{"id":"https://openalex.org/W1979141295","doi":"https://doi.org/10.1186/s12859-015-0477-4","title":"BACA: bubble chArt to compare annotations","display_name":"BACA: bubble chArt to compare annotations","publication_year":2015,"publication_date":"2015-02-04","ids":{"openalex":"https://openalex.org/W1979141295","doi":"https://doi.org/10.1186/s12859-015-0477-4","mag":"1979141295","pmid":"https://pubmed.ncbi.nlm.nih.gov/25652236"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0477-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0477-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0477-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0477-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011752174","display_name":"Vittorio Fortino","orcid":"https://orcid.org/0000-0001-8693-5285"},"institutions":[{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Vittorio Fortino","raw_affiliation_strings":["Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. vittorio.fortino@ttl.fi","Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. vittorio.fortino@ttl.fi","Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. vittorio.fortino@ttl.fi","institution_ids":["https://openalex.org/I2801770344"]},{"raw_affiliation_string":"Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. vittorio.fortino@ttl.fi","institution_ids":["https://openalex.org/I2801770344"]},{"raw_affiliation_string":"Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland","institution_ids":["https://openalex.org/I2801770344"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016170192","display_name":"Harri Alenius","orcid":"https://orcid.org/0000-0003-0106-8923"},"institutions":[{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Harri Alenius","raw_affiliation_strings":["Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. harri.alenius@ttl.fi","Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. harri.alenius@ttl.fi","Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. harri.alenius@ttl.fi","institution_ids":["https://openalex.org/I2801770344"]},{"raw_affiliation_string":"Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. harri.alenius@ttl.fi","institution_ids":["https://openalex.org/I2801770344"]},{"raw_affiliation_string":"Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland","institution_ids":["https://openalex.org/I2801770344"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028682033","display_name":"Dario Greco","orcid":"https://orcid.org/0000-0001-9195-9003"},"institutions":[{"id":"https://openalex.org/I2801770344","display_name":"Finnish Institute of Occupational Health","ror":"https://ror.org/030wyr187","country_code":"FI","type":"facility","lineage":["https://openalex.org/I2801770344"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Dario Greco","raw_affiliation_strings":["Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. dario.greco@ttl.fi","Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. dario.greco@ttl.fi","Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. dario.greco@ttl.fi","institution_ids":["https://openalex.org/I2801770344"]},{"raw_affiliation_string":"Unit of Systems Toxicology, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland. dario.greco@ttl.fi","institution_ids":["https://openalex.org/I2801770344"]},{"raw_affiliation_string":"Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Topeliuksenkatu 41b, 00250, Helsinki, Finland","institution_ids":["https://openalex.org/I2801770344"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028682033"],"corresponding_institution_ids":["https://openalex.org/I2801770344"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9646,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.74165317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"37","last_page":"37"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7566999793052673,"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":0.7566999793052673,"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":0.09040000289678574,"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":0.032499998807907104,"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/chart","display_name":"Chart","score":0.5933520197868347},{"id":"https://openalex.org/keywords/bubble","display_name":"Bubble","score":0.488519549369812},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47419530153274536},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46597954630851746},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.46474689245224},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3822648525238037},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34693318605422974},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18860942125320435},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15023699402809143},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1403648853302002},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10144659876823425},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.058736979961395264}],"concepts":[{"id":"https://openalex.org/C190812933","wikidata":"https://www.wikidata.org/wiki/Q28923","display_name":"Chart","level":2,"score":0.5933520197868347},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.488519549369812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47419530153274536},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46597954630851746},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.46474689245224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3822648525238037},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34693318605422974},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18860942125320435},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15023699402809143},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1403648853302002},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10144659876823425},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.058736979961395264},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0477-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0477-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0477-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25652236","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25652236","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3338948","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4377007","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:www.julkari.fi:10024/125982","is_oa":false,"landing_page_url":"http://www.julkari.fi/handle/10024/125982","pdf_url":null,"source":{"id":"https://openalex.org/S4306402058","display_name":"STM:n Hallinnonalan avoin julkaisuarkisto (Julkari)","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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0477-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0477-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0477-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2883756617","display_name":"Biological Foundation for the Safety Classification of Engineered Nanomaterials (ENM): Systems Biology Approaches to Understand Interactions of ENM with Living Organisms and the Environment","funder_award_id":"309329","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1979141295.pdf","grobid_xml":"https://content.openalex.org/works/W1979141295.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1579822124","https://openalex.org/W1587026990","https://openalex.org/W1969353942","https://openalex.org/W2096561521","https://openalex.org/W2111874188","https://openalex.org/W2122683221","https://openalex.org/W2139703939","https://openalex.org/W2146994504","https://openalex.org/W2161491874","https://openalex.org/W4230096730"],"related_works":["https://openalex.org/W2072214669","https://openalex.org/W2928956957","https://openalex.org/W3137839740","https://openalex.org/W938380018","https://openalex.org/W2369700007","https://openalex.org/W3129210721","https://openalex.org/W2354156280","https://openalex.org/W1613422971","https://openalex.org/W2059848165","https://openalex.org/W2012117814"],"abstract_inverted_index":{"BACKGROUND:":[0],"DAVID":[1,22,68,116],"is":[2,83,88],"the":[3,19,67,92],"most":[4],"popular":[5],"tool":[6,39],"for":[7,31,71],"interpreting":[8],"large":[9,79],"lists":[10],"of":[11,21],"gene/proteins":[12],"classically":[13],"produced":[14],"in":[15,45,85],"high-throughput":[16],"experiments.":[17],"However,":[18],"use":[20],"website":[23],"becomes":[24],"difficult":[25],"when":[26],"analyzing":[27],"multiple":[28,42,78,107],"gene":[29,80],"lists,":[30],"it":[32],"does":[33],"not":[34],"provide":[35],"an":[36],"adequate":[37],"visualization":[38],"to":[40,62,105],"show/compare":[41],"enrichment":[43,73],"results":[44,75],"a":[46,54],"concise":[47],"and":[48,87],"informative":[49],"manner.":[50],"RESULT:":[51],"We":[52],"implemented":[53,84],"new":[55],"R-based":[56],"graphical":[57],"tool,":[58],"BACA":[59,82,101],"(Bubble":[60],"chArt":[61],"Compare":[63],"Annotations),":[64],"which":[65],"uses":[66],"web":[69],"service":[70],"cross-comparing":[72],"analysis":[74],"derived":[76],"from":[77],"lists.":[81],"R":[86,103],"freely":[89],"available":[90],"at":[91],"CRAN":[93],"repository":[94],"(":[95],"http://cran.r-project.org/web/packages/BACA/":[96],").":[97],"CONCLUSION:":[98],"The":[99],"package":[100],"allows":[102],"users":[104],"combine":[106],"annotation":[108],"charts":[109],"into":[110],"one":[111],"output":[112],"graph":[113],"by":[114],"passing":[115],"website.":[117]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
