{"id":"https://openalex.org/W2953389631","doi":"https://doi.org/10.1186/s12859-019-2875-5","title":"Combining learning and constraints for genome-wide protein annotation","display_name":"Combining learning and constraints for genome-wide protein annotation","publication_year":2019,"publication_date":"2019-06-17","ids":{"openalex":"https://openalex.org/W2953389631","doi":"https://doi.org/10.1186/s12859-019-2875-5","mag":"2953389631","pmid":"https://pubmed.ncbi.nlm.nih.gov/31208327"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2875-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2875-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2875-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2875-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001174680","display_name":"Stefano Teso","orcid":"https://orcid.org/0000-0002-2340-9461"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Stefano Teso","raw_affiliation_strings":["Computer Science Department, KULeuven, Celestijnenlaan 200 A bus 2402, Leuven, 3001, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, KULeuven, Celestijnenlaan 200 A bus 2402, Leuven, 3001, Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015906490","display_name":"Luca Masera","orcid":"https://orcid.org/0000-0001-9734-4202"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luca Masera","raw_affiliation_strings":["Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 5, Povo di Trento, 38123, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 5, Povo di Trento, 38123, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109267259","display_name":"Michelangelo Diligenti","orcid":null},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Michelangelo Diligenti","raw_affiliation_strings":["Department of Information Engineering and Mathematics, University of Siena, San Niccol\u00f2, via Roma, 56, Siena, 53100, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Engineering and Mathematics, University of Siena, San Niccol\u00f2, via Roma, 56, Siena, 53100, Italy","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066187890","display_name":"Andrea Passerini","orcid":"https://orcid.org/0000-0002-2765-5395"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andrea Passerini","raw_affiliation_strings":["Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 5, Povo di Trento, 38123, Italy. andrea.passerini@unitn.it","Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 5, Povo di Trento, 38123, Italy"],"raw_orcid":"https://orcid.org/0000-0002-2765-5395","affiliations":[{"raw_affiliation_string":"Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 5, Povo di Trento, 38123, Italy. andrea.passerini@unitn.it","institution_ids":["https://openalex.org/I193223587"]},{"raw_affiliation_string":"Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 5, Povo di Trento, 38123, Italy","institution_ids":["https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066187890"],"corresponding_institution_ids":["https://openalex.org/I193223587"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.0759,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.42035816,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"1","first_page":"338","last_page":"338"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8230999708175659,"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":0.8230999708175659,"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":0.07119999825954437,"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":0.058800000697374344,"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":0.7322400808334351},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6911758184432983},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5515518188476562},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.46945732831954956},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45504677295684814},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.45433667302131653},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.45374804735183716},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44776400923728943},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4423753619194031},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39634788036346436},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3878714442253113},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18871629238128662},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13212254643440247},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12182566523551941}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7322400808334351},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6911758184432983},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5515518188476562},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.46945732831954956},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45504677295684814},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.45433667302131653},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.45374804735183716},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44776400923728943},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4423753619194031},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39634788036346436},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3878714442253113},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18871629238128662},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13212254643440247},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12182566523551941},{"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003657","descriptor_name":"Decision Making","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-019-2875-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2875-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2875-5","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:31208327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31208327","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:lirias2repo.kuleuven.be:123456789/642597","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/123456789/642597","pdf_url":null,"source":{"id":"https://openalex.org/S7407055369","display_name":"Lirias","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Bmc Bioinformatics, vol. 20 (1), Art.No. ARTN 338","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:56c45242a2894bc5a4f3afeca5b710e9","is_oa":true,"landing_page_url":"https://doaj.org/article/56c45242a2894bc5a4f3afeca5b710e9","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 1-14 (2019)","raw_type":"article"},{"id":"pmh:oai:iris.unitn.it:11572/251227","is_oa":false,"landing_page_url":"http://hdl.handle.net/11572/251227","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6580517","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6580517","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:usiena-air.unisi.it:11365/1082441","is_oa":true,"landing_page_url":"http://hdl.handle.net/11365/1082441","pdf_url":null,"source":{"id":"https://openalex.org/S4377196319","display_name":"Use Siena air (University of Siena)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I102064193","host_organization_name":"University of Siena","host_organization_lineage":["https://openalex.org/I102064193"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2875-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2875-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2875-5","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":[],"funders":[{"id":"https://openalex.org/F4320309327","display_name":"Google","ror":"https://ror.org/00njsd438"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953389631.pdf","grobid_xml":"https://content.openalex.org/works/W2953389631.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1144107824","https://openalex.org/W1511160855","https://openalex.org/W1560724230","https://openalex.org/W1585529040","https://openalex.org/W1593732018","https://openalex.org/W1743864981","https://openalex.org/W1821527815","https://openalex.org/W1974188411","https://openalex.org/W1988841006","https://openalex.org/W1995918845","https://openalex.org/W2012336263","https://openalex.org/W2033591223","https://openalex.org/W2048919592","https://openalex.org/W2048947602","https://openalex.org/W2055043387","https://openalex.org/W2057387739","https://openalex.org/W2065516946","https://openalex.org/W2076186660","https://openalex.org/W2085063752","https://openalex.org/W2087574732","https://openalex.org/W2097606916","https://openalex.org/W2101220662","https://openalex.org/W2102221598","https://openalex.org/W2102461176","https://openalex.org/W2103017472","https://openalex.org/W2103453943","https://openalex.org/W2104239076","https://openalex.org/W2105924489","https://openalex.org/W2107067224","https://openalex.org/W2117486996","https://openalex.org/W2119027485","https://openalex.org/W2131562240","https://openalex.org/W2131962941","https://openalex.org/W2136504847","https://openalex.org/W2137683543","https://openalex.org/W2139294595","https://openalex.org/W2140239055","https://openalex.org/W2146408445","https://openalex.org/W2152875974","https://openalex.org/W2153959628","https://openalex.org/W2157544181","https://openalex.org/W2158714788","https://openalex.org/W2159707944","https://openalex.org/W2162142896","https://openalex.org/W2164461702","https://openalex.org/W2166637863","https://openalex.org/W2167821759","https://openalex.org/W2170747616","https://openalex.org/W2201744460","https://openalex.org/W2227395312","https://openalex.org/W2312744322","https://openalex.org/W2323179903","https://openalex.org/W2487770199","https://openalex.org/W2550301226","https://openalex.org/W2615066396","https://openalex.org/W2912565176","https://openalex.org/W2915975108","https://openalex.org/W4211007335"],"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/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W1546381263"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,99,122,190],"advent":[2],"of":[3,23,27,33,55,60,71,92,95,178,187],"high-throughput":[4],"experimental":[5,168],"techniques":[6],"paved":[7],"the":[8,20,47,69,126,131,171,176,185,188,195,200,228],"way":[9],"to":[10,68,214,237,248],"genome-wide":[11],"computational":[12],"analysis":[13],"and":[14,89,106,163,220,230],"predictive":[15,52,83],"annotation":[16,22,91],"studies.":[17],"When":[18],"considering":[19],"joint":[21],"a":[24,34,75,82,96,112,142,146,205],"large":[25],"set":[26],"related":[28],"entities,":[29],"like":[30],"all":[31,93,154],"proteins":[32,94],"certain":[35],"genome,":[36],"many":[37],"candidate":[38],"annotations":[39,73],"could":[40,65],"be":[41,151],"inconsistent,":[42],"or":[43,223],"very":[44],"unlikely,":[45],"given":[46,97,212],"existing":[48],"knowledge.":[49],"A":[50],"sound":[51],"framework":[53],"capable":[54],"accounting":[56],"for":[57,104],"this":[58],"type":[59],"constraints":[61,117,136],"in":[62],"making":[63],"predictions":[64],"substantially":[66,183],"contribute":[67],"quality":[70,186],"machine-generated":[72],"at":[74,199],"genomic":[76],"scale.":[77],"RESULTS:":[78],"We":[79],"present":[80],"OCELOT,":[81],"pipeline":[84],"which":[85],"simultaneously":[86],"addresses":[87],"functional":[88,105],"interaction":[90,108,162],"genome.":[98],"system":[100,191,198,244],"combines":[101],"sequence-based":[102],"predictors":[103],"protein-protein":[107],"(PPI)":[109],"prediction":[110],"with":[111,145,153,204],"consistency":[113],"layer":[114],"enforcing":[115],"(soft)":[116],"as":[118,157,159],"fuzzy":[119],"logic":[120],"rules.":[121],"enforced":[123],"rules":[124,160,182],"represent":[125],"available":[127,207],"prior":[128,179],"knowledge":[129,180],"about":[130],"classification":[132],"task,":[133],"including":[134],"taxonomic":[135],"over":[137],"each":[138],"GO":[139,147],"hierarchy":[140,229],"(e.g.":[141],"protein":[143],"labeled":[144,152],"term":[148],"should":[149],"also":[150,245],"ancestor":[155],"terms)":[156],"well":[158],"combining":[161],"function":[164],"prediction.":[165],"An":[166],"extensive":[167],"evaluation":[169],"on":[170,227,252],"Yeast":[172],"genome":[173],"shows":[174],"that":[175],"integration":[177],"via":[181],"improves":[184],"predictions.":[189],"largely":[192],"outperforms":[193],"GoFDR,":[194],"only":[196,217],"high-ranking":[197],"last":[201],"CAFA":[202],"challenge":[203],"readily":[206],"implementation,":[208],"when":[209,233],"GoFDR":[210,234],"is":[211,235],"access":[213],"intra-genome":[215],"information":[216,239],"(as":[218],"OCELOT),":[219],"has":[221],"comparable":[222],"better":[224],"results":[225],"(depending":[226],"performance":[231],"measure)":[232],"allowed":[236],"use":[238],"from":[240],"other":[241],"genomes.":[242],"Our":[243],"compares":[246],"favorably":[247],"recent":[249],"methods":[250],"based":[251],"deep":[253],"learning.":[254]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
