{"id":"https://openalex.org/W2113781300","doi":"https://doi.org/10.1093/bioinformatics/btn157","title":"Towards the use of argumentation in bioinformatics: a gene expression case study","display_name":"Towards the use of argumentation in bioinformatics: a gene expression case study","publication_year":2008,"publication_date":"2008-06-27","ids":{"openalex":"https://openalex.org/W2113781300","doi":"https://doi.org/10.1093/bioinformatics/btn157","mag":"2113781300","pmid":"https://pubmed.ncbi.nlm.nih.gov/18586728"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn157","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn157","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i304/49052762/bioinformatics_24_13_i304.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i304/49052762/bioinformatics_24_13_i304.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032536651","display_name":"Kenneth McLeod","orcid":"https://orcid.org/0000-0002-2006-6619"},"institutions":[{"id":"https://openalex.org/I32062511","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93","country_code":"GB","type":"education","lineage":["https://openalex.org/I32062511"]},{"id":"https://openalex.org/I4387154614","display_name":"MRC Human Genetics Unit","ror":"https://ror.org/011jsc803","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4387154614","https://openalex.org/I90344618","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Kenneth McLeod","raw_affiliation_strings":["1 Department of Computer Science, Heriot-Watt University and 2MRC Human Genetics Unit, Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Heriot-Watt University and 2MRC Human Genetics Unit, Edinburgh, UK","institution_ids":["https://openalex.org/I32062511","https://openalex.org/I4387154614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079735260","display_name":"Albert Burger","orcid":"https://orcid.org/0000-0002-5492-8635"},"institutions":[{"id":"https://openalex.org/I32062511","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93","country_code":"GB","type":"education","lineage":["https://openalex.org/I32062511"]},{"id":"https://openalex.org/I4387154614","display_name":"MRC Human Genetics Unit","ror":"https://ror.org/011jsc803","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210087105","https://openalex.org/I4387154614","https://openalex.org/I90344618","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Albert Burger","raw_affiliation_strings":["1 Department of Computer Science, Heriot-Watt University and 2MRC Human Genetics Unit, Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Heriot-Watt University and 2MRC Human Genetics Unit, Edinburgh, UK","institution_ids":["https://openalex.org/I32062511","https://openalex.org/I4387154614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032536651"],"corresponding_institution_ids":["https://openalex.org/I32062511","https://openalex.org/I4387154614"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5615,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.68126625,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"24","issue":"13","first_page":"i304","last_page":"i312"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.666100025177002,"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":0.666100025177002,"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":0.06960000097751617,"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/T10885","display_name":"Gene expression and cancer classification","score":0.030899999663233757,"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/argumentation-theory","display_name":"Argumentation theory","score":0.9537938833236694},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7275431156158447},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.7049179077148438},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6621774435043335},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5139274597167969},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3751961588859558},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3439946174621582},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.33051279187202454},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.141057550907135},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.07406595349311829}],"concepts":[{"id":"https://openalex.org/C65059942","wikidata":"https://www.wikidata.org/wiki/Q270105","display_name":"Argumentation theory","level":2,"score":0.9537938833236694},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7275431156158447},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.7049179077148438},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6621774435043335},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5139274597167969},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3751961588859558},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3439946174621582},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.33051279187202454},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.141057550907135},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.07406595349311829},{"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D032701","descriptor_name":"Biomimetics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D032701","descriptor_name":"Biomimetics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D032701","descriptor_name":"Biomimetics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D032701","descriptor_name":"Biomimetics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn157","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn157","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i304/49052762/bioinformatics_24_13_i304.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18586728","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18586728","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.568.9580","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.568.9580","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.macs.hw.ac.uk/bisel/downloads/kcm_ismb_08.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2718635","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2718635","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn157","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn157","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/13/i304/49052762/bioinformatics_24_13_i304.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113781300.pdf","grobid_xml":"https://content.openalex.org/works/W2113781300.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W10172367","https://openalex.org/W22447144","https://openalex.org/W144900376","https://openalex.org/W1502374275","https://openalex.org/W1523712082","https://openalex.org/W1553600843","https://openalex.org/W1573503065","https://openalex.org/W1677682185","https://openalex.org/W1968956228","https://openalex.org/W1979320841","https://openalex.org/W2002520185","https://openalex.org/W2020955676","https://openalex.org/W2029696490","https://openalex.org/W2034885653","https://openalex.org/W2068144010","https://openalex.org/W2104126268","https://openalex.org/W2114739726","https://openalex.org/W2130714423","https://openalex.org/W2136887407","https://openalex.org/W2155493185","https://openalex.org/W2292976884","https://openalex.org/W2408185001","https://openalex.org/W2734202852","https://openalex.org/W2914263187","https://openalex.org/W4229802642","https://openalex.org/W4254401811","https://openalex.org/W6600917162","https://openalex.org/W6609644740","https://openalex.org/W6614942400","https://openalex.org/W6655547353","https://openalex.org/W6657691947","https://openalex.org/W6682885334","https://openalex.org/W6740696149"],"related_works":["https://openalex.org/W2141332034","https://openalex.org/W4256185029","https://openalex.org/W4388437769","https://openalex.org/W2337488240","https://openalex.org/W2762454042","https://openalex.org/W2064153856","https://openalex.org/W52290235","https://openalex.org/W3007362904","https://openalex.org/W2404647514","https://openalex.org/W1667647204"],"abstract_inverted_index":{"MOTIVATION:":[0],"Due":[1],"to":[2,31,40,51,88,127],"different":[3],"experimental":[4],"setups":[5],"and":[6,35,76,113],"various":[7],"interpretations":[8],"of":[9,28,37,48,72,78],"results,":[10],"the":[11,33,38,46,73,91,96,106,157,164],"data":[12,75,131,147],"contained":[13],"in":[14,132],"online":[15],"bioinformatics":[16],"resources":[17,30],"can":[18,124,148],"be":[19,125,149],"inconsistent,":[20],"therefore,":[21],"making":[22],"it":[23,59],"more":[24],"difficult":[25],"for":[26,156],"users":[27,53],"these":[29],"assess":[32],"suitability":[34],"correctness":[36],"answers":[39],"their":[41],"queries.":[42],"This":[43,119],"work":[44],"investigates":[45],"role":[47],"argumentation":[49,86,108,123,138,154],"systems":[50],"help":[52],"evaluate":[54],"such":[55],"answers.":[56],"More":[57],"specifically,":[58],"looks":[60],"closely":[61],"at":[62],"a":[63,84,114],"gene":[64,98,145,158],"expression":[65,99,146,159],"case":[66],"study,":[67],"creating":[68],"an":[69],"appropriate":[70],"representation":[71],"underlying":[74],"series":[77],"rules":[79,155],"that":[80,122],"are":[81,161],"used":[82,126],"by":[83,95],"third-party":[85],"engine":[87,109,139],"reason":[89],"over":[90],"query":[92],"results":[93],"provided":[94],"mouse":[97],"database":[100],"EMAGE.":[101],"RESULTS:":[102],"A":[103],"prototype":[104],"using":[105],"ASPIC":[107,137],"has":[110],"been":[111],"implemented":[112],"preliminary":[115],"evaluation":[116,120],"carried":[117],"out.":[118],"suggested":[121],"deal":[128],"with":[129],"inconsistent":[130],"biological":[133],"resources.":[134],"AVAILABILITY:":[135],"The":[136,153],"is":[140],"available":[141,162],"from":[142,151,163],"http://www.argumentation.org.":[143],"EMAGE":[144],"obtained":[150],"http://genex.hgu.mrc.ac.uk.":[152],"example":[160],"lead":[165],"author":[166],"upon":[167],"request.":[168]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
