{"id":"https://openalex.org/W2000844908","doi":"https://doi.org/10.1186/1471-2105-9-198","title":"Improving protein function prediction methods with integrated literature data","display_name":"Improving protein function prediction methods with integrated literature data","publication_year":2008,"publication_date":"2008-04-15","ids":{"openalex":"https://openalex.org/W2000844908","doi":"https://doi.org/10.1186/1471-2105-9-198","mag":"2000844908","pmid":"https://pubmed.ncbi.nlm.nih.gov/18412966"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-198","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-198","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-198","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-198","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013875055","display_name":"Aaron Gabow","orcid":null},"institutions":[{"id":"https://openalex.org/I1288162130","display_name":"University of Colorado Hospital","ror":"https://ror.org/006jjmw19","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288162130","https://openalex.org/I4210087413"]},{"id":"https://openalex.org/I4210087413","display_name":"University of Colorado Health","ror":"https://ror.org/0107w4315","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087413"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aaron P Gabow","raw_affiliation_strings":["Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO 80045, USA. gabow@cbio.mskcc.org","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO 80045, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO 80045, USA. gabow@cbio.mskcc.org","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO 80045, USA","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I4210087413","https://openalex.org/I1288162130","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041931115","display_name":"Sonia M. Leach","orcid":"https://orcid.org/0000-0003-2910-069X"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]},{"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","US"],"is_corresponding":true,"raw_author_name":"Sonia M Leach","raw_affiliation_strings":["Department of Electrical Engineering (ESAT), Research Division SCD, Katholieke Universiteit Leuven, B-3001, Leuven, Belgium","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","Department of Electrical Engineering (ESAT), Research Division SCD, Katholieke Universiteit Leuven, Leuven, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering (ESAT), Research Division SCD, Katholieke Universiteit Leuven, B-3001, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Electrical Engineering (ESAT), Research Division SCD, Katholieke Universiteit Leuven, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111881812","display_name":"William A. Baumgartner","orcid":null},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William A Baumgartner","raw_affiliation_strings":["Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041860080","display_name":"Lawrence Hunter","orcid":"https://orcid.org/0000-0003-1455-3370"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lawrence E Hunter","raw_affiliation_strings":["Department of Computer Science, University of Colorado at Boulder, Boulder, CO, 80309, USA","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","Department of Computer Science, University of Colorado at Boulder, Boulder, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Colorado at Boulder, Boulder, CO, 80309, USA","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Computer Science, University of Colorado at Boulder, Boulder, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091405758","display_name":"Debra S. Goldberg","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debra S Goldberg","raw_affiliation_strings":["Department of Computer Science, University of Colorado at Boulder, Boulder, CO, 80309, USA","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","Department of Computer Science, University of Colorado at Boulder, Boulder, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Colorado at Boulder, Boulder, CO, 80309, USA","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6101, PO Box 6511, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Computer Science, University of Colorado at Boulder, Boulder, USA","institution_ids":["https://openalex.org/I188538660"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5013875055","https://openalex.org/A5041931115"],"corresponding_institution_ids":["https://openalex.org/I1288162130","https://openalex.org/I4210087413","https://openalex.org/I51713134","https://openalex.org/I921990950","https://openalex.org/I99464096"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.6677,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.8982276,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"9","issue":"1","first_page":"198","last_page":"198"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.983299970626831,"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":0.983299970626831,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.004000000189989805,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0020000000949949026,"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/protein-function-prediction","display_name":"Protein function prediction","score":0.6650601029396057},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6294585466384888},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.5516400337219238},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.5393528938293457},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5346704125404358},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4960246980190277},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4903426170349121},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4726150333881378},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.46190956234931946},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4349590539932251},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36482155323028564},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3125142455101013},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2567834258079529},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18197351694107056},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16303029656410217}],"concepts":[{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.6650601029396057},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6294585466384888},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.5516400337219238},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.5393528938293457},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5346704125404358},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4960246980190277},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4903426170349121},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4726150333881378},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.46190956234931946},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4349590539932251},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36482155323028564},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3125142455101013},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2567834258079529},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18197351694107056},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16303029656410217},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016206","descriptor_name":"Databases, Bibliographic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016206","descriptor_name":"Databases, Bibliographic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016206","descriptor_name":"Databases, Bibliographic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-198","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-198","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-198","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:18412966","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18412966","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:042c8550b6e9457594c42e2891768f12","is_oa":false,"landing_page_url":"https://doaj.org/article/042c8550b6e9457594c42e2891768f12","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 198 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2375131","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2375131","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:10.1186/1471-2105-9-198","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-198","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-198","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/G5169022270","display_name":null,"funder_award_id":"R01 LM008111","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6508667619","display_name":null,"funder_award_id":"R01 LM009254","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G7344667414","display_name":"Starter Grant: Modeling Evolution of Gene and Protein Interactions","funder_award_id":"0630250","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2000844908.pdf","grobid_xml":"https://content.openalex.org/works/W2000844908.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1486817521","https://openalex.org/W1544224697","https://openalex.org/W1566012138","https://openalex.org/W1956694423","https://openalex.org/W1976316416","https://openalex.org/W1994803330","https://openalex.org/W2011986160","https://openalex.org/W2015954361","https://openalex.org/W2042210880","https://openalex.org/W2044514479","https://openalex.org/W2048140075","https://openalex.org/W2057885377","https://openalex.org/W2058766645","https://openalex.org/W2102281458","https://openalex.org/W2103017472","https://openalex.org/W2106093878","https://openalex.org/W2107717979","https://openalex.org/W2111193511","https://openalex.org/W2119043225","https://openalex.org/W2121048111","https://openalex.org/W2122683551","https://openalex.org/W2123500593","https://openalex.org/W2124617249","https://openalex.org/W2126991359","https://openalex.org/W2131456688","https://openalex.org/W2132582966","https://openalex.org/W2136992683","https://openalex.org/W2137786672","https://openalex.org/W2138312771","https://openalex.org/W2152881983","https://openalex.org/W2155320925","https://openalex.org/W2159203162","https://openalex.org/W2165797737","https://openalex.org/W2171403830","https://openalex.org/W2171674404","https://openalex.org/W2952213200","https://openalex.org/W4236956086","https://openalex.org/W4252706339","https://openalex.org/W4300022934"],"related_works":["https://openalex.org/W2094822546","https://openalex.org/W4388708026","https://openalex.org/W1528887219","https://openalex.org/W1969080446","https://openalex.org/W4255644844","https://openalex.org/W2181394498","https://openalex.org/W2287132924","https://openalex.org/W2131407941","https://openalex.org/W2125650596","https://openalex.org/W2586268529"],"abstract_inverted_index":{"BACKGROUND:":[0],"Determining":[1],"the":[2,12,17,34,59,72,84,102,116,127,148,169,177,204,215,225,242,255,322],"function":[3,25,131,278,327],"of":[4,30,55,62,74,86,118,150,171,228],"uncharacterized":[5],"proteins":[6,56,64,119,181,238],"is":[7,143,182,260,271,290],"a":[8,23,40,79,163,272,291],"major":[9],"challenge":[10],"in":[11,33,65,99,126,134,141,321],"post-genomic":[13],"era":[14],"due":[15,146],"to":[16,27,147,185,203,240,318],"problem's":[18],"complexity":[19],"and":[20,43,88,137,174,221],"scale.":[21],"Identifying":[22],"protein's":[24],"contributes":[26],"an":[28,121],"understanding":[29],"its":[31,37,44],"role":[32],"involved":[35],"pathways,":[36],"suitability":[38],"as":[39,101],"drug":[41],"target,":[42],"potential":[45],"for":[46,82,196,245,276,294],"protein":[47,303],"modifications.":[48],"Several":[49],"graph-theoretic":[50,130,277,326],"approaches":[51],"predict":[52],"unidentified":[53],"functions":[54,256],"by":[57],"using":[58],"functional":[60],"annotations":[61],"better-characterized":[63],"protein-protein":[66,155,172],"interaction":[67,166,304,323],"networks.":[68],"We":[69,95,110],"systematically":[70],"consider":[71],"use":[73],"literature":[75,284],"co-occurrence":[76,87,117,158,175,198,230,247,263,288,312],"data,":[77,176,248],"introduce":[78],"new":[80],"method":[81,195,244],"quantifying":[83,197],"reliability":[85,199],"test":[89],"how":[90],"performance":[91,100,125,142,202],"differs":[92],"across":[93],"species.":[94],"also":[96],"quantify":[97],"changes":[98],"prediction":[103,132,190,279,328],"algorithms":[104,191,329],"annotate":[105],"with":[106,157,162,257,301],"increased":[107],"specificity.":[108],"RESULTS:":[109],"find":[111],"that":[112,287,325],"including":[113],"information":[114],"on":[115],"within":[120],"abstract":[122,235],"greatly":[123],"boosts":[124],"Functional":[128],"Flow":[129],"algorithm":[133],"yeast,":[135],"fly":[136],"worm.":[138],"This":[139],"increase":[140],"not":[144],"simply":[145],"presence":[149],"additional":[151,316],"edges":[152],"since":[153],"supplementing":[154,161],"interactions":[156,173],"data":[159,264,270,289,313],"outperforms":[160],"comparably-sized":[164],"genetic":[165],"dataset.":[167],"Through":[168],"combination":[170],"neighborhood":[178],"around":[179,211],"unknown":[180],"quickly":[183],"connected":[184],"well-characterized":[186],"nodes":[187],"which":[188,213],"global":[189],"can":[192,330],"exploit.":[193,331],"Our":[194],"shows":[200],"superior":[201],"other":[205],"methods,":[206],"particularly":[207,299],"at":[208,232],"threshold":[209],"values":[210],"10%":[212],"yield":[214],"best":[216],"trade":[217],"off":[218],"between":[219],"coverage":[220],"accuracy.":[222],"In":[223],"contrast,":[224],"traditional":[226],"way":[227],"asserting":[229],"when":[231],"least":[233],"one":[234],"mentions":[236],"both":[237],"proves":[239,266],"be":[241],"worst":[243],"generating":[246],"introducing":[249],"too":[250],"many":[251],"false":[252],"positives.":[253],"Annotating":[254],"greater":[258],"specificity":[259],"harder,":[261],"but":[262],"still":[265],"beneficial.":[267],"CONCLUSION:":[268],"Co-occurrence":[269],"valuable":[273],"supplemental":[274],"source":[275],"algorithms.":[280],"A":[281],"rapidly":[282],"growing":[283],"corpus":[285],"ensures":[286],"readily-available":[292],"resource":[293],"nearly":[295],"every":[296],"studied":[297],"organism,":[298],"those":[300],"small":[302],"databases.":[305],"Though":[306],"arguably":[307],"biased":[308],"toward":[309],"known":[310],"genes,":[311],"provides":[314],"critical":[315],"links":[317],"well-studied":[319],"regions":[320],"network":[324]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":30},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
