{"id":"https://openalex.org/W4390971134","doi":"https://doi.org/10.1109/bibm58861.2023.10385722","title":"Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations","display_name":"Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390971134","doi":"https://doi.org/10.1109/bibm58861.2023.10385722"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385722","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","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/A5050082998","display_name":"Isabella Grassucci","orcid":"https://orcid.org/0000-0002-2484-8570"},"institutions":[{"id":"https://openalex.org/I4210134348","display_name":"National Cancer Institute","ror":"https://ror.org/044ybef51","country_code":"MY","type":"government","lineage":["https://openalex.org/I105292261","https://openalex.org/I4210134348"]}],"countries":["MY"],"is_corresponding":true,"raw_author_name":"Isabella Grassucci","raw_affiliation_strings":["National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","institution_ids":["https://openalex.org/I4210134348"]},{"raw_affiliation_string":"UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034647396","display_name":"Eleonora Sperandio","orcid":"https://orcid.org/0000-0002-8572-6788"},"institutions":[{"id":"https://openalex.org/I4210134348","display_name":"National Cancer Institute","ror":"https://ror.org/044ybef51","country_code":"MY","type":"government","lineage":["https://openalex.org/I105292261","https://openalex.org/I4210134348"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Eleonora Sperandio","raw_affiliation_strings":["National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","institution_ids":["https://openalex.org/I4210134348"]},{"raw_affiliation_string":"UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071183779","display_name":"Fabio Ticconi","orcid":"https://orcid.org/0000-0001-8905-6657"},"institutions":[{"id":"https://openalex.org/I4210134348","display_name":"National Cancer Institute","ror":"https://ror.org/044ybef51","country_code":"MY","type":"government","lineage":["https://openalex.org/I105292261","https://openalex.org/I4210134348"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Fabio Ticconi","raw_affiliation_strings":["National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","institution_ids":["https://openalex.org/I4210134348"]},{"raw_affiliation_string":"UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046032709","display_name":"Alice Massacci","orcid":"https://orcid.org/0000-0001-7780-809X"},"institutions":[{"id":"https://openalex.org/I4210134348","display_name":"National Cancer Institute","ror":"https://ror.org/044ybef51","country_code":"MY","type":"government","lineage":["https://openalex.org/I105292261","https://openalex.org/I4210134348"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Alice Massacci","raw_affiliation_strings":["National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","institution_ids":["https://openalex.org/I4210134348"]},{"raw_affiliation_string":"UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038917395","display_name":"Sara Baldinelli","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134348","display_name":"National Cancer Institute","ror":"https://ror.org/044ybef51","country_code":"MY","type":"government","lineage":["https://openalex.org/I105292261","https://openalex.org/I4210134348"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Sara Baldinelli","raw_affiliation_strings":["National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","institution_ids":["https://openalex.org/I4210134348"]},{"raw_affiliation_string":"UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009416445","display_name":"Martina Betti","orcid":"https://orcid.org/0009-0003-4462-2207"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210139435","display_name":"Institute for Experimental Endocrinology and Oncology","ror":"https://ror.org/04sn06036","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Martina Betti","raw_affiliation_strings":["National Research Council,Institute of Experimental Endocrinology and Oncology,Naples,Italy","Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy"],"affiliations":[{"raw_affiliation_string":"National Research Council,Institute of Experimental Endocrinology and Oncology,Naples,Italy","institution_ids":["https://openalex.org/I4210139435"]},{"raw_affiliation_string":"Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy","institution_ids":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066981430","display_name":"Matteo Pallocca","orcid":"https://orcid.org/0000-0002-7756-3579"},"institutions":[{"id":"https://openalex.org/I4210134348","display_name":"National Cancer Institute","ror":"https://ror.org/044ybef51","country_code":"MY","type":"government","lineage":["https://openalex.org/I105292261","https://openalex.org/I4210134348"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Matteo Pallocca","raw_affiliation_strings":["National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"National Cancer Institute,UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena,Rome,Italy","institution_ids":["https://openalex.org/I4210134348"]},{"raw_affiliation_string":"UOSD Biostatistics, Bioinformatics and Clinical Trial Center, IRCSS Regina Elena, National Cancer Institute, Rome, Italy","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5050082998"],"corresponding_institution_ids":["https://openalex.org/I4210134348"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.33827857,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":null,"first_page":"3638","last_page":"3641"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9993000030517578,"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":0.9930999875068665,"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":0.7806776762008667},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6777281761169434},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5675792098045349},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5033852458000183},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4810783565044403},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.4691772758960724},{"id":"https://openalex.org/keywords/soundness","display_name":"Soundness","score":0.44678768515586853},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43570220470428467},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4345897138118744},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.4153105318546295},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.36585599184036255},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35389843583106995},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08760347962379456}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7806776762008667},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6777281761169434},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5675792098045349},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5033852458000183},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4810783565044403},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.4691772758960724},{"id":"https://openalex.org/C39920170","wikidata":"https://www.wikidata.org/wiki/Q693083","display_name":"Soundness","level":2,"score":0.44678768515586853},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43570220470428467},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4345897138118744},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4153105318546295},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36585599184036255},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35389843583106995},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08760347962379456},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385722","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1950829641","https://openalex.org/W2014677321","https://openalex.org/W2049295422","https://openalex.org/W2103017472","https://openalex.org/W2123879591","https://openalex.org/W2130410032","https://openalex.org/W2345356016","https://openalex.org/W2605897695","https://openalex.org/W3175752499","https://openalex.org/W4255738661","https://openalex.org/W4328052644","https://openalex.org/W6749258240"],"related_works":["https://openalex.org/W1511249877","https://openalex.org/W1578828174","https://openalex.org/W2950376466","https://openalex.org/W2000943029","https://openalex.org/W2621980927","https://openalex.org/W2002878601","https://openalex.org/W2199396573","https://openalex.org/W4302559785","https://openalex.org/W2140496290","https://openalex.org/W2949331520"],"abstract_inverted_index":{"Bioinformatics":[0],"and":[1,25,35,127,138],"Data":[2],"Science":[3],"are":[4,21],"routinely":[5],"challenged":[6],"to":[7,103,133,153],"take":[8],"out":[9],"intelligible":[10],"results":[11],"from":[12],"huge":[13],"amounts":[14],"of":[15,41,53,57,91,114,164],"data.":[16],"These":[17],"results,":[18],"in":[19,44,107,124,161],"turn,":[20],"conveyed":[22],"through":[23],"plots":[24],"visualizations":[26],"that":[27,87],"should":[28],"be":[29,151],"easily":[30],"reproducible":[31],"for":[32,76],"scientific":[33],"soundness":[34],"ethical":[36],"reasons.":[37],"This":[38],"process":[39,96],"is":[40,60],"critical":[42],"importance":[43],"Genomics,":[45],"when":[46],"dealing":[47],"with":[48,98],"large":[49],"multi-omics":[50],"datasets.":[51],"One":[52],"the":[54,92,112,115],"final":[55],"steps":[56],"these":[58],"analyses":[59],"Gene":[61,93,141],"Set":[62,142],"enrichment,":[63],"where":[64],"web":[65],"tools":[66],"represent":[67],"a":[68,73,84,89,131],"valuable":[69],"resource":[70],"but":[71],"not":[72],"reliable":[74],"surrogate":[75],"standardized,":[77],"high-quality":[78,105],"visualizations.":[79],"Here":[80],"we":[81,146],"present":[82,120],"Auto-GO,":[83],"software":[85],"framework":[86],"proposes":[88],"standardization":[90],"Functional":[94],"Enrichment":[95,143],"along":[97],"an":[99,108],"R":[100],"package":[101],"able":[102],"produce":[104],"visualization":[106],"automated":[109],"manner,":[110],"improving":[111],"reproducibility":[113],"whole":[116],"analytical":[117],"process.":[118],"We":[119],"three":[121],"use":[122],"cases":[123],"Cancer":[125],"Transcriptomics":[126],"Epigenomics":[128],"datasets":[129],"as":[130],"proof-of-concept":[132],"visualize":[134],"Multiple":[135],"Differential":[136],"Expression":[137],"Single":[139],"Sample":[140],"Analysis.":[144],"Finally,":[145],"show":[147],"how":[148],"it":[149],"can":[150],"employed":[152],"shear":[154],"light":[155],"on":[156],"publicly":[157],"available":[158],"datasets,":[159],"even":[160],"small":[162],"casuistry":[163],"Rare":[165],"Cancers.":[166]},"counts_by_year":[],"updated_date":"2025-12-21T01:58:51.020947","created_date":"2025-10-10T00:00:00"}
