{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:00:37Z","timestamp":1773277237233,"version":"3.50.1"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,1,25]],"date-time":"2008-01-25T00:00:00Z","timestamp":1201219200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-50","type":"journal-article","created":{"date-parts":[[2008,1,25]],"date-time":"2008-01-25T19:20:33Z","timestamp":1201288833000},"source":"Crossref","is-referenced-by-count":50,"title":["Defining functional distances over Gene Ontology"],"prefix":"10.1186","volume":"9","author":[{"given":"Angela","family":"del Pozo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florencio","family":"Pazos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,1,25]]},"reference":[{"issue":"3","key":"2035_CR1","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bib\/bbl004","volume":"7","author":"I Friedberg","year":"2006","unstructured":"Friedberg I: Automated protein function prediction-the genomic challenge. Brief Bioinform 2006, 7(3):225\u2013242.","journal-title":"Brief Bioinform"},{"issue":"6","key":"2035_CR2","first-page":"246","volume":"2","author":"B Smith","year":"2004","unstructured":"Smith B, Kumar A: Controlled vocabularies in bioinformatics: a case study in the gene ontology. DDT: BIOSILICO 2004, 2(6):246\u2013252.","journal-title":"DDT: BIOSILICO"},{"issue":"1","key":"2035_CR3","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1007\/s101420000005","volume":"1","author":"S Rison","year":"2000","unstructured":"Rison S, Hodgman T, Thornton J: Comparison of functional annotation schemes for genomes. Funct Integr Genomics 2000, 1(1):56\u201369.","journal-title":"Funct Integr Genomics"},{"issue":"3","key":"2035_CR4","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.sbi.2005.05.010","volume":"15","author":"A Valencia","year":"2005","unstructured":"Valencia A: Automatic annotation of protein function. Current Opinion in Structural Biology 2005, 15(3):267\u201374.","journal-title":"Current Opinion in Structural Biology"},{"issue":"4","key":"2035_CR5","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1128\/MMBR.57.4.862-952.1993","volume":"57","author":"M Riley","year":"1993","unstructured":"Riley M: Functions of the gene products of Escherichia coli. Microbiol Rev 1993, 57(4):862\u2013952.","journal-title":"Microbiol Rev"},{"key":"2035_CR6","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1007\/PL00006122","volume":"V44","author":"J Tamames","year":"1997","unstructured":"Tamames J, Casari G, Ouzounis C, Valencia A: Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes. Journal of Molecular Evolution 1997, V44: 66\u201373.","journal-title":"Journal of Molecular Evolution"},{"issue":"6\u20137","key":"2035_CR7","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1002\/cfg.435","volume":"5","author":"C Mungall","year":"2004","unstructured":"Mungall C: Obol: integrating language and meaning in bio-ontologies: Conference Papers. Comp Funct Genomics 2004, 5(6\u20137):509\u2013520.","journal-title":"Comp Funct Genomics"},{"issue":"5","key":"2035_CR8","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2005-6-5-r46","volume":"6","author":"B Smith","year":"2005","unstructured":"Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C: Relations in biomedical ontologies. Genome Biology 2005, 6(5):R46.","journal-title":"Genome Biology"},{"key":"2035_CR9","unstructured":"Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, (32 Database):D258\u201361."},{"issue":"10","key":"2035_CR10","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","volume":"19","author":"P Lord","year":"2003","unstructured":"Lord P, Stevens R, Brass A, Goble C: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19(10):1275\u201383.","journal-title":"Bioinformatics"},{"key":"2035_CR11","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1186\/1471-2105-7-135","volume":"7","author":"P Zhang","year":"2006","unstructured":"Zhang P, Zhang J, Sheng H, Russo J, Osborne B, Buetow K: Gene functional similarity search tool (GF-SST). BMC Bioinformatics 2006, 7: 135.","journal-title":"BMC Bioinformatics"},{"key":"2035_CR12","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2105-7-302","volume":"7","author":"A Schlicker","year":"2006","unstructured":"Schlicker A, Domingues F, Rahnenfuhrer J, Lengauer T: A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7: 302.","journal-title":"BMC Bioinformatics"},{"key":"2035_CR13","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1145\/1099554.1099658","volume-title":"In CIKM '05: Proceedings of the 14th ACM international conference on Information and knowledge management","author":"F Couto","year":"2005","unstructured":"Couto F, Silva M, Coutinho P: Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. In In CIKM '05: Proceedings of the 14th ACM international conference on Information and knowledge management. New York, NY, USA: ACM Press; 2005:343\u2013344."},{"issue":"10","key":"2035_CR14","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","volume":"23","author":"JZ Wang","year":"2007","unstructured":"Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF: A new method to measure the semantic similarity of GO term. Bioinformatics 2007, 23(10):1274\u20131281.","journal-title":"Bioinformatics"},{"key":"2035_CR15","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1613\/jair.514","volume":"11","author":"P Resnik","year":"1999","unstructured":"Resnik P: Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research 1999, 11: 95\u2013130.","journal-title":"Journal of Artificial Intelligence Research"},{"key":"2035_CR16","doi-asserted-by":"publisher","first-page":"D201","DOI":"10.1093\/nar\/gki106","volume":"33","author":"NJ Mulder","year":"2005","unstructured":"Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH: InterPro, progress and status in 2005. Nucleic Acids Res 2005, 33: D201\u20135.","journal-title":"Nucleic Acids Res"},{"key":"2035_CR17","doi-asserted-by":"crossref","unstructured":"Huang D, Sherman B, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler M, Lane H, Lempicki R: DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 2007, (35 Web Server):W169\u2013175.","DOI":"10.1093\/nar\/gkm415"},{"issue":"8","key":"2035_CR18","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","volume":"96","author":"M Pellegrini","year":"1999","unstructured":"Pellegrini M, Marcotte E, Thompson M, Eisenberg D, Yeates T: Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles. Proc Natl Acad Sci USA 1999, 96(8):4285\u20134288.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"15","key":"2035_CR19","doi-asserted-by":"publisher","first-page":"7176","DOI":"10.1073\/pnas.90.15.7176","volume":"90","author":"BT Korber","year":"1993","unstructured":"Korber BT, Farber R, Wolpert D, Lapedes A: Covariation of Mutations in the V3 Loop of Human Immunodeficiency Virus Type 1 Envelope Protein: An Information Theoretic Analysis. PNAS 1993, 90(15):7176\u20137180.","journal-title":"PNAS"},{"key":"2035_CR20","volume-title":"Tech Rep 03-05-01","author":"D Verma","year":"2003","unstructured":"Verma D, Meil\u0103 M: A Comparison of Spectral Clustering Algorithms. In Tech Rep 03\u201305\u201301. University of Washington Department of Computer Science; 2003."},{"key":"2035_CR21","first-page":"849","volume-title":"In Advances in Neural Information Processing Systems 14","author":"A Ng","year":"2002","unstructured":"Ng A, Jordan M, Weiss Y: On Spectral Clustering: Analysis and an algorithm. In In Advances in Neural Information Processing Systems 14. Edited by: Dietterich TG, Becker S, Ghahramani Z. Cambridge, MA: MIT Press; 2002:849\u2013856."},{"key":"2035_CR22","volume-title":"Pattern Classification","author":"R Duda","year":"2001","unstructured":"Duda R, Hart P, Stork D: Pattern Classification. Wiley; 2001."},{"issue":"4","key":"2035_CR23","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1101\/gr.461403","volume":"13","author":"E Camon","year":"2003","unstructured":"Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Jand Cox MaslenA, Apweiler R: The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Research 2003, 13(4):662\u2013672.","journal-title":"Genome Research"},{"key":"2035_CR24","unstructured":"Guide to GO Evidence Codes[ http:\/\/www.geneontology.org\/GO.evidence.shtml ]"},{"issue":"13","key":"2035_CR25","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","volume":"22","author":"W Li","year":"2006","unstructured":"Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658\u20131659.","journal-title":"Bioinformatics"},{"key":"2035_CR26","unstructured":"Gene Ontology Annotation (GOA) Database[ http:\/\/www.ebi.ac.uk\/GOA ]"},{"key":"2035_CR27","volume-title":"Number 92 in CBMS Regional Conference Series in Mathematics, American Mathematical Society","author":"F Chung","year":"1997","unstructured":"Chung F: Spectral Graph Theory. Number 92 in CBMS Regional Conference Series in Mathematics, American Mathematical Society 1997."},{"key":"2035_CR28","volume-title":"NIPS2000","author":"M Meil\u0103","year":"2000","unstructured":"Meil\u0103 M, Shi J: Learning Segmentation by Random Walks. NIPS2000 2000."},{"key":"2035_CR29","volume-title":"Tech Rep 451","author":"M Meil\u0103","year":"2004","unstructured":"Meil\u0103 M: The Multicut Lemma. In Tech Rep 451. University of Washington Statistics; 2004."},{"key":"2035_CR30","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","volume":"23","author":"M Letunic","year":"2007","unstructured":"Letunic M, Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23: 127\u2013128.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-50.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-50\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-50.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,1]],"date-time":"2020-05-01T06:14:59Z","timestamp":1588313699000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-50"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,1,25]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2035"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-50","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,25]]},"article-number":"50"}}