{"id":"https://openalex.org/W3149377746","doi":"https://doi.org/10.1109/jbhi.2021.3106787","title":"A Network-Based Analysis of Disease Modules From a Taxonomic Perspective","display_name":"A Network-Based Analysis of Disease Modules From a Taxonomic Perspective","publication_year":2021,"publication_date":"2021-08-24","ids":{"openalex":"https://openalex.org/W3149377746","doi":"https://doi.org/10.1109/jbhi.2021.3106787","mag":"3149377746","pmid":"https://pubmed.ncbi.nlm.nih.gov/34428165"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2021.3106787","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3106787","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Giorgio Grani","orcid":"https://orcid.org/0000-0002-0388-1283"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giorgio Grani","raw_affiliation_strings":["Translational and Precision Medicine Department, Sapienza University of Rome, Rome, Italy"],"raw_orcid":"https://orcid.org/0000-0002-0388-1283","affiliations":[{"raw_affiliation_string":"Translational and Precision Medicine Department, Sapienza University of Rome, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lorenzo Madeddu","orcid":"https://orcid.org/0000-0002-5702-8691"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lorenzo Madeddu","raw_affiliation_strings":["Translational and Precision Medicine Department, Sapienza University of Rome, Rome, Italy"],"raw_orcid":"https://orcid.org/0000-0002-5702-8691","affiliations":[{"raw_affiliation_string":"Translational and Precision Medicine Department, Sapienza University of Rome, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":null,"display_name":"Paola Velardi","orcid":"https://orcid.org/0000-0003-0884-1499"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paola Velardi","raw_affiliation_strings":["Department of Computer Science, Sapienza University of Rome, Rome, Italy"],"raw_orcid":"https://orcid.org/0000-0003-0884-1499","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sapienza University of Rome, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":null,"apc_paid":null,"fwci":0.3701,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.54368313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"26","issue":"4","first_page":"1773","last_page":"1781"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9294999837875366,"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":0.9294999837875366,"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":0.013799999840557575,"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":0.012600000016391277,"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/perspective","display_name":"Perspective (graphical)","score":0.7566999793052673},{"id":"https://openalex.org/keywords/categorical-variable","display_name":"Categorical variable","score":0.6934999823570251},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5256999731063843},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.46709999442100525},{"id":"https://openalex.org/keywords/human-disease","display_name":"Human disease","score":0.38420000672340393},{"id":"https://openalex.org/keywords/social-network-analysis","display_name":"Social network analysis","score":0.28619998693466187},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.2728999853134155}],"concepts":[{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.7566999793052673},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.6934999823570251},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.656499981880188},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5256999731063843},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5199000239372253},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.46709999442100525},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4122999906539917},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.38420000672340393},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.37470000982284546},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35830000042915344},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29910001158714294},{"id":"https://openalex.org/C114713312","wikidata":"https://www.wikidata.org/wiki/Q7551269","display_name":"Social network analysis","level":3,"score":0.28619998693466187},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.2728999853134155},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.26579999923706055},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2630999982357025},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2605000138282776},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2542000114917755}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/jbhi.2021.3106787","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3106787","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:34428165","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34428165","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":"IEEE journal of biomedical and health informatics","raw_type":null},{"id":"pmh:oai:iris.uniroma1.it:11573/1566301","is_oa":false,"landing_page_url":"http://hdl.handle.net/11573/1566301","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1575657597","display_name":null,"funder_award_id":"20182022","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320337140","display_name":"Dipartimento di Informatica, Sapienza Universit\u00e0 di Roma","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1544009106","https://openalex.org/W2041617939","https://openalex.org/W2056782561","https://openalex.org/W2062533676","https://openalex.org/W2067305633","https://openalex.org/W2083045667","https://openalex.org/W2110553827","https://openalex.org/W2119412782","https://openalex.org/W2156695919","https://openalex.org/W2159092541","https://openalex.org/W2160202099","https://openalex.org/W2168301815","https://openalex.org/W2169433327","https://openalex.org/W2179281170","https://openalex.org/W2577490495","https://openalex.org/W2826750344","https://openalex.org/W2922196565","https://openalex.org/W2938214930","https://openalex.org/W2950213033","https://openalex.org/W2964198126","https://openalex.org/W2983166786","https://openalex.org/W3021030584","https://openalex.org/W3053581598","https://openalex.org/W4211100568","https://openalex.org/W4235145261","https://openalex.org/W4238448376","https://openalex.org/W4240681178","https://openalex.org/W4254977667","https://openalex.org/W6636975626"],"related_works":[],"abstract_inverted_index":{"OBJECTIVE:":[0],"Human-curated":[1],"diseaseontologies":[2],"are":[3,25,53,83],"widely":[4],"used":[5,86],"for":[6],"diagnostic":[7],"evaluation,":[8],"treatment":[9],"and":[10,15,60,94,99,124,162,191,213,217,225,231],"data":[11],"comparisons":[12],"over":[13],"time,":[14],"clinical":[16,127],"decision":[17],"support.":[18],"The":[19,133],"classification":[20,229],"principles":[21],"underlying":[22],"these":[23],"ontologies":[24,52,161],"guided":[26],"by":[27,150],"the":[28,58,79,102,136,152,166,170,205],"analysis":[29],"of":[30,63,73,111,121,126,135,157,165,220],"observable":[31],"pathological":[32],"similarities":[33,149],"between":[34,154,189],"disorders,":[35],"often":[36],"based":[37],"on":[38,147],"anatomical":[39],"or":[40],"histological":[41],"principles.":[42],"Although,":[43],"thanks":[44],"to":[45,56,89,95,129,143,180,192,209],"recent":[46],"advances":[47],"in":[48,78,87,139,159,169],"molecular":[49],"biology,":[50],"disease":[51,74,148,199,228],"slowly":[54],"changing":[55],"integrate":[57],"etiological":[59],"genetic":[61],"origins":[62],"diseases,":[64,222],"nosology":[65],"still":[66],"reflects":[67],"this":[68,140,194],"\"reductionist\"":[69],"perspective.":[70],"Proximity":[71],"relationships":[72,123],"modules":[75],"(hereafter":[76],"DMs)":[77],"human":[80,221,227],"interactome":[81],"network":[82,234],"now":[84],"increasingly":[85],"diagnostics,":[88],"identify":[90,232],"pathobiologically":[91],"similar":[92],"diseases":[93,158],"support":[96],"drug":[97],"repurposing":[98],"discovery.":[100],"On":[101],"other":[103],"hand,":[104],"similarity":[105,219],"relations":[106,188],"induced":[107],"from":[108,186],"structural":[109,163,216],"proximity":[110,156,164,187],"DMs":[112,168],"also":[113],"have":[114],"several":[115],"limitations,":[116],"such":[117],"as":[118],"incomplete":[119],"knowledge":[120],"disease-gene":[122,238],"reliability":[125],"trials":[128],"assess":[130],"their":[131],"validity.":[132],"purpose":[134],"study":[137],"described":[138],"paper":[141],"is":[142],"shed":[144],"more":[145],"light":[146],"analyzing":[151],"relationship":[153],"categorical":[155,218],"human-curated":[160,198],"related":[167,178],"interactome.":[171],"METHOD:":[172],"We":[173,202],"propose":[174],"a":[175,183,197],"method":[176,207],"(and":[177],"algorithms)":[179],"automatically":[181],"induce":[182],"hierarchical":[184],"structure":[185,195],"DMs,":[190],"compare":[193],"with":[196],"taxonomy.":[200],"RESULTS:":[201],"demonstrate":[203],"that":[204],"proposed":[206],"allows":[208],"systematically":[210],"analyze":[211],"commonalities":[212],"differences":[214],"among":[215],"help":[223],"refine":[224],"extend":[226],"systems,":[230],"promising":[233],"areas":[235],"where":[236],"new":[237],"interactions":[239],"can":[240],"be":[241],"discovered.":[242]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2021-04-13T00:00:00"}
