobid_xml":"https://content.openalex.org/works/W2132099158.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W9185232","https://openalex.org/W1490056294","https://openalex.org/W1544423579","https://openalex.org/W1902027874","https://openalex.org/W1965610986","https://openalex.org/W1970167211","https://openalex.org/W1972901468","https://openalex.org/W1983578042","https://openalex.org/W1987224493","https://openalex.org/W1994689936","https://openalex.org/W1998660410","https://openalex.org/W2010045529","https://openalex.org/W2028239056","https://openalex.org/W2028302672","https://openalex.org/W2031868269","https://openalex.org/W2033616183","https://openalex.org/W2033930261","https://openalex.org/W2055629176","https://openalex.org/W2059745395","https://openalex.org/W2076105288","https://openalex.org/W2083045667","https://openalex.org/W2089955605","https://openalex.org/W2101992647","https://openalex.org/W2144181601","https://openalex.org/W2146440114","https://openalex.org/W2149184178","https://openalex.org/W2164394064","https://openalex.org/W2167106533","https://openalex.org/W2168846334","https://openalex.org/W4211164442","https://openalex.org/W4285719527","https://openalex.org/W4298222125"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W4386392971"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1],"bio-medicine,":[2],"exploratory":[3],"studies":[4,245],"and":[5,20,97,104,117,137,143,192,195,199,222,226,258,282,285,298,333,342],"hypothesis":[6,49,78,154],"generation":[7,155],"often":[8,64],"begin":[9],"with":[10,23,81,92,211,237,260,308],"researching":[11],"existing":[12,82],"literature":[13,38,115],"to":[14,45,68,89,266,278,304,338],"identify":[15,305],"a":[16,40,47,52,86,110,128,169,238,309],"set":[17,239],"of":[18,37,102,113,135,164,203,208,240,254,323],"factors":[19,241,306],"their":[21,77],"association":[22],"diseases,":[24],"phenotypes,":[25],"or":[26,50],"biological":[27,53],"processes.":[28],"Many":[29],"scientists":[30],"are":[31,187],"overwhelmed":[32],"by":[33,329,345],"the":[34,132,144,149,184,255,268,274,324,330,340,346],"sheer":[35],"volume":[36],"on":[39,289],"disease":[41,141,233],"when":[42],"they":[43],"plan":[44],"generate":[46],"new":[48,70,302],"study":[51,328],"phenomenon.":[54],"The":[55,152,176,206,292],"situation":[56],"is":[57,79,85,109,126,168,215,235,276,295,317,336],"even":[58],"worse":[59],"for":[60,320],"junior":[61],"investigators":[62],"who":[63],"find":[65],"it":[66],"difficult":[67],"formulate":[69],"hypotheses":[71,303],"or,":[72],"more":[73,188],"importantly,":[74],"corroborate":[75],"if":[76],"consistent":[80],"literature.":[83],"It":[84,270],"daunting":[87],"task":[88],"be":[90],"abreast":[91],"so":[93],"much":[94],"being":[95,318],"published":[96,150],"also":[98],"remember":[99],"all":[100],"combinations":[101],"direct":[103,221,281],"indirect":[105,223,283],"associations.":[106],"Fortunately":[107],"there":[108,125],"growing":[111],"trend":[112],"using":[114,197,248],"mining":[116],"knowledge":[118,263,287],"discovery":[119,288],"tools":[120],"in":[121,140,147,190,217,300],"biomedical":[122],"research.":[123],"However,":[124],"still":[127],"large":[129],"gap":[130],"between":[131],"huge":[133],"amount":[134],"effort":[136,146],"resources":[138],"invested":[139],"research":[142],"little":[145],"harvesting":[148],"knowledge.":[151],"proposed":[153,177,293],"framework":[156,294],"(HGF)":[157],"finds":[158],"\"crisp":[159],"semantic":[160,213],"associations\"":[161],"among":[162],"entities":[163,230],"interest":[165],"-":[166],"that":[167,273],"step":[170],"towards":[171],"bridging":[172],"such":[173],"gaps.":[174],"METHODOLOGY:":[175],"HGF":[178,275],"shares":[179],"similar":[180],"end":[181],"goals":[182],"like":[183],"SWAN":[185],"but":[186],"holistic":[189],"nature":[191],"was":[193,264,271],"designed":[194],"implemented":[196],"scalable":[198],"efficient":[200],"computational":[201],"models":[202],"disease-disease":[204],"interaction.":[205],"integration":[207],"mapping":[209],"ontologies":[210],"latent":[212],"analysis":[214,253],"critical":[216],"capturing":[218],"domain":[219,331],"specific":[220],"\"crisp\"":[224,280],"associations,":[225,284],"making":[227],"assertions":[228,343],"about":[229],"(such":[231],"as":[232],"X":[234],"associated":[236,307,334],"Z).":[242],"RESULTS:":[243],"Pilot":[244],"were":[246],"performed":[247,265],"two":[249],"diseases.":[250],"A":[251,311,326],"comparative":[252],"computed":[256,344],"\"associations\"":[257],"\"assertions\"":[259],"curated":[261],"expert":[262],"validate":[267,339],"results.":[269],"observed":[272],"able":[277],"capture":[279],"provide":[286],"demand.":[290],"CONCLUSIONS:":[291],"fast,":[296],"efficient,":[297],"robust":[299],"generating":[301],"disease.":[310],"full":[312],"integrated":[313],"Web":[314],"service":[315],"application":[316],"developed":[319],"wide":[321],"dissemination":[322],"HGF.":[325,347],"large-scale":[327],"experts":[332],"researchers":[335],"underway":[337],"associations":[341]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
