{"id":"https://openalex.org/W2918631818","doi":"https://doi.org/10.1186/s12859-019-2639-2","title":"FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments","display_name":"FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments","publication_year":2019,"publication_date":"2019-02-15","ids":{"openalex":"https://openalex.org/W2918631818","doi":"https://doi.org/10.1186/s12859-019-2639-2","mag":"2918631818","pmid":"https://pubmed.ncbi.nlm.nih.gov/30767762"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2639-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2639-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2639-2","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/track/pdf/10.1186/s12859-019-2639-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089211537","display_name":"Giovanni Scala","orcid":"https://orcid.org/0000-0002-9037-1782"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I2800229700","display_name":"Helsinki Institute of Physics","ror":"https://ror.org/01x2x1522","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I2800229700","https://openalex.org/I63548447","https://openalex.org/I94722563","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Giovanni Scala","raw_affiliation_strings":["BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Institute of Biotechnology, University of Helsinki, Viikinkaari 5d, Helsinki, FI-00014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, Viikinkaari 5d, Helsinki, FI-00014, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041632230","display_name":"Angela Serra","orcid":"https://orcid.org/0000-0002-3374-1492"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Angela Serra","raw_affiliation_strings":["BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038612379","display_name":"Veer Singh Marwah","orcid":"https://orcid.org/0000-0002-8272-0655"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Veer Singh Marwah","raw_affiliation_strings":["BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003627670","display_name":"Laura Aliisa Saarim\u00e4ki","orcid":"https://orcid.org/0000-0003-1996-286X"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Laura Aliisa Saarim\u00e4ki","raw_affiliation_strings":["BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]}]},{"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/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]},{"id":"https://openalex.org/I2800229700","display_name":"Helsinki Institute of Physics","ror":"https://ror.org/01x2x1522","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I2800229700","https://openalex.org/I63548447","https://openalex.org/I94722563","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Dario Greco","raw_affiliation_strings":["BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","Institute of Biotechnology, University of Helsinki, Viikinkaari 5d, Helsinki, FI-00014, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioMediTech Institute, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylp\u00f6n katu 34 - Arvo building, Tampere, FI-33014, Finland","institution_ids":["https://openalex.org/I166825849","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, Viikinkaari 5d, Helsinki, FI-00014, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":1538,"currency":"EUR","value_usd":1658},"fwci":1.8965,"has_fulltext":true,"cited_by_count":43,"citation_normalized_percentile":{"value":0.8634917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"79","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9574000239372253,"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":0.9574000239372253,"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":0.017400000244379044,"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":0.01209999993443489,"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":0.6684608459472656},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6500300168991089},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.5823047757148743},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5682686567306519},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5452060103416443},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.49898409843444824},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.494625061750412},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4753013551235199},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.44675374031066895},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.4355786442756653},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40986859798431396},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3398928642272949},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.32560306787490845},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30074840784072876},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24196869134902954},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22725054621696472},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15735837817192078},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09336850047111511}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6684608459472656},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6500300168991089},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.5823047757148743},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5682686567306519},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5452060103416443},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.49898409843444824},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.494625061750412},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4753013551235199},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.44675374031066895},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.4355786442756653},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40986859798431396},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3398928642272949},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.32560306787490845},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30074840784072876},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24196869134902954},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22725054621696472},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15735837817192078},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09336850047111511},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","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/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1186/s12859-019-2639-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2639-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2639-2","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:30767762","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30767762","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:tampub.uta.fi:10024/105824","is_oa":true,"landing_page_url":"http://tampub.uta.fi/handle/10024/105824","pdf_url":null,"source":{"id":"https://openalex.org/S4306401860","display_name":"Tampere University Institutional Repository (Tampere University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I150589677","host_organization_name":"Tampere University of Applied Sciences","host_organization_lineage":["https://openalex.org/I150589677"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"publishedVersion"},{"id":"pmh:oai:doaj.org/article:7f0b5a04777a4cbf935c68c466a527fb","is_oa":true,"landing_page_url":"https://doaj.org/article/7f0b5a04777a4cbf935c68c466a527fb","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-7 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5380090","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6376640","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:helda.helsinki.fi:10138/299134","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/299134","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:helda.helsinki.fi:10138/311067","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/311067","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6376640","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6376640","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:trepo.tuni.fi:10024/105824","is_oa":true,"landing_page_url":"https://trepo.tuni.fi/handle/10024/105824","pdf_url":null,"source":{"id":"https://openalex.org/S4306401860","display_name":"Tampere University Institutional Repository (Tampere University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I150589677","host_organization_name":"Tampere University of Applied Sciences","host_organization_lineage":["https://openalex.org/I150589677"],"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":"","raw_type":"publishedVersion"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2639-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2639-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2639-2","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/G541198402","display_name":null,"funder_award_id":"292307","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5816991477","display_name":null,"funder_award_id":"275151 and 292307","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7626961633","display_name":null,"funder_award_id":"275151","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2918631818.pdf","grobid_xml":"https://content.openalex.org/works/W2918631818.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1979141295","https://openalex.org/W1989277387","https://openalex.org/W2035618305","https://openalex.org/W2082382210","https://openalex.org/W2096086497","https://openalex.org/W2103017472","https://openalex.org/W2110256992","https://openalex.org/W2124649657","https://openalex.org/W2124954099","https://openalex.org/W2158217645","https://openalex.org/W2345356016","https://openalex.org/W4233698560","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2551839783","https://openalex.org/W4386401670","https://openalex.org/W2059565715","https://openalex.org/W2956207900","https://openalex.org/W2901823680","https://openalex.org/W2790781282","https://openalex.org/W4285233331","https://openalex.org/W2110256992","https://openalex.org/W4313887725","https://openalex.org/W2334025507"],"abstract_inverted_index":{"BACKGROUND:":[0],"Functional":[1],"annotation":[2],"of":[3,24,26,67,83,90,150,165,190,226,247,258,274],"genes":[4,27],"is":[5,46,96,111,137,199,208,215],"an":[6,142,278],"essential":[7,47],"step":[8],"in":[9,127,222,264],"omics":[10,41,84],"data":[11],"analysis.":[12],"Multiple":[13],"databases":[14],"and":[15,35,79,117,123,167,207,249,254,261,271,277],"methods":[16],"are":[17,71],"currently":[18,112],"available":[19,73,209],"to":[20,50,58,74,77,101,120,129,154,162,168,185,281],"summarize":[21,125,155],"the":[22,52,75,88,103,135,146,156,187,239],"functions":[23],"sets":[25],"into":[28,43],"higher":[29,65,163],"level":[30,66],"representations,":[31],"such":[32],"as":[33,201],"ontologies":[34],"molecular":[36],"pathways.":[37],"Annotating":[38],"results":[39,104,131,157],"from":[40,242],"experiments":[42,91,194,276],"functional":[44,81,94,152,188,259],"categories":[45],"not":[48],"only":[49],"understand":[51],"underlying":[53],"regulatory":[54],"dynamics":[55],"but":[56],"also":[57,133],"compare":[59,80],"multiple":[60,193,224,275],"experimental":[61],"conditions":[62],"at":[63,173,195,210],"a":[64,113,179,202,216,269],"abstraction.":[68],"Several":[69],"tools":[70,119],"already":[72],"community":[76],"represent":[78],"profiles":[82],"experiments.":[85],"However,":[86],"when":[87,106,134],"number":[89],"and/or":[92],"enriched":[93,240],"terms":[95,260],"high,":[97],"it":[98],"becomes":[99],"difficult":[100],"interpret":[102,282],"even":[105],"graphically":[107,121],"represented.":[108],"Therefore,":[109],"there":[110],"need":[114],"for":[115],"interactive":[116,256],"user-friendly":[118,180],"navigate":[122],"further":[124],"annotations":[126,153,189,241],"order":[128],"facilitate":[130],"interpretation":[132,166],"dimensionality":[136],"high.":[138],"RESULTS:":[139],"We":[140,177],"developed":[141],"approach":[143],"that":[144,183,220],"exploits":[145],"intrinsic":[147],"hierarchical":[148],"structure":[149],"several":[151],"obtained":[158],"through":[159],"enrichment":[160],"analyses":[161],"levels":[164],"map":[169],"gene":[170],"related":[171,235],"information":[172],"each":[174],"summarized":[175],"level.":[176],"built":[178],"graphical":[181,218],"interface":[182],"allows":[184,268],"visualize":[186],"one":[191],"or":[192,228,251],"once.":[196],"The":[197],"tool":[198,219],"implemented":[200],"R-Shiny":[203],"application":[204],"called":[205],"FunMappOne":[206,214,267],"https://github.com/grecolab/FunMappOne":[211],".":[212],"CONCLUSION:":[213],"R-shiny":[217],"takes":[221],"input":[223],"lists":[225],"human":[227],"mouse":[229],"genes,":[230],"optionally":[231],"along":[232],"with":[233],"their":[234],"modification":[236],"magnitudes,":[237],"computes":[238],"Gene":[243],"Ontology,":[244],"Kyoto":[245],"Encyclopedia":[246],"Genes":[248],"Genomes,":[250],"Reactome":[252],"databases,":[253],"reports":[255],"maps":[257],"pathways":[262],"organized":[263],"rational":[265],"groups.":[266],"fast":[270],"convenient":[272],"comparison":[273],"easy":[279],"way":[280],"results.":[283]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
