{"id":"https://openalex.org/W2134340731","doi":"https://doi.org/10.1093/bib/bbt058","title":"Extracting reaction networks from databases-opening Pandora's box","display_name":"Extracting reaction networks from databases-opening Pandora's box","publication_year":2013,"publication_date":"2013-08-14","ids":{"openalex":"https://openalex.org/W2134340731","doi":"https://doi.org/10.1093/bib/bbt058","mag":"2134340731","pmid":"https://pubmed.ncbi.nlm.nih.gov/23946492"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbt058","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt058","pdf_url":"https://academic.oup.com/bib/article-pdf/15/6/973/432455/bbt058.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/15/6/973/432455/bbt058.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054647246","display_name":"Liam G. Fearnley","orcid":"https://orcid.org/0000-0003-2198-5411"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"L. G. Fearnley","raw_affiliation_strings":["Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","Queensland Node of Metabolomics Australia","Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland"],"affiliations":[{"raw_affiliation_string":"Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Queensland Node of Metabolomics Australia","institution_ids":[]},{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","institution_ids":[]},{"raw_affiliation_string":"Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018252802","display_name":"Melissa J. Davis","orcid":"https://orcid.org/0000-0003-4864-7033"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"M. J. Davis","raw_affiliation_strings":["Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","Queensland Node of Metabolomics Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","institution_ids":[]},{"raw_affiliation_string":"Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","institution_ids":[]},{"raw_affiliation_string":"Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Queensland Node of Metabolomics Australia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023552489","display_name":"Mark A. Ragan","orcid":"https://orcid.org/0000-0003-1672-7020"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"M. A. Ragan","raw_affiliation_strings":["Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","Queensland Node of Metabolomics Australia","Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia"],"affiliations":[{"raw_affiliation_string":"Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","institution_ids":[]},{"raw_affiliation_string":"Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","institution_ids":[]},{"raw_affiliation_string":"Queensland Node of Metabolomics Australia","institution_ids":[]},{"raw_affiliation_string":"Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061172047","display_name":"Lars K. Nielsen","orcid":"https://orcid.org/0000-0001-8191-3511"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"L. K. Nielsen","raw_affiliation_strings":["Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","Queensland Node of Metabolomics Australia"],"affiliations":[{"raw_affiliation_string":"Synthetic Biology Group at the Australian Institute for Bioengineering and Nanotechnology (AIBN), is Professor of Biological Engineering in the School of Chemical Engineering at The University of Queensland and heads the","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Computational Biology division of the Institute for Molecular Bioscience at The University of Queensland","institution_ids":[]},{"raw_affiliation_string":"Computational Biology at the Institute for Molecular Bioscience, professor in the School of Information Technology and Electrical Engineering at The University of Queensland and Director of the Australian Research Council Centre of Excellence in Bioinformatics","institution_ids":[]},{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Queensland Node of Metabolomics Australia","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5018252802"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.2995,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.63066124,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"15","issue":"6","first_page":"973","last_page":"983"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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":0.9994000196456909,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9990000128746033,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9990000128746033,"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/computer-science","display_name":"Computer science","score":0.7657774686813354},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.7092307806015015},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.47375398874282837},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.47363510727882385},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.45963603258132935},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.45482686161994934},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.4417978823184967},{"id":"https://openalex.org/keywords/crosstalk","display_name":"Crosstalk","score":0.41637617349624634},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.41429704427719116},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3893032371997833},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36194050312042236},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.15305709838867188},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1408044695854187},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.09372028708457947}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7657774686813354},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.7092307806015015},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.47375398874282837},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.47363510727882385},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.45963603258132935},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.45482686161994934},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.4417978823184967},{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.41637617349624634},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.41429704427719116},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3893032371997833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36194050312042236},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.15305709838867188},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1408044695854187},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.09372028708457947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bbt058","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt058","pdf_url":"https://academic.oup.com/bib/article-pdf/15/6/973/432455/bbt058.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23946492","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23946492","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/263628","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/263628","pdf_url":"http://hdl.handle.net/11343/263628","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1004.1088","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1004.1088","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bib.oxfordjournals.org/content/15/6/973.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1009.437","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1009.437","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://europepmc.org/backend/ptpmcrender.fcgi?accid%3DPMC4239801%26blobtype%3Dpdf","raw_type":"text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:319586","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4239801","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4239801","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbt058","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt058","pdf_url":"https://academic.oup.com/bib/article-pdf/15/6/973/432455/bbt058.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1884015662","display_name":null,"funder_award_id":"DP110103384","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G2218789016","display_name":null,"funder_award_id":"LM007885","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134340731.pdf","grobid_xml":"https://content.openalex.org/works/W2134340731.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1964362163","https://openalex.org/W1969709265","https://openalex.org/W1972429412","https://openalex.org/W1983196674","https://openalex.org/W1996529795","https://openalex.org/W1996572869","https://openalex.org/W1998767819","https://openalex.org/W1999824494","https://openalex.org/W1999895438","https://openalex.org/W2006933206","https://openalex.org/W2012284471","https://openalex.org/W2024653949","https://openalex.org/W2041652393","https://openalex.org/W2056365020","https://openalex.org/W2069157810","https://openalex.org/W2081781433","https://openalex.org/W2082773579","https://openalex.org/W2087563523","https://openalex.org/W2089465951","https://openalex.org/W2092755129","https://openalex.org/W2095304455","https://openalex.org/W2096595244","https://openalex.org/W2096766502","https://openalex.org/W2096824774","https://openalex.org/W2100980426","https://openalex.org/W2104108767","https://openalex.org/W2114124738","https://openalex.org/W2116398954","https://openalex.org/W2118053673","https://openalex.org/W2120433529","https://openalex.org/W2124479173","https://openalex.org/W2125904022","https://openalex.org/W2129110097","https://openalex.org/W2130410032","https://openalex.org/W2132218677","https://openalex.org/W2132992030","https://openalex.org/W2142302575","https://openalex.org/W2150908245","https://openalex.org/W2151784069","https://openalex.org/W2152172878","https://openalex.org/W2159482845","https://openalex.org/W2163500926","https://openalex.org/W2165090547","https://openalex.org/W4210347168","https://openalex.org/W4233334497","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2120890012","https://openalex.org/W2101315668","https://openalex.org/W2155492529","https://openalex.org/W2300879143","https://openalex.org/W4283723149","https://openalex.org/W4252504573","https://openalex.org/W2028703400","https://openalex.org/W2286239702","https://openalex.org/W2089305230","https://openalex.org/W782572168"],"abstract_inverted_index":{"Large":[0],"quantities":[1],"of":[2,7,40,62,86,96,136,143,170],"information":[3,53],"describing":[4,101],"the":[5,19,38,50,71,84,92,119,141,159,168],"mechanisms":[6],"biological":[8,52],"pathways":[9,31,63],"continue":[10],"to":[11,36,64,166],"be":[12],"collected":[13],"in":[14,25,33,55,114,140,163],"publicly":[15],"available":[16],"databases.":[17],"At":[18],"same":[20],"time,":[21],"experiments":[22,41],"have":[23,127],"increased":[24],"scale,":[26],"and":[27,42,69,74,118,139],"biologists":[28],"increasingly":[29],"use":[30],"defined":[32],"online":[34],"databases":[35],"interpret":[37],"results":[39],"generate":[43],"hypotheses.":[44],"Emerging":[45],"computational":[46,148],"techniques":[47],"that":[48,110],"exploit":[49],"rich":[51],"captured":[54],"reaction":[56,67,99,131,154],"systems":[57],"require":[58],"formal":[59],"standardized":[60],"descriptions":[61],"extract":[65],"these":[66],"networks":[68,155],"avoid":[70],"alternative:":[72],"time-consuming":[73],"largely":[75],"manual":[76],"literature-based":[77],"network":[78,100,132],"reconstruction.":[79],"Here,":[80],"we":[81,161],"systematically":[82],"evaluate":[83],"effects":[85],"commonly":[87],"used":[88],"knowledge":[89,125],"representations":[90,121],"on":[91],"seemingly":[93],"simple":[94],"task":[95],"extracting":[97],"a":[98,105],"signal":[102],"transduction":[103],"from":[104,151],"pathway":[106,120,137,172],"database.":[107],"We":[108],"show":[109],"this":[111,164],"process":[112],"is":[113],"fact":[115],"surprisingly":[116],"difficult,":[117],"adopted":[122],"by":[123],"various":[124],"bases":[126],"dramatic":[128],"consequences":[129],"for":[130],"extraction,":[133],"connectivity,":[134],"capture":[135],"crosstalk":[138],"modelling":[142],"cell-cell":[144],"interactions.":[145],"Researchers":[146],"constructing":[147],"models":[149],"built":[150],"automatically":[152],"extracted":[153],"must":[156],"therefore":[157],"consider":[158],"issues":[160],"outline":[162],"review":[165],"maximize":[167],"value":[169],"existing":[171],"knowledge.":[173]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
