{"id":"https://openalex.org/W2065589669","doi":"https://doi.org/10.1186/1471-2105-8-243","title":"Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks","display_name":"Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks","publication_year":2007,"publication_date":"2007-07-10","ids":{"openalex":"https://openalex.org/W2065589669","doi":"https://doi.org/10.1186/1471-2105-8-243","mag":"2065589669","pmid":"https://pubmed.ncbi.nlm.nih.gov/17620146"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-243","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-243","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-243.pdf","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://link.springer.com/content/pdf/10.1186/1471-2105-8-243.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079940014","display_name":"Nikolai Daraselia","orcid":null},"institutions":[{"id":"https://openalex.org/I4210158425","display_name":"Ariadne Diagnostics (United States)","ror":"https://ror.org/04mzbw652","country_code":"US","type":"company","lineage":["https://openalex.org/I4210158425"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikolai Daraselia","raw_affiliation_strings":["Ariadne Genomics, Inc, Rockville, MD 20850, USA. nikolai@ariadnegenomics.com <nikolai@ariadnegenomics.com>","Ariadne Genomics, Inc, Rockville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ariadne Genomics, Inc, Rockville, MD 20850, USA. nikolai@ariadnegenomics.com <nikolai@ariadnegenomics.com>","institution_ids":["https://openalex.org/I4210158425"]},{"raw_affiliation_string":"Ariadne Genomics, Inc, Rockville, USA","institution_ids":["https://openalex.org/I4210158425"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049213055","display_name":"Anton Yuryev","orcid":"https://orcid.org/0000-0003-1021-4849"},"institutions":[{"id":"https://openalex.org/I4210158425","display_name":"Ariadne Diagnostics (United States)","ror":"https://ror.org/04mzbw652","country_code":"US","type":"company","lineage":["https://openalex.org/I4210158425"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anton Yuryev","raw_affiliation_strings":["Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","Ariadne Genomics, Inc, Rockville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I4210158425"]},{"raw_affiliation_string":"Ariadne Genomics, Inc, Rockville, USA","institution_ids":["https://openalex.org/I4210158425"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004512619","display_name":"Sergei Egorov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210158425","display_name":"Ariadne Diagnostics (United States)","ror":"https://ror.org/04mzbw652","country_code":"US","type":"company","lineage":["https://openalex.org/I4210158425"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergei Egorov","raw_affiliation_strings":["Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","Ariadne Genomics, Inc, Rockville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I4210158425"]},{"raw_affiliation_string":"Ariadne Genomics, Inc, Rockville, USA","institution_ids":["https://openalex.org/I4210158425"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018702135","display_name":"Ilya Mazo","orcid":"https://orcid.org/0000-0002-8587-4895"},"institutions":[{"id":"https://openalex.org/I4210158425","display_name":"Ariadne Diagnostics (United States)","ror":"https://ror.org/04mzbw652","country_code":"US","type":"company","lineage":["https://openalex.org/I4210158425"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ilya Mazo","raw_affiliation_strings":["Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","Ariadne Genomics, Inc, Rockville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I4210158425"]},{"raw_affiliation_string":"Ariadne Genomics, Inc, Rockville, USA","institution_ids":["https://openalex.org/I4210158425"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087149978","display_name":"Yaroslav Ispolatov","orcid":"https://orcid.org/0000-0002-0201-3396"},"institutions":[{"id":"https://openalex.org/I4210158425","display_name":"Ariadne Diagnostics (United States)","ror":"https://ror.org/04mzbw652","country_code":"US","type":"company","lineage":["https://openalex.org/I4210158425"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Iaroslav Ispolatov","raw_affiliation_strings":["Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","Ariadne Genomics, Inc, Rockville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ariadne Genomics, Inc, 9430 Key West Ave., Suite 313, Rockville, MD, 20850, USA","institution_ids":["https://openalex.org/I4210158425"]},{"raw_affiliation_string":"Ariadne Genomics, Inc, Rockville, USA","institution_ids":["https://openalex.org/I4210158425"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5049213055"],"corresponding_institution_ids":["https://openalex.org/I4210158425"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.5975,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.93567729,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"243","last_page":"243"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8737000226974487,"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":0.8737000226974487,"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":0.12020000070333481,"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":0.0007999999797903001,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8622124791145325},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6903369426727295},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5054836273193359},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5050807595252991},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.4803805947303772},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4793068468570709},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4430786371231079},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43785494565963745},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.43609780073165894},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.41655397415161133},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.38807007670402527},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36980658769607544},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29497164487838745},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24538511037826538},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22482901811599731},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1877770721912384},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0939379334449768}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8622124791145325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6903369426727295},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5054836273193359},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5050807595252991},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.4803805947303772},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4793068468570709},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4430786371231079},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43785494565963745},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.43609780073165894},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.41655397415161133},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38807007670402527},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36980658769607544},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29497164487838745},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24538511037826538},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22482901811599731},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1877770721912384},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0939379334449768},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000592","qualifier_name":"standards","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":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-243","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-243","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-243.pdf","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:17620146","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17620146","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:458e51d199b646bba63757de8a655456","is_oa":true,"landing_page_url":"https://doaj.org/article/458e51d199b646bba63757de8a655456","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 8, Iss 1, p 243 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1940026","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1940026","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:10.1186/1471-2105-8-243","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-243","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-8-243.pdf","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/G1831323167","display_name":null,"funder_award_id":"R01 GM068954","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2904278360","display_name":null,"funder_award_id":"1 R01 GM068954-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4673364362","display_name":null,"funder_award_id":"5R44RR021304-03","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G6442512130","display_name":null,"funder_award_id":"R44 RR021304","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065589669.pdf","grobid_xml":"https://content.openalex.org/works/W2065589669.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W85880394","https://openalex.org/W201288405","https://openalex.org/W1523095068","https://openalex.org/W1644749979","https://openalex.org/W1970863518","https://openalex.org/W1977224551","https://openalex.org/W1983532638","https://openalex.org/W1992107140","https://openalex.org/W1998261914","https://openalex.org/W2011303928","https://openalex.org/W2012895254","https://openalex.org/W2033588290","https://openalex.org/W2040778567","https://openalex.org/W2046482984","https://openalex.org/W2056119436","https://openalex.org/W2083654996","https://openalex.org/W2084089807","https://openalex.org/W2091978351","https://openalex.org/W2092689087","https://openalex.org/W2092795373","https://openalex.org/W2099100406","https://openalex.org/W2100585269","https://openalex.org/W2102037268","https://openalex.org/W2102155970","https://openalex.org/W2103017472","https://openalex.org/W2103907281","https://openalex.org/W2106093878","https://openalex.org/W2115539205","https://openalex.org/W2116117181","https://openalex.org/W2117223578","https://openalex.org/W2118446779","https://openalex.org/W2127563440","https://openalex.org/W2128936012","https://openalex.org/W2131456688","https://openalex.org/W2134788911","https://openalex.org/W2134789671","https://openalex.org/W2141490615","https://openalex.org/W2144563318","https://openalex.org/W2146119511","https://openalex.org/W2152495216","https://openalex.org/W2156737316","https://openalex.org/W2160238006","https://openalex.org/W2160521949","https://openalex.org/W2163258133","https://openalex.org/W2164071427","https://openalex.org/W2166711445","https://openalex.org/W2167289895","https://openalex.org/W2171602500","https://openalex.org/W2171674404","https://openalex.org/W3124010868"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2086443788","https://openalex.org/W4299646404","https://openalex.org/W3030863237","https://openalex.org/W2142508559","https://openalex.org/W2022059553","https://openalex.org/W2128542713","https://openalex.org/W1963847445","https://openalex.org/W2088387316","https://openalex.org/W2536992799"],"abstract_inverted_index":{"BACKGROUND:":[0],"Uncovering":[1],"cellular":[2],"roles":[3],"of":[4,10,45,48,58,138,173,180,194,216,280,287,374,383],"a":[5,8,55,133,199,222,248,319],"protein":[6,85,124,139,155,210,322],"is":[7,54,332],"task":[9],"tremendous":[11],"importance":[12],"and":[13,27,84,118,126,166,169,212,278,348],"complexity":[14],"that":[15,60,179,295,310,370],"requires":[16],"dedicated":[17],"experimental":[18],"work":[19],"as":[20,22,35,391],"well":[21],"often":[23,32,89],"sophisticated":[24],"data":[25,116],"mining":[26],"processing":[28,119],"tools.":[29],"Protein":[30,339],"functions,":[31],"referred":[33],"to":[34,40,69,104,122,178,334],"its":[36,306,325],"annotations,":[37],"are":[38,66,88],"believed":[39],"manifest":[41],"themselves":[42],"through":[43],"topology":[44,87],"the":[46,63,92,106,115,147,154,159,164,171,174,191,203,208,258,266,276,288,292,300,344,350,362,365,371],"networks":[47,211,388],"inter-proteins":[49],"interactions.":[50,380],"In":[51,102,190],"particular,":[52],"there":[53],"growing":[56],"body":[57],"evidence":[59,393],"proteins":[61,76,226,384],"performing":[62],"same":[64],"function":[65],"more":[67],"likely":[68],"interact":[70],"with":[71,75,77,252,316,327,361],"each":[72],"other":[73,78],"than":[74,237],"functions.":[79],"However,":[80],"since":[81],"functional":[82,140,311,340,357,396],"annotation":[83,125,141,156,214,229,264,303,313,353],"network":[86,235,245,330],"studied":[90],"separately,":[91],"direct":[93],"relationship":[94],"between":[95,205],"them":[96],"has":[97],"not":[98],"been":[99],"comprehensively":[100],"demonstrated.":[101],"addition":[103],"having":[105],"general":[107],"biological":[108,228,262],"significance,":[109],"such":[110],"demonstration":[111],"would":[112],"further":[113],"validate":[114],"extraction":[117,137,176],"methods":[120],"used":[121,183],"compose":[123],"protein-protein":[127],"interactions":[128],"datasets.":[129],"RESULTS:":[130],"We":[131,220,255,308],"developed":[132],"method":[134],"for":[135,394],"automatic":[136,175],"from":[142,158],"scientific":[143],"text":[144],"based":[145],"on":[146],"Natural":[148],"Language":[149],"Processing":[150],"(NLP)":[151],"technology.":[152,272],"For":[153],"extracted":[157,268,342],"entire":[160],"PubMed,":[161],"we":[162,197],"evaluated":[163],"precision":[165],"recall":[167],"rates,":[168],"compared":[170],"performance":[172],"technology":[177,346],"manual":[181],"curation":[182],"in":[184,207,275,318,364,385],"public":[185,301],"Gene":[186],"Ontology":[187],"(GO)":[188],"annotation.":[189],"second":[192],"part":[193],"our":[195,270],"presentation,":[196],"reported":[198],"large-scale":[200],"investigation":[201],"into":[202],"correspondence":[204],"communities":[206,246,331],"literature-based":[209],"GO":[213,253,261,281,302,312,352,356],"groups":[215,230,282,293],"functionally":[217],"related":[218],"proteins.":[219],"found":[221],"comprehensive":[223],"two-way":[224],"match:":[225],"within":[227,291],"form":[231],"significantly":[232,298],"denser":[233],"linked":[234,244],"clusters":[236],"expected":[238],"by":[239,269,343,378],"chance":[240],"and,":[241],"conversely,":[242],"densely":[243],"exhibit":[247],"pronounced":[249],"non-random":[250],"overlap":[251,326],"groups.":[254],"also":[256],"expanded":[257],"publicly":[259],"available":[260],"process":[263],"using":[265],"relations":[267],"NLP":[271,345],"An":[273],"increase":[274],"number":[277],"size":[279],"without":[283,304],"any":[284],"noticeable":[285],"decrease":[286],"link":[289],"density":[290],"indicated":[294],"this":[296],"expansion":[297],"broadens":[299],"diluting":[305],"quality.":[307],"revealed":[309],"correlates":[314,359],"mostly":[315,360],"clustering":[317,363,382],"physical":[320,366,386],"interaction":[321,367,387],"network,":[323,368],"while":[324],"indirect":[328],"regulatory":[329],"two":[333],"three":[335],"times":[336],"smaller.":[337],"CONCLUSION:":[338],"annotations":[341],"expand":[347],"enrich":[349],"existing":[351],"system.":[354],"The":[355],"modularity":[358],"suggesting":[369],"essential":[372],"role":[373],"structural":[375],"organization":[376],"maintained":[377],"these":[379],"Reciprocally,":[381],"can":[389],"serve":[390],"an":[392],"their":[395],"similarity.":[397]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}