{"id":"https://openalex.org/W4206338776","doi":"https://doi.org/10.1186/s12859-022-04565-6","title":"Assigning protein function from domain-function associations using DomFun","display_name":"Assigning protein function from domain-function associations using DomFun","publication_year":2022,"publication_date":"2022-01-15","ids":{"openalex":"https://openalex.org/W4206338776","doi":"https://doi.org/10.1186/s12859-022-04565-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/35033002"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04565-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04565-6","pdf_url":null,"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://doi.org/10.1186/s12859-022-04565-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038281376","display_name":"Elena Rojano","orcid":"https://orcid.org/0000-0002-2678-710X"},"institutions":[{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Elena Rojano","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040063827","display_name":"Fernando M. Jabato","orcid":"https://orcid.org/0000-0001-7498-1962"},"institutions":[{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Fernando M. Jabato","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032959797","display_name":"James R. Perkins","orcid":"https://orcid.org/0000-0003-4108-096X"},"institutions":[{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"James R. Perkins","raw_affiliation_strings":["CIBER of Rare Diseases, Av. Monforte de Lemos, 3-5. Pabellon 11. Planta 0, 28029, Madrid, Spain. jimrperkins@gmail.com","Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain. jimrperkins@gmail.com","Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain. jimrperkins@gmail.com","Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain"],"raw_orcid":"https://orcid.org/0000-0003-4108-096X","affiliations":[{"raw_affiliation_string":"CIBER of Rare Diseases, Av. Monforte de Lemos, 3-5. Pabellon 11. Planta 0, 28029, Madrid, Spain. jimrperkins@gmail.com","institution_ids":["https://openalex.org/I4210111366"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain. jimrperkins@gmail.com","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain. jimrperkins@gmail.com","institution_ids":["https://openalex.org/I82767444","https://openalex.org/I4210164724"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088333668","display_name":"J. Caballero","orcid":"https://orcid.org/0000-0002-1821-5742"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 C\u00f3rdoba-Caballero","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031958805","display_name":"Federico Garc\u00eda-Criado","orcid":"https://orcid.org/0000-0002-5123-8348"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Federico Garc\u00eda-Criado","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036351252","display_name":"Ian Sillitoe","orcid":"https://orcid.org/0000-0003-1091-9144"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ian Sillitoe","raw_affiliation_strings":["Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081250379","display_name":"Christine Orengo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christine Orengo","raw_affiliation_strings":["Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065049632","display_name":"Juan A. G. Ranea","orcid":"https://orcid.org/0000-0003-0327-1837"},"institutions":[{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan A. G. Ranea","raw_affiliation_strings":["CIBER of Rare Diseases, Av. Monforte de Lemos, 3-5. Pabellon 11. Planta 0, 28029, Madrid, Spain","Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIBER of Rare Diseases, Av. Monforte de Lemos, 3-5. Pabellon 11. Planta 0, 28029, Madrid, Spain","institution_ids":["https://openalex.org/I4210111366"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038138862","display_name":"Pedro Seoane","orcid":"https://orcid.org/0000-0002-3020-1415"},"institutions":[{"id":"https://openalex.org/I4210111366","display_name":"Centre for Biomedical Network Research on Rare Diseases","ror":"https://ror.org/01ygm5w19","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210111366"]},{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pedro Seoane-Zonjic","raw_affiliation_strings":["CIBER of Rare Diseases, Av. Monforte de Lemos, 3-5. Pabellon 11. Planta 0, 28029, Madrid, Spain","Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIBER of Rare Diseases, Av. Monforte de Lemos, 3-5. Pabellon 11. Planta 0, 28029, Madrid, Spain","institution_ids":["https://openalex.org/I4210111366"]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of Malaga, Bulevar Louis Pasteur, 31, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Institute of Biomedical Research in Malaga (IBIMA), Dr. Miguel D\u00edaz Recio, 28, 29010, Malaga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5038281376"],"corresponding_institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.6467,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.83366609,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"23","issue":"1","first_page":"43","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.949999988079071,"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":0.949999988079071,"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":0.023099999874830246,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.005100000184029341,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.7093230485916138},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.686380922794342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6711349487304688},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.6612725257873535},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6286042332649231},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5965701937675476},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.572731614112854},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4828115403652191},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.4754619002342224},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46811550855636597},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4644510746002197},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.3168645203113556},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30763787031173706},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2534526288509369},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24243658781051636},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14680761098861694},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13558396697044373}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7093230485916138},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.686380922794342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6711349487304688},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.6612725257873535},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6286042332649231},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5965701937675476},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.572731614112854},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4828115403652191},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.4754619002342224},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46811550855636597},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4644510746002197},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.3168645203113556},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30763787031173706},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2534526288509369},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24243658781051636},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14680761098861694},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13558396697044373},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, 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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","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":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","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},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-022-04565-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04565-6","pdf_url":null,"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:35033002","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35033002","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:www.repositoriosalud.es:10668/20261","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8761305/pdf","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04565-6","source":{"id":"https://openalex.org/S4377196114","display_name":"RISalud Institutional Health Repository of Andaluc\u00eda","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"},{"id":"pmh:oai:doaj.org/article:04cbfecf2a7e4f32bcde7c8858ce38c0","is_oa":true,"landing_page_url":"https://doaj.org/article/04cbfecf2a7e4f32bcde7c8858ce38c0","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 23, Iss 1, Pp 1-19 (2022)","raw_type":"article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10142850","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10142850/","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":"   BMC Bioinformatics , 23  (1)    , Article 43. (2022)      ","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8761305","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8761305","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04565-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04565-6","pdf_url":null,"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/G1125178396","display_name":null,"funder_award_id":"PID2019-108096RB-C21","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G2239537280","display_name":null,"funder_award_id":"SAF2016-78041-C2-1-R","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"},{"id":"https://openalex.org/G23007851","display_name":null,"funder_award_id":"PID2019-108096RB-C21","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3805965999","display_name":null,"funder_award_id":"UMA18-FEDERJA-102","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G3858781183","display_name":null,"funder_award_id":"I Ayudas del Plan Propio, D.2","funder_id":"https://openalex.org/F4320311265","funder_display_name":"Universidad de M\u00e1laga"},{"id":"https://openalex.org/G5516262562","display_name":null,"funder_award_id":"PI-0075-2017","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G5555131222","display_name":null,"funder_award_id":"PID2019","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G6240419514","display_name":null,"funder_award_id":"UMA18-FEDERJA","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G6284536590","display_name":null,"funder_award_id":"PID2019-105010RB-I00","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G7625767729","display_name":null,"funder_award_id":"UMA18-FEDERJA-102","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8875107625","display_name":null,"funder_award_id":"PID2019-108096RB-C21","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"}],"funders":[{"id":"https://openalex.org/F4320310214","display_name":"Fundaci\u00f3n Ram\u00f3n Areces","ror":"https://ror.org/04ra91131"},{"id":"https://openalex.org/F4320311265","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28"},{"id":"https://openalex.org/F4320315062","display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","ror":null},{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"},{"id":"https://openalex.org/F4320332805","display_name":"Smithsonian Conservation Biology Institute","ror":"https://ror.org/04hnzva96"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1892752174","https://openalex.org/W1970371025","https://openalex.org/W1975170514","https://openalex.org/W1998490996","https://openalex.org/W2031903428","https://openalex.org/W2068072987","https://openalex.org/W2089467986","https://openalex.org/W2090146405","https://openalex.org/W2092612709","https://openalex.org/W2100383158","https://openalex.org/W2103017472","https://openalex.org/W2108067237","https://openalex.org/W2122576958","https://openalex.org/W2145126338","https://openalex.org/W2159482845","https://openalex.org/W2227395312","https://openalex.org/W2302133857","https://openalex.org/W2558272290","https://openalex.org/W2603053732","https://openalex.org/W2792504918","https://openalex.org/W2810862813","https://openalex.org/W2943402909","https://openalex.org/W2947872911","https://openalex.org/W2950595506","https://openalex.org/W2959593662","https://openalex.org/W3021518969","https://openalex.org/W3022588147","https://openalex.org/W3048937775","https://openalex.org/W3089704999","https://openalex.org/W4210561386","https://openalex.org/W4230371842","https://openalex.org/W4233698560"],"related_works":["https://openalex.org/W2551839783","https://openalex.org/W4386401670","https://openalex.org/W2956207900","https://openalex.org/W2790781282","https://openalex.org/W2334025507","https://openalex.org/W2901913417","https://openalex.org/W2952660917","https://openalex.org/W1797688090","https://openalex.org/W1977065177","https://openalex.org/W33421173"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"function":[2,141,189,257],"prediction":[3,190],"remains":[4],"a":[5,17],"key":[6],"challenge.":[7],"Domain":[8],"composition":[9],"affects":[10],"protein":[11,24,44,317],"function.":[12],"Here":[13],"we":[14,202,215,274],"present":[15],"DomFun,":[16],"Ruby":[18,333],"gem":[19,334],"that":[20,91,124,308],"uses":[21],"associations":[22,39,107,298],"between":[23],"domains":[25,61],"and":[26,59,75,98,133,168,198,285,329],"functions,":[27],"calculated":[28],"using":[29,81,125,291,299],"multiple":[30,95],"indices":[31],"based":[32],"on":[33,264],"tripartite":[34,54],"network":[35],"analysis.":[36],"These":[37],"domain-function":[38,106,297],"are":[40],"combined":[41,108],"at":[42,342,351],"the":[43,68,79,82,94,114,153,220,235,265],"level,":[45],"to":[46,113,128,143,187,206,234,314],"generate":[47],"protein-function":[48],"predictions.":[49],"RESULTS:":[50],"We":[51,77,121,172],"analysed":[52],"16":[53],"networks":[55],"connecting":[56],"homologous":[57],"superfamily":[58],"FunFam":[60,105],"from":[62,67,323,337],"CATH-Gene3D":[63],"with":[64,109,209,225,230,247,258],"functional":[65],"annotations":[66,193],"three":[69],"Gene":[70],"Ontology":[71],"(GO)":[72],"sub-ontologies,":[73],"KEGG,":[74],"Reactome.":[76,199,286],"validated":[78],"results":[80,135,205,261],"CAFA":[83,158,210,226,252],"3":[84,159,211,253],"benchmark":[85,177,271],"platform":[86],"for":[87,104,138,191,212,219,283],"GO":[88,139,144],"annotation,":[89],"finding":[90],"out":[92],"of":[93,164],"association":[96],"metrics":[97],"domain":[99,321],"datasets":[100],"tested,":[101],"Simpson":[102,228,294],"index":[103,229,295],"Stouffer's":[110,231,300],"method":[111,155,232],"leads":[112],"best":[115,289],"performance":[116,130,218,237,246],"in":[117,156,162,238,251],"almost":[118,239],"all":[119,240],"scenarios.":[120,241],"also":[122,173,279],"found":[123,137,203,208,216,350],"FunFams":[126],"led":[127,233],"better":[129,134],"than":[131],"superfamilies,":[132],"were":[136],"molecular":[140],"compared":[142],"biological":[145],"process":[146],"terms.":[147],"DomFun":[148,243,332],"performed":[149],"as":[150,152,196,320],"well":[151],"highest-performing":[154],"certain":[157],"evaluation":[160,266],"procedures":[161],"terms":[163],"[Formula:":[165,169],"see":[166,170],"text]":[167,171],"implemented":[174,306],"our":[175,269],"own":[176,270],"procedure,":[178,272],"Pathway":[179],"Prediction":[180],"Performance":[181],"(PPP),":[182],"which":[183],"can":[184,278,310,348],"be":[185,311,349],"used":[186],"validate":[188],"additional":[192],"sources,":[194,325],"such":[195,319],"KEGG":[197,284],"Using":[200],"PPP,":[201,273],"similar":[204],"those":[207],"GO,":[213,259],"moreover":[214],"good":[217],"other":[221,248,316,324],"annotation":[222],"sources.":[223],"As":[224],"3,":[227],"top":[236],"CONCLUSIONS:":[242],"shows":[244],"competitive":[245],"methods":[249],"evaluated":[250],"when":[254,290],"predicting":[255],"proteins":[256],"although":[260],"vary":[262],"depending":[263],"procedure.":[267],"Through":[268],"have":[275],"shown":[276],"it":[277,309],"make":[280],"accurate":[281],"predictions":[282],"It":[287],"performs":[288],"FunFams,":[292],"combining":[293],"derived":[296],"method.":[301],"The":[302,331],"tool":[303],"has":[304],"been":[305],"so":[307],"easily":[312],"adapted":[313],"incorporate":[315],"features,":[318],"data":[322],"amino":[326],"acid":[327],"k-mers":[328],"motifs.":[330],"is":[335],"available":[336],"https://rubygems.org/gems/DomFun":[338],".":[339,344,353],"Code":[340],"maintained":[341],"https://github.com/ElenaRojano/DomFun":[343],"Validation":[345],"procedure":[346],"scripts":[347],"https://github.com/ElenaRojano/DomFun_project":[352]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
