{"id":"https://openalex.org/W2156540941","doi":"https://doi.org/10.3217/jucs-013-12-1881","title":"An Ontology-based Approach to Support Text Mining and Information Retrieval in the Biological Domain","display_name":"An Ontology-based Approach to Support Text Mining and Information Retrieval in the Biological Domain","publication_year":2020,"publication_date":"2020-04-07","ids":{"openalex":"https://openalex.org/W2156540941","doi":"https://doi.org/10.3217/jucs-013-12-1881","mag":"2156540941"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:7000026","is_oa":true,"landing_page_url":"https://zenodo.org/record/7000026","pdf_url":"https://zenodo.org/record/7000026","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"JUCS - Journal of Universal Computer Science 13((12)) 1881-1907","raw_type":"info:eu-repo/semantics/article"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/7000026","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049147763","display_name":"Khaled Khelif","orcid":null},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Khaled Khelif","raw_affiliation_strings":["French Institute for Research in Computer Science and Automation"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"French Institute for Research in Computer Science and Automation","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044327360","display_name":"Pascal Barbry","orcid":"https://orcid.org/0000-0001-9632-6483"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pascal Barbry","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5043179188","display_name":"Rose Dieng-Kuntz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rose Dieng-Kuntz","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0745,"has_fulltext":true,"cited_by_count":41,"citation_normalized_percentile":{"value":0.37495088,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":null,"first_page":"1881","last_page":"1907"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9933000206947327,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9866999983787537,"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":0.8920633792877197},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7837193012237549},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6712064743041992},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5221621990203857},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.4944040775299072},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.45869842171669006},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.4226875305175781},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4189854562282562},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34738683700561523}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8920633792877197},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7837193012237549},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6712064743041992},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5221621990203857},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.4944040775299072},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.45869842171669006},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.4226875305175781},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4189854562282562},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34738683700561523},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:zenodo.org:7000026","is_oa":true,"landing_page_url":"https://zenodo.org/record/7000026","pdf_url":"https://zenodo.org/record/7000026","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"JUCS - Journal of Universal Computer Science 13((12)) 1881-1907","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.123.1649","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.123.1649","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.jucs.org/jucs_13_12/an_ontology_based_approach/jucs_13_12_1881_1907_khelif.pdf","raw_type":"text"},{"id":"doi:10.3217/jucs-013-12-1881","is_oa":true,"landing_page_url":"https://doi.org/10.3217/jucs-013-12-1881","pdf_url":null,"source":{"id":"https://openalex.org/S4306400660","display_name":"TUGraz OPEN Library (Graz University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4092182","host_organization_name":"Graz University of Technology","host_organization_lineage":["https://openalex.org/I4092182"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"DataPaper"},{"id":"mag:2156540941","is_oa":false,"landing_page_url":"http://dblp.uni-trier.de/db/journals/jucs/jucs13.html#KhelifDB07","pdf_url":null,"source":{"id":"https://openalex.org/S58563349","display_name":"JUCS - Journal of Universal Computer Science","issn_l":"0948-695X","issn":["0948-695X","0948-6968"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310317875","host_organization_name":"Verlag der Technischen Universit\u00e4t Graz","host_organization_lineage":["https://openalex.org/P4310317875"],"host_organization_lineage_names":["Verlag der Technischen Universit\u00e4t Graz"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"JUCS - Journal of Universal Computer Science","raw_type":null}],"best_oa_location":{"id":"pmh:oai:zenodo.org:7000026","is_oa":true,"landing_page_url":"https://zenodo.org/record/7000026","pdf_url":"https://zenodo.org/record/7000026","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"JUCS - Journal of Universal Computer Science 13((12)) 1881-1907","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.5400000214576721}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2156540941.pdf","grobid_xml":"https://content.openalex.org/works/W2156540941.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W4508078","https://openalex.org/W13024833","https://openalex.org/W90740718","https://openalex.org/W109123980","https://openalex.org/W122706658","https://openalex.org/W1099821490","https://openalex.org/W1521396122","https://openalex.org/W1522202524","https://openalex.org/W1541884542","https://openalex.org/W1580236550","https://openalex.org/W1967411628","https://openalex.org/W1972793074","https://openalex.org/W1974775483","https://openalex.org/W1990530231","https://openalex.org/W2010487328","https://openalex.org/W2053673723","https://openalex.org/W2061327015","https://openalex.org/W2064148497","https://openalex.org/W2103017472","https://openalex.org/W2110989128","https://openalex.org/W2114561888","https://openalex.org/W2120973168","https://openalex.org/W2126875431","https://openalex.org/W2131630280","https://openalex.org/W2137881949","https://openalex.org/W2150650678","https://openalex.org/W2154082132","https://openalex.org/W2154687603","https://openalex.org/W2157272674","https://openalex.org/W2168384920","https://openalex.org/W2468598294","https://openalex.org/W2758614577","https://openalex.org/W2977768578"],"related_works":["https://openalex.org/W1974775483","https://openalex.org/W1980466622","https://openalex.org/W2704992846","https://openalex.org/W2110989128","https://openalex.org/W1923813304","https://openalex.org/W2026285882","https://openalex.org/W2946987804","https://openalex.org/W2152523033","https://openalex.org/W1565580039","https://openalex.org/W102005480","https://openalex.org/W2383759688","https://openalex.org/W2360075568","https://openalex.org/W2080787340","https://openalex.org/W1983989393","https://openalex.org/W2063575587","https://openalex.org/W2745399624","https://openalex.org/W2123979981","https://openalex.org/W3016592075","https://openalex.org/W2983339271","https://openalex.org/W2128251740"],"abstract_inverted_index":{"Abstract:":[0],"This":[1,68],"paper":[2],"describes":[3],"an":[4],"ontology-based":[5,51],"approach":[6,69],"aiming":[7],"at":[8,16],"helping":[9],"biologists":[10,59,74],"to":[11,60,72,95],"annotate":[12],"their":[13,18,87],"documents":[14],"and":[15,38,55,83],"facilitating":[17],"information":[19],"retrieval":[20],"task.":[21],"Our":[22],"approach,":[23],"based":[24],"on":[25,30,64,76],"semantic":[26,33,52],"web":[27],"technologies,":[28],"relies":[29],"formalised":[31],"ontologies,":[32],"annotations":[34,53,66],"of":[35,50,86,99],"scientific":[36],"articles":[37],"knowledge":[39],"extraction":[40],"from":[41],"texts.":[42],"We":[43],"propose":[44],"a":[45,56],"method/system":[46],"for":[47],"the":[48,81,84],"generation":[49],"(MeatAnnot)":[54],"system":[57],"allowing":[58],"draw":[61],"advanced":[62],"inferences":[63],"these":[65],"(MeatSearch).":[67],"was":[70],"proposed":[71],"support":[73],"working":[75],"DNA":[77],"microarray":[78],"experiments":[79],"in":[80],"validation":[82],"interpretation":[85],"results,":[88],"but":[89],"it":[90],"can":[91],"probably":[92],"be":[93],"extended":[94],"other":[96],"massive":[97],"analyses":[98],"biological":[100],"events":[101],"(as":[102],"provided":[103],"by":[104],"proteomics,":[105],"metabolomics\u2026).":[106]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-17T05:52:16.776730","created_date":"2025-10-10T00:00:00"}
