{"id":"https://openalex.org/W2154693238","doi":"https://doi.org/10.1186/1471-2105-13-s1-s4","title":"User centered and ontology based information retrieval system for life sciences","display_name":"User centered and ontology based information retrieval system for life sciences","publication_year":2012,"publication_date":"2012-01-25","ids":{"openalex":"https://openalex.org/W2154693238","doi":"https://doi.org/10.1186/1471-2105-13-s1-s4","mag":"2154693238"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s1-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s1-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S4","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002227583","display_name":"Mohameth Fran\u00e7ois Sy","orcid":"https://orcid.org/0000-0002-4603-9838"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mohameth-Fran\u00e7ois Sy","raw_affiliation_strings":["LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072128914","display_name":"Sylvie Ranwez","orcid":"https://orcid.org/0000-0002-8707-0313"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sylvie Ranwez","raw_affiliation_strings":["LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019212344","display_name":"Jacky Montmain","orcid":"https://orcid.org/0000-0003-0918-5788"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jacky Montmain","raw_affiliation_strings":["LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060085686","display_name":"Armelle R\u00e9gnault","orcid":null},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Armelle Regnault","raw_affiliation_strings":["Inserm/Institut Multi-Organismes, Immunologie, H\u00e9matologie et Pneumologie (ITMO IHP), 175, rue du Chevaleret, 75013, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inserm/Institut Multi-Organismes, Immunologie, H\u00e9matologie et Pneumologie (ITMO IHP), 175, rue du Chevaleret, 75013, Paris, France","institution_ids":["https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007319413","display_name":"Michel Crampes","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michel Crampes","raw_affiliation_strings":["LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LGI2P Research Centre, EMA/Site EERIE, Parc scientifique G. Besse, 30 035, N\u00eemes cedex 1, France","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025043496","display_name":"Vincent Ranwez","orcid":"https://orcid.org/0000-0002-9308-7541"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Ranwez","raw_affiliation_strings":["Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS Universit\u00e9 Montpellier II, place E. Bataillon, CC 064, 34 095, Montpellier cedex 05, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS Universit\u00e9 Montpellier II, place E. Bataillon, CC 064, 34 095, Montpellier cedex 05, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I19894307","https://openalex.org/I4210105943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5072128914"],"corresponding_institution_ids":[],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.8228,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.91600676,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"S1","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":0.9998000264167786,"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":0.9998000264167786,"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":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9715999960899353,"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":0.8584390878677368},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.787222146987915},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6371383666992188},{"id":"https://openalex.org/keywords/query-expansion","display_name":"Query expansion","score":0.5314888954162598},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.4517008662223816}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8584390878677368},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.787222146987915},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6371383666992188},{"id":"https://openalex.org/C99016210","wikidata":"https://www.wikidata.org/wiki/Q5488129","display_name":"Query expansion","level":2,"score":0.5314888954162598},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.4517008662223816},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-13-s1-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s1-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:HAL:inserm-00662993v1","is_oa":false,"landing_page_url":"https://inserm.hal.science/inserm-00662993","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2012, 13 Suppl 1 (Suppl 1), pp.S4. &#x27E8;10.1186/1471-2105-13-S1-S4&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:087bc64d676f4a28b21480397681b55f","is_oa":false,"landing_page_url":"https://doaj.org/article/087bc64d676f4a28b21480397681b55f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss Suppl 1, p S4 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s1-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s1-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S1-S4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.5199999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2154693238.pdf","grobid_xml":"https://content.openalex.org/works/W2154693238.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W42500033","https://openalex.org/W79702431","https://openalex.org/W179879056","https://openalex.org/W1490588581","https://openalex.org/W1500117362","https://openalex.org/W1532325895","https://openalex.org/W1548930048","https://openalex.org/W1550436572","https://openalex.org/W1587615950","https://openalex.org/W1587714055","https://openalex.org/W1596876523","https://openalex.org/W1647729745","https://openalex.org/W1659833910","https://openalex.org/W1668989518","https://openalex.org/W1907013787","https://openalex.org/W1956559956","https://openalex.org/W1972275086","https://openalex.org/W2010160850","https://openalex.org/W2030507931","https://openalex.org/W2034473480","https://openalex.org/W2040998119","https://openalex.org/W2044986849","https://openalex.org/W2052182675","https://openalex.org/W2053673723","https://openalex.org/W2068086934","https://openalex.org/W2068802535","https://openalex.org/W2071601409","https://openalex.org/W2075377384","https://openalex.org/W2084168100","https://openalex.org/W2084242198","https://openalex.org/W2087739686","https://openalex.org/W2096939566","https://openalex.org/W2105106523","https://openalex.org/W2107703929","https://openalex.org/W2114296069","https://openalex.org/W2117463461","https://openalex.org/W2132232128","https://openalex.org/W2132784310","https://openalex.org/W2136480620","https://openalex.org/W2140519398","https://openalex.org/W2140887277","https://openalex.org/W2145258036","https://openalex.org/W2147131251","https://openalex.org/W2152200716","https://openalex.org/W2154724067","https://openalex.org/W2166344872","https://openalex.org/W2170618878","https://openalex.org/W2244375307","https://openalex.org/W2571454102","https://openalex.org/W4213009331","https://openalex.org/W4233441984","https://openalex.org/W4241601953","https://openalex.org/W4293690910","https://openalex.org/W6632561075"],"related_works":["https://openalex.org/W2161902337","https://openalex.org/W2393185060","https://openalex.org/W4206732572","https://openalex.org/W2090912237","https://openalex.org/W2114566577","https://openalex.org/W1999370257","https://openalex.org/W4308654829","https://openalex.org/W2380444954","https://openalex.org/W2148473175","https://openalex.org/W59960109"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Because":[2],"of":[3,7,59,87,143,155,183,216,231,242],"the":[4,42,52,57,85,97,107,121,141,203,229,288],"increasing":[5],"number":[6],"electronic":[8],"resources,":[9],"designing":[10],"efficient":[11],"tools":[12],"to":[13,96,115,139,158,172,178,191,198,250,293],"retrieve":[14],"and":[15,31,51,63,90,109,149,167,213,224],"exploit":[16],"them":[17],"is":[18,45,56,80,99,147,185,269,277],"a":[19,152,179,188,210,278,282],"major":[20],"challenge.":[21],"Some":[22],"improvements":[23],"have":[24,110],"been":[25],"offered":[26],"by":[27,68,106,219],"semantic":[28,189],"Web":[29],"technologies":[30],"applications":[32,50],"based":[33,260],"on":[34,113,136,237],"domain":[35,137],"ontologies.":[36],"In":[37],"life":[38],"science,":[39],"for":[40,93],"instance,":[41],"Gene":[43],"Ontology":[44],"widely":[46],"exploited":[47],"in":[48,187,254,265,286],"genomic":[49],"Medical":[53],"Subject":[54],"Headings":[55],"basis":[58],"biomedical":[60],"publications":[61],"indexation":[62],"information":[64,131,234,261,292],"retrieval":[65,132,235,262],"process":[66],"proposed":[67],"PubMed.":[69],"However":[70],"current":[71],"search":[72],"engines":[73],"suffer":[74],"from":[75],"two":[76,238],"main":[77],"drawbacks:":[78],"there":[79],"limited":[81],"user":[82,160,283],"interaction":[83],"with":[84,176],"list":[86],"retrieved":[88,148],"resources":[89],"no":[91,111],"explanation":[92],"their":[94,117,124],"adequacy":[95,175],"query":[98,156,221],"provided.":[100],"Users":[101],"may":[102],"thus":[103],"be":[104],"confused":[105],"selection":[108,182],"idea":[112],"how":[114],"adapt":[116],"queries":[118],"so":[119],"that":[120,134,146,150,195],"results":[122,157],"match":[123,202],"expectations.":[125],"Results":[126],"This":[127,275],"paper":[128,267],"describes":[129],"an":[130],"system":[133,236,263,289],"relies":[135],"ontology":[138,165,259],"widen":[140],"set":[142],"relevant":[144,291],"documents":[145,174,184],"uses":[151],"graphical":[153,193],"rendering":[154],"favor":[159],"interactions.":[161],"Semantic":[162],"proximities":[163],"between":[164],"concepts":[166,222],"aggregating":[168],"models":[169],"are":[170],"used":[171],"assess":[173],"respect":[177],"query.":[180],"The":[181,258],"displayed":[186],"map":[190],"provide":[192,294],"indications":[194],"make":[196],"explicit":[197],"what":[199],"extent":[200],"they":[201],"user's":[204],"query;":[205],"this":[206,233,266],"man/machine":[207],"interface":[208],"favors":[209],"more":[211],"interactive":[212],"iterative":[214],"exploration":[215],"data":[217],"corpus,":[218],"facilitating":[220],"weighting":[223],"visual":[225],"explanation.":[226],"We":[227],"illustrate":[228],"benefit":[230],"using":[232],"case":[239],"studies":[240],"one":[241],"which":[243,287],"aiming":[244],"at":[245],"collecting":[246],"human":[247],"genes":[248],"related":[249],"transcription":[251],"factors":[252],"involved":[253],"hemopoiesis":[255],"pathway.":[256],"Conclusions":[257],"described":[264],"(OBIRS)":[268],"freely":[270],"available":[271],"at:":[272],"http://www.ontotoolkit.mines-ales.fr/ObirsClient/":[273],".":[274],"environment":[276],"first":[279],"step":[280],"towards":[281],"centred":[284],"application":[285],"enlightens":[290],"decision":[295],"help.":[296]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
