{"id":"https://openalex.org/W1996838831","doi":"https://doi.org/10.1186/1471-2105-10-319","title":"Generation of Gene Ontology benchmark datasets with various types of positive signal","display_name":"Generation of Gene Ontology benchmark datasets with various types of positive signal","publication_year":2009,"publication_date":"2009-10-07","ids":{"openalex":"https://openalex.org/W1996838831","doi":"https://doi.org/10.1186/1471-2105-10-319","mag":"1996838831","pmid":"https://pubmed.ncbi.nlm.nih.gov/19811632"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-319","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-319","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-319","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/10.1186/1471-2105-10-319","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030987435","display_name":"Petri T\u00f6r\u00f6nen","orcid":"https://orcid.org/0000-0003-4764-9790"},"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/I4210122519","display_name":"Biocenter Finland","ror":"https://ror.org/03aay6c48","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210122519"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Petri T\u00f6r\u00f6nen","raw_affiliation_strings":["The Holm Group, Biocenter II, Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland. petri.toronen@helsinki.fi","Institute of Biotechnology, The Holm Group, Biocenter II, University of Helsinki, PO Box 56, 00014, Finland"],"affiliations":[{"raw_affiliation_string":"The Holm Group, Biocenter II, Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland. petri.toronen@helsinki.fi","institution_ids":["https://openalex.org/I4210122519","https://openalex.org/I133731052"]},{"raw_affiliation_string":"Institute of Biotechnology, The Holm Group, Biocenter II, University of Helsinki, PO Box 56, 00014, Finland","institution_ids":["https://openalex.org/I4210122519","https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070244169","display_name":"Petri Pehkonen","orcid":null},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Petri Pehkonen","raw_affiliation_strings":["Department of Biosciences, University of Kuopio, P.O. Box 1627, 70211, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Biosciences, University of Kuopio, P.O. Box 1627, 70211, Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064498279","display_name":"Liisa Holm","orcid":"https://orcid.org/0000-0002-7807-2966"},"institutions":[{"id":"https://openalex.org/I4210122519","display_name":"Biocenter Finland","ror":"https://ror.org/03aay6c48","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210122519"]},{"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"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Liisa Holm","raw_affiliation_strings":["Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014, Finland","Institute of Biotechnology, The Holm Group, Biocenter II, University of Helsinki, PO Box 56, 00014, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Institute of Biotechnology, The Holm Group, Biocenter II, University of Helsinki, PO Box 56, 00014, Finland","institution_ids":["https://openalex.org/I4210122519","https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5030987435"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4210122519"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5375,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.65451608,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"10","issue":"1","first_page":"319","last_page":"319"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973999857902527,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6951125264167786},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.681365966796875},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.613460898399353},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5733805298805237},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5712389945983887},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.521372377872467},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48907166719436646},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.46632009744644165},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4533015489578247},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4257754385471344},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.4240378737449646},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2372739613056183},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1537611186504364}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6951125264167786},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.681365966796875},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.613460898399353},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5733805298805237},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5712389945983887},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.521372377872467},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48907166719436646},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.46632009744644165},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4533015489578247},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4257754385471344},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.4240378737449646},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2372739613056183},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1537611186504364},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"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}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-10-319","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-319","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-319","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:19811632","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19811632","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:doaj.org/article:5da2dd7f565748b2a01e8ba301b191f6","is_oa":true,"landing_page_url":"https://doaj.org/article/5da2dd7f565748b2a01e8ba301b191f6","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":"BMC Bioinformatics, Vol 10, Iss 1, p 319 (2009)","raw_type":"article"},{"id":"pmh:oai:helda.helsinki.fi:10138/162828","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/162828","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:2762998","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2762998","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-319","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-319","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-319","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":[{"id":"https://metadata.un.org/sdg/17","score":0.4099999964237213,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1996838831.pdf","grobid_xml":"https://content.openalex.org/works/W1996838831.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1788898868","https://openalex.org/W1981106668","https://openalex.org/W1983126247","https://openalex.org/W1987678450","https://openalex.org/W2004958539","https://openalex.org/W2015705446","https://openalex.org/W2021129827","https://openalex.org/W2045729458","https://openalex.org/W2054881132","https://openalex.org/W2071828122","https://openalex.org/W2073116379","https://openalex.org/W2080915318","https://openalex.org/W2096373458","https://openalex.org/W2096603500","https://openalex.org/W2097795961","https://openalex.org/W2098647860","https://openalex.org/W2100437550","https://openalex.org/W2103017472","https://openalex.org/W2107755054","https://openalex.org/W2111903862","https://openalex.org/W2117870677","https://openalex.org/W2120024428","https://openalex.org/W2121044470","https://openalex.org/W2122683221","https://openalex.org/W2125905177","https://openalex.org/W2127833142","https://openalex.org/W2129287762","https://openalex.org/W2134736660","https://openalex.org/W2135230352","https://openalex.org/W2137786672","https://openalex.org/W2140954822","https://openalex.org/W2142635246","https://openalex.org/W2144907278","https://openalex.org/W2170040895","https://openalex.org/W3154566661","https://openalex.org/W4236956086","https://openalex.org/W4256170606","https://openalex.org/W4379510236"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W4230315250","https://openalex.org/W2086519370","https://openalex.org/W2087343574"],"abstract_inverted_index":{"The":[0,41],"presented":[1],"methods":[2,11],"aid":[3],"the":[4,52],"development":[5],"and":[6,21,37,47],"evaluation":[7],"of":[8],"GO":[9,35,38],"analysis":[10],"as":[12],"they":[13],"enable":[14],"thorough":[15],"testing":[16],"with":[17],"different":[18,22],"signal":[19,23],"types":[20],"levels.":[24],"As":[25],"an":[26],"example,":[27],"our":[28],"comparisons":[29],"reveal":[30],"clear":[31],"differences":[32],"between":[33],"compared":[34],"clustering":[36],"de-correlation":[39],"methods.":[40],"implementation":[42],"is":[43,48],"coded":[44],"in":[45],"Matlab":[46],"freely":[49],"available":[50],"at":[51],"dedicated":[53],"website":[54],"http://ekhidna.biocenter.helsinki.fi/users/petri/public/POSGODA/POSGODA.html.":[55]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}