{"id":"https://openalex.org/W2062163602","doi":"https://doi.org/10.1186/1471-2105-9-78","title":"OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression","display_name":"OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression","publication_year":2008,"publication_date":"2008-01-31","ids":{"openalex":"https://openalex.org/W2062163602","doi":"https://doi.org/10.1186/1471-2105-9-78","mag":"2062163602","pmid":"https://pubmed.ncbi.nlm.nih.gov/18237434"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-78","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-78","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-78","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/10.1186/1471-2105-9-78","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041860080","display_name":"Lawrence Hunter","orcid":"https://orcid.org/0000-0003-1455-3370"},"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":true,"raw_author_name":"Lawrence Hunter","raw_affiliation_strings":["Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Larry.Hunter@uchsc.edu","Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Larry.Hunter@uchsc.edu","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083081872","display_name":"Zhiyong Lu","orcid":"https://orcid.org/0000-0001-9998-916X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiyong Lu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA","National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390"]},{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA#TAB#","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009055817","display_name":"James Firby","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"James Firby","raw_affiliation_strings":["PowerSet, Inc., San Francisco, CA, 94107, USA","PowerSet, Inc., San Francisco, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PowerSet, Inc., San Francisco, CA, 94107, USA","institution_ids":[]},{"raw_affiliation_string":"PowerSet, Inc., San Francisco, USA","institution_ids":[]}]},{"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":["Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA","Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017417252","display_name":"H. L. Johnson","orcid":"https://orcid.org/0000-0003-1873-2085"},"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":"Helen L Johnson","raw_affiliation_strings":["Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA","Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067047360","display_name":"Philip V. Ogren","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip V Ogren","raw_affiliation_strings":["Department of Computer Science, University of Colorado, Boulder, CO, 80303, USA","Dept. of Computer Science, Univ. of Colorado, Boulder, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Colorado, Boulder, CO, 80303, USA","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Dept. of Computer Science, Univ. of Colorado, Boulder, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062221063","display_name":"Kevin Bretonnel Cohen","orcid":"https://orcid.org/0000-0003-1749-8290"},"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":"K Bretonnel Cohen","raw_affiliation_strings":["Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA","Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I921990950"]},{"raw_affiliation_string":"Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, USA","institution_ids":["https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5041860080"],"corresponding_institution_ids":["https://openalex.org/I921990950"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":7.7942,"has_fulltext":true,"cited_by_count":154,"citation_normalized_percentile":{"value":0.98199819,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"9","issue":"1","first_page":"78","last_page":"78"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.996999979019165,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.996999979019165,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.000699999975040555,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.7579847574234009},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7187486290931702},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.6405684351921082},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5207255482673645},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.49783873558044434},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.49109578132629395},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4589167535305023},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.43401241302490234},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4319707155227661},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39421576261520386},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37306511402130127},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.24221262335777283},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13577419519424438}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7579847574234009},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7187486290931702},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.6405684351921082},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5207255482673645},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.49783873558044434},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.49109578132629395},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4589167535305023},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.43401241302490234},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4319707155227661},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39421576261520386},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37306511402130127},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.24221262335777283},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13577419519424438},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007722","descriptor_name":"Health Knowledge, Attitudes, Practice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007722","descriptor_name":"Health Knowledge, Attitudes, Practice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007722","descriptor_name":"Health Knowledge, Attitudes, Practice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":"Q000502","qualifier_name":"physiology","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:10.1186/1471-2105-9-78","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-78","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-78","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:18237434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18237434","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2275248","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2275248","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:82586eba5c0545448fd2f5fb6bdbf257","is_oa":false,"landing_page_url":"https://doaj.org/article/82586eba5c0545448fd2f5fb6bdbf257","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 78 (2008)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-78","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-78","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-78","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":[{"display_name":"Quality Education","score":0.5899999737739563,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G147733325","display_name":null,"funder_award_id":"R01-LM-009254","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G1591429387","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/G2289874961","display_name":null,"funder_award_id":"R01-NLM-009254","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G2964837984","display_name":null,"funder_award_id":"R01NLM008111","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"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/W2062163602.pdf","grobid_xml":"https://content.openalex.org/works/W2062163602.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W25333297","https://openalex.org/W37492685","https://openalex.org/W199456390","https://openalex.org/W1546045375","https://openalex.org/W1550258693","https://openalex.org/W1600005654","https://openalex.org/W1608124137","https://openalex.org/W1623698862","https://openalex.org/W1954715867","https://openalex.org/W1965745145","https://openalex.org/W1976097579","https://openalex.org/W1976316416","https://openalex.org/W1981276685","https://openalex.org/W1981492645","https://openalex.org/W1989570518","https://openalex.org/W1999117234","https://openalex.org/W2000844908","https://openalex.org/W2016928406","https://openalex.org/W2020492692","https://openalex.org/W2038721957","https://openalex.org/W2043099927","https://openalex.org/W2044514479","https://openalex.org/W2061166439","https://openalex.org/W2071993998","https://openalex.org/W2079982743","https://openalex.org/W2091803989","https://openalex.org/W2092419931","https://openalex.org/W2093618552","https://openalex.org/W2096489769","https://openalex.org/W2098201295","https://openalex.org/W2103017472","https://openalex.org/W2103427999","https://openalex.org/W2104965688","https://openalex.org/W2112454182","https://openalex.org/W2120433106","https://openalex.org/W2122139846","https://openalex.org/W2122904379","https://openalex.org/W2123273303","https://openalex.org/W2129113459","https://openalex.org/W2137881949","https://openalex.org/W2145946200","https://openalex.org/W2148130205","https://openalex.org/W2150650678","https://openalex.org/W2152698860","https://openalex.org/W2155325862","https://openalex.org/W2155723007","https://openalex.org/W2156930958","https://openalex.org/W2161299591","https://openalex.org/W2162629891","https://openalex.org/W2166057395","https://openalex.org/W2166474856","https://openalex.org/W2167072947","https://openalex.org/W2167289895","https://openalex.org/W2169918010","https://openalex.org/W2169974160","https://openalex.org/W2182888718","https://openalex.org/W2187363965","https://openalex.org/W2549843171","https://openalex.org/W2917056928","https://openalex.org/W2999905431","https://openalex.org/W4205948809","https://openalex.org/W4230872509","https://openalex.org/W4235505822"],"related_works":["https://openalex.org/W842810586","https://openalex.org/W4319940250","https://openalex.org/W2352298027","https://openalex.org/W2092919065","https://openalex.org/W3138801416","https://openalex.org/W4236762297","https://openalex.org/W2369351710","https://openalex.org/W2594363579","https://openalex.org/W2572241437","https://openalex.org/W4379379356"],"abstract_inverted_index":{"BACKGROUND:":[0],"Information":[1],"extraction":[2,60,93,191,208],"(IE)":[3],"efforts":[4,238,249],"are":[5],"widely":[6],"acknowledged":[7],"to":[8,186,188,227,242,251],"be":[9,240],"important":[10,23],"in":[11,20,28,58,64,114,126,145,255],"harnessing":[12],"the":[13,36,53,56,80,164,173,206,220,244],"rapid":[14],"advance":[15],"of":[16,42,55,82,137,150,176,183,198,205,215,232,236,246],"biomedical":[17,177],"knowledge,":[18],"particularly":[19],"areas":[21],"where":[22],"factual":[24],"information":[25,59,92,190,195,207,262],"is":[26,112,210,223,270],"published":[27],"a":[29,110,115,148,228],"diverse":[30,68],"literature.":[31],"Here":[32],"we":[33],"report":[34],"on":[35,122],"design,":[37],"implementation":[38],"and":[39,72,84,87,107,157,250],"several":[40],"evaluations":[41],"OpenDMAP,":[43],"an":[44,74,216],"ontology-driven,":[45],"integrated":[46],"concept":[47],"analysis":[48],"system.":[49],"It":[50],"significantly":[51],"advances":[52,163],"state":[54],"art":[57],"by":[61],"leveraging":[62],"knowledge":[63,221],"ontological":[65],"resources,":[66],"integrating":[67],"text":[69],"processing":[70],"applications,":[71],"using":[73],"expanded":[75],"pattern":[76],"language":[77],"that":[78,109,219,257],"allows":[79],"mixing":[81],"syntactic":[83],"semantic":[85],"elements":[86,214],"variable":[88],"ordering.":[89],"RESULTS:":[90],"OpenDMAP":[91,162,267],"systems":[94,139,256],"were":[95,120],"produced":[96],"for":[97,167,261],"extracting":[98,168,194],"protein":[99],"transport":[100,152],"assertions":[101,105,108],"(transport),":[102],"protein-protein":[103,169],"interaction":[104,155,170],"(interaction)":[106],"gene":[111],"expressed":[113],"cell":[116],"type":[117],"(expression).":[118],"Evaluations":[119],"performed":[121],"each":[123,136],"system,":[124],"resulting":[125],"F-scores":[127],"ranging":[128],"from":[129,172,213],".26-.72":[130],"(precision":[131],".39-.85,":[132],"recall":[133],".16-.85).":[134],"Additionally,":[135],"these":[138,237],"was":[140],"run":[141],"over":[142],"all":[143],"abstracts":[144],"MEDLINE,":[146],"producing":[147],"total":[149],"72,460":[151],"instances,":[153],"265,795":[154],"instances":[156],"176,153":[158],"expression":[159],"instances.":[160],"CONCLUSION:":[161],"performance":[165,184],"standards":[166],"predications":[171],"full":[174],"texts":[175],"research":[178],"articles.":[179],"Furthermore,":[180],"this":[181],"level":[182],"appears":[185],"generalize":[187],"other":[189],"tasks,":[192],"including":[193],"about":[196],"predicates":[197],"more":[199],"than":[200],"two":[201],"arguments.":[202],"The":[203,234,264],"output":[204],"system":[209],"always":[211],"constructed":[212,230],"ontology,":[217],"ensuring":[218],"representation":[222],"grounded":[224],"with":[225],"respect":[226],"carefully":[229],"model":[231],"reality.":[233],"results":[235],"can":[239],"used":[241],"increase":[243],"efficiency":[245],"manual":[247],"curation":[248],"provide":[252],"additional":[253],"features":[254],"integrate":[258],"multiple":[259],"sources":[260],"extraction.":[263],"open":[265],"source":[266],"code":[268],"library":[269],"freely":[271],"available":[272],"at":[273],"http://bionlp.sourceforge.net/":[274]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":33},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":12}],"updated_date":"2026-08-22T07:34:49.880490","created_date":"2025-10-10T00:00:00"}
