{"id":"https://openalex.org/W3126250723","doi":"https://doi.org/10.1186/s13040-021-00239-w","title":"Gene function finding through cross-organism ensemble learning","display_name":"Gene function finding through cross-organism ensemble learning","publication_year":2021,"publication_date":"2021-02-12","ids":{"openalex":"https://openalex.org/W3126250723","doi":"https://doi.org/10.1186/s13040-021-00239-w","mag":"3126250723"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-021-00239-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00239-w","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-021-00239-w","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-021-00239-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079648393","display_name":"Gianluca Moro","orcid":"https://orcid.org/0000-0002-3663-7877"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Gianluca Moro","raw_affiliation_strings":["DISI - University of Bologna, Via dell\u2019Universit\u00e0, Cesena (FC), Italy","DISI - University of Bologna, Via dell'Universit\u00e0, Cesena (FC), Italy"],"affiliations":[{"raw_affiliation_string":"DISI - University of Bologna, Via dell\u2019Universit\u00e0, Cesena (FC), Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"DISI - University of Bologna, Via dell'Universit\u00e0, Cesena (FC), Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085346183","display_name":"Marco Masseroli","orcid":"https://orcid.org/0000-0003-2574-1174"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Masseroli","raw_affiliation_strings":["DEIB, Politecnico di Milano, Piazza L. Da Vinci 32, Milan, 20133, Italy"],"affiliations":[{"raw_affiliation_string":"DEIB, Politecnico di Milano, Piazza L. Da Vinci 32, Milan, 20133, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079648393"],"corresponding_institution_ids":["https://openalex.org/I9360294"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3246,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.5481531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"14","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9975000023841858,"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":0.9898999929428101,"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/organism","display_name":"Organism","score":0.7612932920455933},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7450007200241089},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.693777322769165},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5519996881484985},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5511332750320435},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5448246002197266},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.5345873832702637},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.48057055473327637},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4685426950454712},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3331730365753174},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3041088879108429},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20450693368911743},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.15621787309646606},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1030052900314331}],"concepts":[{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.7612932920455933},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7450007200241089},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.693777322769165},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5519996881484985},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5511332750320435},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5448246002197266},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.5345873832702637},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.48057055473327637},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4685426950454712},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3331730365753174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3041088879108429},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20450693368911743},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15621787309646606},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1030052900314331},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-021-00239-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00239-w","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-021-00239-w","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmh:oai:cris.unibo.it:11585/808531","is_oa":true,"landing_page_url":"https://biodatamining.biomedcentral.com/articles/10.1186/s13040-021-00239-w","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:bd629922d6864a23a09702e4f93135bd","is_oa":true,"landing_page_url":"https://doaj.org/article/bd629922d6864a23a09702e4f93135bd","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 14, Iss 1, Pp 1-21 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7879670","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7879670","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:re.public.polimi.it:11311/1162654","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1162654","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s13040-021-00239-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00239-w","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-021-00239-w","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3796392728","display_name":null,"funder_award_id":"693174","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"}],"funders":[{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3126250723.pdf","grobid_xml":"https://content.openalex.org/works/W3126250723.grobid-xml"},"referenced_works_count":99,"referenced_works":["https://openalex.org/W14097345","https://openalex.org/W189297676","https://openalex.org/W1480890459","https://openalex.org/W1508353027","https://openalex.org/W1534477342","https://openalex.org/W1553869793","https://openalex.org/W1570448133","https://openalex.org/W1597538863","https://openalex.org/W1597559145","https://openalex.org/W1605688901","https://openalex.org/W1829419243","https://openalex.org/W1880262756","https://openalex.org/W1912057618","https://openalex.org/W1922686488","https://openalex.org/W1981735184","https://openalex.org/W1985213868","https://openalex.org/W2001004762","https://openalex.org/W2012690341","https://openalex.org/W2015981827","https://openalex.org/W2020832641","https://openalex.org/W2022163189","https://openalex.org/W2022472106","https://openalex.org/W2034310798","https://openalex.org/W2038759777","https://openalex.org/W2050644191","https://openalex.org/W2051678411","https://openalex.org/W2052968292","https://openalex.org/W2054118996","https://openalex.org/W2058616517","https://openalex.org/W2059414555","https://openalex.org/W2065702910","https://openalex.org/W2069849680","https://openalex.org/W2072062223","https://openalex.org/W2075178605","https://openalex.org/W2076743129","https://openalex.org/W2077814585","https://openalex.org/W2082607144","https://openalex.org/W2084168100","https://openalex.org/W2091273188","https://openalex.org/W2100849409","https://openalex.org/W2104094955","https://openalex.org/W2106093878","https://openalex.org/W2107580398","https://openalex.org/W2107743791","https://openalex.org/W2113142309","https://openalex.org/W2117486996","https://openalex.org/W2119043225","https://openalex.org/W2121893605","https://openalex.org/W2131482353","https://openalex.org/W2133465414","https://openalex.org/W2134932622","https://openalex.org/W2138842411","https://openalex.org/W2141773193","https://openalex.org/W2144899297","https://openalex.org/W2146341620","https://openalex.org/W2147444893","https://openalex.org/W2148440006","https://openalex.org/W2155341884","https://openalex.org/W2155440340","https://openalex.org/W2156690298","https://openalex.org/W2159583324","https://openalex.org/W2164219008","https://openalex.org/W2165698076","https://openalex.org/W2166468869","https://openalex.org/W2168662600","https://openalex.org/W2168930979","https://openalex.org/W2169896388","https://openalex.org/W2181347294","https://openalex.org/W2184777435","https://openalex.org/W2215094294","https://openalex.org/W2223216628","https://openalex.org/W2227395312","https://openalex.org/W2293073759","https://openalex.org/W2294893199","https://openalex.org/W2314128852","https://openalex.org/W2353702165","https://openalex.org/W2528445297","https://openalex.org/W2559655401","https://openalex.org/W2565684071","https://openalex.org/W2612647668","https://openalex.org/W2754307534","https://openalex.org/W2768579653","https://openalex.org/W2792177509","https://openalex.org/W2892464364","https://openalex.org/W2893958209","https://openalex.org/W2914862438","https://openalex.org/W3144008936","https://openalex.org/W3145828585","https://openalex.org/W3153661842","https://openalex.org/W4230723324","https://openalex.org/W4238844819","https://openalex.org/W4242446209","https://openalex.org/W4246066782","https://openalex.org/W4247272746","https://openalex.org/W4254300870","https://openalex.org/W4256568565","https://openalex.org/W4405648826","https://openalex.org/W6639619044","https://openalex.org/W6686516128"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W2074740504","https://openalex.org/W3013644380","https://openalex.org/W1996935079","https://openalex.org/W3210243923","https://openalex.org/W2145833061","https://openalex.org/W2258998699","https://openalex.org/W1998405066","https://openalex.org/W2171737904","https://openalex.org/W2029483977"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Structured":[2],"biological":[3,20],"information":[4],"about":[5],"genes":[6,40],"and":[7,16,37,41,54,96,213,219,249,278,289,345],"proteins":[8,42],"is":[9,136,190,299],"a":[10,33,70,84,101,120,129,139,268],"valuable":[11,48,330],"resource":[12],"to":[13,77,127,137,149,152,163,193,216,220,283,297,322,332,346],"improve":[14],"discovery":[15],"understanding":[17],"of":[18,39,43,83,90,111,122,258,274],"complex":[19],"processes":[21],"via":[22],"machine":[23,141],"learning":[24,74,142,211,310],"algorithms.":[25],"Gene":[26],"Ontology":[27],"(GO)":[28],"controlled":[29],"annotations":[30,49,82,89,107,124,169,182,197,277,287,343,349],"describe,":[31],"in":[32,117,125,161,198],"structured":[34],"form,":[35],"features":[36],"functions":[38],"many":[44],"organisms.":[45,62],"However,":[46],"such":[47],"are":[50,56,328],"not":[51],"always":[52],"reliable":[53,313],"sometimes":[55],"incomplete,":[57],"especially":[58],"for":[59,170,183],"rarely":[60],"studied":[61],"Here,":[63],"we":[64],"present":[65],"GeFF":[66,104],"(Gene":[67],"Function":[68],"Finder),":[69],"novel":[71,206,307,315],"cross-organism":[72,260,308],"ensemble":[73,210,261,294,309],"method":[75,207,229,296,311],"able":[76,192],"reliably":[78],"predict":[79],"new":[80,180,195,276,342],"GO":[81,88,236],"target":[85,200],"organism":[86,93,172],"from":[87,108,173],"another":[91],"source":[92],"evolutionarily":[94],"related":[95],"better":[97],"studied.":[98],"Results":[99],"Using":[100],"supervised":[102,140],"method,":[103],"predicts":[105,179],"unknown":[106,181,196],"random":[109],"perturbations":[110],"existing":[112],"annotations.":[113,156],"The":[114,133,157,253],"perturbation":[115],"consists":[116],"randomly":[118],"deleting":[119],"fraction":[121],"known":[123,168,348],"order":[126],"produce":[128],"reduced":[130,146],"annotation":[131,147,335],"set.":[132],"key":[134],"idea":[135],"train":[138],"algorithm":[143],"with":[144,208,230,267],"the":[145,154,166,184,187,228,256,259,271,293,334,340],"set":[148],"predict,":[150],"namely":[151],"rebuild,":[153],"original":[155,167],"resulting":[158],"prediction":[159,188,295],"model,":[160],"addition":[162],"accurately":[164],"rebuilding":[165],"an":[171,221,323],"their":[174,235,279],"perturbed":[175],"version,":[176],"also":[177,191],"effectively":[178],"organism.":[185],"Moreover,":[186],"model":[189,224],"discover":[194],"different":[199,209,232],"organisms":[201,233],"without":[202],"retraining.We":[203],"combined":[204],"our":[205],"approaches":[212],"compared":[214],"them":[215],"each":[217],"other":[218],"equivalent":[222],"single":[223],"technique.":[225],"We":[226],"tested":[227],"five":[231],"using":[234],"annotations:":[237],"Homo":[238],"sapiens":[239],",":[240,243,246],"Mus":[241],"musculus":[242],"Bos":[244],"taurus":[245],"Gallus":[247],"gallus":[248],"Dictyostelium":[250],"discoideum":[251],".":[252,304],"outcomes":[254],"demonstrate":[255],"effectiveness":[257],"approach,":[262],"which":[263],"can":[264],"be":[265],"customized":[266],"trade-off":[269],"between":[270],"desired":[272],"number":[273],"predicted":[275,290,314],"precision.A":[280],"Web":[281],"application":[282],"browse":[284],"both":[285,331],"input":[286],"used":[288],"ones,":[291],"choosing":[292],"use,":[298],"publicly":[300],"available":[301],"at":[302],"http://tiny.cc/geff/":[303],"Conclusions":[305],"Our":[306],"provides":[312],"gene":[316],"annotations,":[317],"i.e.,":[318],"functions,":[319],"ranked":[320],"according":[321],"associated":[324],"likelihood":[325],"value.":[326],"They":[327],"very":[329],"speed":[333],"curation,":[336],"focusing":[337],"it":[338],"on":[339],"prioritized":[341],"predicted,":[344],"complement":[347],"available.":[350]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2021-02-15T00:00:00"}
