{"id":"https://openalex.org/W2140795069","doi":"https://doi.org/10.1093/nar/gkl812","title":"A Protein Classification Benchmark collection for machine learning","display_name":"A Protein Classification Benchmark collection for machine learning","publication_year":2006,"publication_date":"2006-11-18","ids":{"openalex":"https://openalex.org/W2140795069","doi":"https://doi.org/10.1093/nar/gkl812","mag":"2140795069","pmid":"https://pubmed.ncbi.nlm.nih.gov/17142240"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl812","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D232/3826826/gkl812.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D232/3826826/gkl812.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007548695","display_name":"Paolo Sonego","orcid":"https://orcid.org/0000-0002-8576-0169"},"institutions":[{"id":"https://openalex.org/I91080651","display_name":"International Centre for Genetic Engineering and Biotechnology","ror":"https://ror.org/043bgf219","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I91080651"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"P. Sonego","raw_affiliation_strings":["Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy","institution_ids":["https://openalex.org/I91080651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061176048","display_name":"Mircea Pacurar","orcid":null},"institutions":[{"id":"https://openalex.org/I902798049","display_name":"National Center for Genetic Engineering and Biotechnology","ror":"https://ror.org/047aswc67","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I902798049"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"M. Pacurar","raw_affiliation_strings":["INTERNATIONAL CENTRE FOR GENETIC ENGINEERING & BIOTECHNOLOGY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INTERNATIONAL CENTRE FOR GENETIC ENGINEERING & BIOTECHNOLOGY","institution_ids":["https://openalex.org/I902798049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103192931","display_name":"Sunny Dhir","orcid":"https://orcid.org/0000-0002-3790-8333"},"institutions":[{"id":"https://openalex.org/I902798049","display_name":"National Center for Genetic Engineering and Biotechnology","ror":"https://ror.org/047aswc67","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I902798049"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"S. Dhir","raw_affiliation_strings":["INTERNATIONAL CENTRE FOR GENETIC ENGINEERING & BIOTECHNOLOGY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INTERNATIONAL CENTRE FOR GENETIC ENGINEERING & BIOTECHNOLOGY","institution_ids":["https://openalex.org/I902798049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037717293","display_name":"Attila Kert\u00e9sz\u2010Farkas","orcid":"https://orcid.org/0000-0001-8110-7253"},"institutions":[{"id":"https://openalex.org/I227486990","display_name":"University of Szeged","ror":"https://ror.org/01pnej532","country_code":"HU","type":"education","lineage":["https://openalex.org/I227486990"]},{"id":"https://openalex.org/I4210152167","display_name":"MTA-SZTE Research Group on Artificial Intelligence","ror":"https://ror.org/0507fk326","country_code":"HU","type":"facility","lineage":["https://openalex.org/I227486990","https://openalex.org/I4210152167","https://openalex.org/I7597260"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"A. Kertesz-Farkas","raw_affiliation_strings":["Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary","1Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary","institution_ids":["https://openalex.org/I4210152167","https://openalex.org/I227486990","https://openalex.org/I7597260"]},{"raw_affiliation_string":"1Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary","institution_ids":["https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020008023","display_name":"Andr\u00e1s Kocsor","orcid":null},"institutions":[{"id":"https://openalex.org/I227486990","display_name":"University of Szeged","ror":"https://ror.org/01pnej532","country_code":"HU","type":"education","lineage":["https://openalex.org/I227486990"]},{"id":"https://openalex.org/I4210152167","display_name":"MTA-SZTE Research Group on Artificial Intelligence","ror":"https://ror.org/0507fk326","country_code":"HU","type":"facility","lineage":["https://openalex.org/I227486990","https://openalex.org/I4210152167","https://openalex.org/I7597260"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"A. Kocsor","raw_affiliation_strings":["Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary","1Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary","institution_ids":["https://openalex.org/I4210152167","https://openalex.org/I227486990","https://openalex.org/I7597260"]},{"raw_affiliation_string":"1Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi v\u00e9rtan\u00fak tere 1.H-6720 Szeged, Hungary","institution_ids":["https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091123400","display_name":"Zolt\u00e1n G\u00e1sp\u00e1ri","orcid":"https://orcid.org/0000-0002-8692-740X"},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]},{"id":"https://openalex.org/I2800351701","display_name":"HUN-REN Szegedi Biol\u00f3giai Kutat\u00f3k\u00f6zpont","ror":"https://ror.org/016gb1631","country_code":"HU","type":"facility","lineage":["https://openalex.org/I2800351701","https://openalex.org/I7597260"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Z. Gaspari","raw_affiliation_strings":["Bioinformatics Group, Biological Research CentreHungarian Academy of Sciences, Temesv\u00e1ri krt. 62, H-6701 Szeged, Hungary","Institute of Chemistry, E\u00f6tv\u00f6s Lor\u00e1nd UniversityP\u00e1zm\u00e1ny P\u00e9ter s\u00e9t\u00e1ny 1/A, H-1117 Budapest, Hungary","3Bioinformatics Group, Biological Research CentreHungarian Academy of Sciences, Temesv\u00e1ri krt. 62, H-6701 Szeged, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Biological Research CentreHungarian Academy of Sciences, Temesv\u00e1ri krt. 62, H-6701 Szeged, Hungary","institution_ids":["https://openalex.org/I2800351701","https://openalex.org/I7597260"]},{"raw_affiliation_string":"Institute of Chemistry, E\u00f6tv\u00f6s Lor\u00e1nd UniversityP\u00e1zm\u00e1ny P\u00e9ter s\u00e9t\u00e1ny 1/A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I106118109"]},{"raw_affiliation_string":"3Bioinformatics Group, Biological Research CentreHungarian Academy of Sciences, Temesv\u00e1ri krt. 62, H-6701 Szeged, Hungary","institution_ids":["https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112240969","display_name":"J.A.M. Leunissen","orcid":null},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"J. A.M. Leunissen","raw_affiliation_strings":["Laboratory of Bioinformatics, Wageningen University and Research CentrePO Box 8128, 6700 ET Wageningen, The Netherlands","4Laboratory of Bioinformatics, Wageningen University and Research CentrePO Box 8128, 6700 ET Wageningen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Wageningen University and Research CentrePO Box 8128, 6700 ET Wageningen, The Netherlands","institution_ids":["https://openalex.org/I913481162"]},{"raw_affiliation_string":"4Laboratory of Bioinformatics, Wageningen University and Research CentrePO Box 8128, 6700 ET Wageningen, The Netherlands","institution_ids":["https://openalex.org/I913481162"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111872342","display_name":"S. Pongor","orcid":null},"institutions":[{"id":"https://openalex.org/I902798049","display_name":"National Center for Genetic Engineering and Biotechnology","ror":"https://ror.org/047aswc67","country_code":"TH","type":"facility","lineage":["https://openalex.org/I1332092204","https://openalex.org/I902798049"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"S. Pongor","raw_affiliation_strings":["INTERNATIONAL CENTRE FOR GENETIC ENGINEERING & BIOTECHNOLOGY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INTERNATIONAL CENTRE FOR GENETIC ENGINEERING & BIOTECHNOLOGY","institution_ids":["https://openalex.org/I902798049"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.4547,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.88684788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"35","issue":"Database","first_page":"D232","last_page":"D236"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.996999979019165,"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/benchmark","display_name":"Benchmark (surveying)","score":0.5966224670410156},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5937144160270691},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5469037890434265},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5390135645866394},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5159443020820618},{"id":"https://openalex.org/keywords/biological-classification","display_name":"Biological classification","score":0.5001044273376465},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49290895462036133},{"id":"https://openalex.org/keywords/multiclass-classification","display_name":"Multiclass classification","score":0.4878987967967987},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.4646448791027069},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.42782366275787354},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3809836208820343},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32695692777633667},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.26353150606155396},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.25707343220710754}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5966224670410156},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5937144160270691},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5469037890434265},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5390135645866394},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5159443020820618},{"id":"https://openalex.org/C48702757","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Biological classification","level":2,"score":0.5001044273376465},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49290895462036133},{"id":"https://openalex.org/C123860398","wikidata":"https://www.wikidata.org/wiki/Q6934605","display_name":"Multiclass classification","level":3,"score":0.4878987967967987},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.4646448791027069},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.42782366275787354},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3809836208820343},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32695692777633667},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.26353150606155396},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.25707343220710754},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","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/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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":10,"locations":[{"id":"doi:10.1093/nar/gkl812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl812","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D232/3826826/gkl812.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:17142240","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17142240","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.280.7171","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.280.7171","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/aa/05/Nucleic_Acids_Res_2007_Jan_16_35(Database_issue)_D232-D236.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.323.7502","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.323.7502","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.bioinformatics.nl/~jackl/Sonego_NAR_2007.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.324.399","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.399","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/35/suppl_1/D232.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:edit.elte.hu:10831/92876","is_oa":true,"landing_page_url":"http://hdl.handle.net/10831/92876","pdf_url":null,"source":{"id":"https://openalex.org/S4306400126","display_name":"ELTE Digital Institutional Repository (EDIT) (E\u00f6tv\u00f6s Lor\u00e1nd University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I106118109","host_organization_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","host_organization_lineage":["https://openalex.org/I106118109"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1344676","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1344676/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   NUCLEIC ACIDS RESEARCH , 35    D232-D236.   (2007)      ","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2284741","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1669728","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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1669728","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl812","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:wur:oai:library.wur.nl:wurpubs/357851","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/a-protein-classification-benchmark-collection-for-machine-learnin","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"Nucleic acids research, 35, D232 - D236","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl812","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_1/D232/3826826/gkl812.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.4399999976158142,"display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322192","display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia","ror":"https://ror.org/02ks8qq67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140795069.pdf","grobid_xml":"https://content.openalex.org/works/W2140795069.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W391985582","https://openalex.org/W1483944095","https://openalex.org/W1536719366","https://openalex.org/W1554663460","https://openalex.org/W1570448133","https://openalex.org/W1969761972","https://openalex.org/W1973714307","https://openalex.org/W1980868419","https://openalex.org/W2014744153","https://openalex.org/W2055043387","https://openalex.org/W2063081141","https://openalex.org/W2074231493","https://openalex.org/W2083060511","https://openalex.org/W2084787613","https://openalex.org/W2087064593","https://openalex.org/W2090388864","https://openalex.org/W2093460686","https://openalex.org/W2097413543","https://openalex.org/W2105438341","https://openalex.org/W2111691661","https://openalex.org/W2118619377","https://openalex.org/W2121702291","https://openalex.org/W2121950477","https://openalex.org/W2124158580","https://openalex.org/W2125725297","https://openalex.org/W2136570298","https://openalex.org/W2143292980","https://openalex.org/W2148603752","https://openalex.org/W2155606054","https://openalex.org/W2283504545","https://openalex.org/W2324212613","https://openalex.org/W2625382302","https://openalex.org/W2799061466","https://openalex.org/W2911964244","https://openalex.org/W4229880569","https://openalex.org/W4236236547","https://openalex.org/W4388297464"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2024731242","https://openalex.org/W2136729892","https://openalex.org/W2041862730","https://openalex.org/W2321188917","https://openalex.org/W2140795069"],"abstract_inverted_index":{"Protein":[0,18],"classification":[1,84,106,129,136,139,187],"by":[2],"machine":[3,36],"learning":[4,37],"algorithms":[5],"is":[6,43,69,79],"now":[7],"widely":[8],"used":[9],"in":[10,25,52,75,100,110],"structural":[11,108],"and":[12,49,64,66,94,113,127],"functional":[13,126],"annotation":[14],"of":[15,35,62,82,107,134,147,170,186],"proteins.":[16],"The":[17,58],"Classification":[19],"Benchmark":[20],"collection":[21,59],"(http://hydra.icgeb.trieste.it/benchmark)":[22],"was":[23],"created":[24],"order":[26],"to":[27],"provide":[28],"standard":[29],"datasets":[30,61],"on":[31,87,91,96,117,174],"which":[32],"the":[33,105,111,132,138,148,171],"performance":[34,188],"methods":[38,54],"can":[39,141],"be":[40,142],"compared.":[41],"It":[42],"primarily":[44],"meant":[45],"for":[46],"method":[47],"developers":[48],"users":[50],"interested":[51],"comparing":[53],"under":[55],"standardized":[56],"conditions.":[57],"contains":[60],"sequences":[63,119],"structures,":[65,121],"each":[67,157],"set":[68,185],"subdivided":[70],"into":[71],"positive/negative,":[72],"training/test":[73],"sets":[74],"several":[76],"ways.":[77],"There":[78],"a":[80,184],"total":[81],"6405":[83],"tasks,":[85],"3297":[86],"protein":[88,92,97],"sequences,":[89],"3095":[90],"structures":[93],"10":[95],"coding":[98],"regions":[99],"DNA.":[101],"Typical":[102],"tasks":[103,140],"include":[104],"domains":[109],"SCOP":[112],"CATH":[114],"databases":[115],"based":[116,173],"their":[118],"or":[120,177],"as":[122,124,151,181,183],"well":[123,182],"various":[125,145,175,192],"taxonomic":[128],"problems.":[130],"In":[131],"case":[133],"hierarchical":[135],"schemes,":[137],"defined":[143],"at":[144],"levels":[146],"hierarchy":[149],"(such":[150],"classes,":[152],"folds,":[153],"superfamilies,":[154],"etc.).":[155],"For":[156],"dataset":[158],"there":[159],"are":[160],"distance":[161],"matrices":[162],"available":[163],"that":[164],"contain":[165],"all":[166,168],"vs.":[167],"comparison":[169,179],"data,":[172],"sequence":[176],"structure":[178],"methods,":[180],"measures":[189],"computed":[190],"with":[191],"classifier":[193],"algorithms.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}