{"id":"https://openalex.org/W2112580417","doi":"https://doi.org/10.1186/1752-0509-6-29","title":"Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks","display_name":"Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks","publication_year":2012,"publication_date":"2012-05-01","ids":{"openalex":"https://openalex.org/W2112580417","doi":"https://doi.org/10.1186/1752-0509-6-29","mag":"2112580417","pmid":"https://pubmed.ncbi.nlm.nih.gov/22548703"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-29","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-29","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-29","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-29","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042595420","display_name":"Daniel C. Kirouac","orcid":"https://orcid.org/0000-0002-9601-1913"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel C Kirouac","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"funder","lineage":["https://openalex.org/I87048295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK, CB10 1SD"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK, CB10 1SD","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024274332","display_name":"Jennifer L. Swantek","orcid":null},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer Swantek","raw_affiliation_strings":["Immunology & Inflammation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, 06877-0368, USA"],"affiliations":[{"raw_affiliation_string":"Immunology & Inflammation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, 06877-0368, USA","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002748007","display_name":"John M. Burke","orcid":"https://orcid.org/0000-0002-1412-5539"},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John M Burke","raw_affiliation_strings":["Immunology & Inflammation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, 06877-0368, USA"],"affiliations":[{"raw_affiliation_string":"Immunology & Inflammation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, 06877-0368, USA","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060106170","display_name":"Douglas A. Lauffenburger","orcid":"https://orcid.org/0000-0002-0050-989X"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas A Lauffenburger","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063426870","display_name":"Peter K. Sorger","orcid":"https://orcid.org/0000-0002-3364-1838"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter K Sorger","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5063426870"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210155419"],"apc_list":null,"apc_paid":null,"fwci":15.2291,"has_fulltext":true,"cited_by_count":79,"citation_normalized_percentile":{"value":0.99411562,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"6","issue":"1","first_page":"29","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.991599977016449,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.7760791778564453},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6380189657211304},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6339765191078186},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.5172408223152161},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49757006764411926},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.49033594131469727},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.4395255744457245},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3991546034812927},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12028554081916809}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.7760791778564453},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6380189657211304},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6339765191078186},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.5172408223152161},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49757006764411926},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.49033594131469727},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4395255744457245},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3991546034812927},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12028554081916809},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"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":"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":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","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":"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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-6-29","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-29","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-29","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:22548703","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22548703","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 systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:43b84b27e58248a38238d86d95f03f84","is_oa":true,"landing_page_url":"https://doaj.org/article/43b84b27e58248a38238d86d95f03f84","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 6, Iss 1, p 29 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2439989","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436686","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-29","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-29","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-29","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.6399999856948853}],"awards":[{"id":"https://openalex.org/G733519322","display_name":null,"funder_award_id":"U54-HG006097","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112580417.pdf","grobid_xml":"https://content.openalex.org/works/W2112580417.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1499561015","https://openalex.org/W1644749979","https://openalex.org/W1964321121","https://openalex.org/W1964343149","https://openalex.org/W1969709265","https://openalex.org/W1977943300","https://openalex.org/W1980492226","https://openalex.org/W1985911638","https://openalex.org/W1991980854","https://openalex.org/W1995996823","https://openalex.org/W2006944023","https://openalex.org/W2010636476","https://openalex.org/W2010890545","https://openalex.org/W2011736622","https://openalex.org/W2017987256","https://openalex.org/W2018953646","https://openalex.org/W2023120194","https://openalex.org/W2034269086","https://openalex.org/W2038682262","https://openalex.org/W2040827479","https://openalex.org/W2043364653","https://openalex.org/W2046783953","https://openalex.org/W2051310004","https://openalex.org/W2054035764","https://openalex.org/W2061767013","https://openalex.org/W2068999270","https://openalex.org/W2069728939","https://openalex.org/W2070658593","https://openalex.org/W2075161553","https://openalex.org/W2077997913","https://openalex.org/W2096595244","https://openalex.org/W2104039751","https://openalex.org/W2105372361","https://openalex.org/W2107591926","https://openalex.org/W2108726522","https://openalex.org/W2113613985","https://openalex.org/W2114830914","https://openalex.org/W2123973944","https://openalex.org/W2126606094","https://openalex.org/W2126841263","https://openalex.org/W2129937975","https://openalex.org/W2131989143","https://openalex.org/W2132997183","https://openalex.org/W2134046693","https://openalex.org/W2135738422","https://openalex.org/W2137304236","https://openalex.org/W2138155367","https://openalex.org/W2139348859","https://openalex.org/W2141152663","https://openalex.org/W2142302575","https://openalex.org/W2143877670","https://openalex.org/W2143969914","https://openalex.org/W2144014661","https://openalex.org/W2144092904","https://openalex.org/W2145899141","https://openalex.org/W2146883006","https://openalex.org/W2148866736","https://openalex.org/W2149363804","https://openalex.org/W2153258203","https://openalex.org/W2155037464","https://openalex.org/W2159241859","https://openalex.org/W2159675211","https://openalex.org/W2163480486","https://openalex.org/W2164298117","https://openalex.org/W2167334954","https://openalex.org/W2170272380","https://openalex.org/W2171283231","https://openalex.org/W2296679604","https://openalex.org/W4211017114","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2063905494","https://openalex.org/W3214348031","https://openalex.org/W2101998831","https://openalex.org/W2158714033","https://openalex.org/W1922372990","https://openalex.org/W2032694615","https://openalex.org/W2153577994","https://openalex.org/W2086904135","https://openalex.org/W2043924719","https://openalex.org/W2127864418"],"abstract_inverted_index":{"Wide":[0],"inconsistencies":[1,36],"among":[2],"interaction":[3],"databases,":[4,57],"pathway":[5,18],"annotations,":[6,74],"and":[7,10,26,44,127],"the":[8,59,131],"numbers":[9],"identities":[11],"of":[12,46,61,72,139],"nodes":[13],"associated":[14],"with":[15,103],"a":[16,20,70,87,107],"given":[17],"pose":[19],"major":[21],"challenge":[22],"for":[23,54,119],"deriving":[24],"causal":[25],"mechanistic":[27,122],"insight":[28],"from":[29,84,106],"network":[30,101],"graphs.":[31],"We":[32],"speculate":[33],"that":[34],"these":[35],"are":[37],"at":[38],"least":[39],"partially":[40],"attributable":[41],"to":[42,79,97],"cell,":[43],"context-specificity":[45],"cellular":[47],"signal":[48,110,140],"transduction,":[49],"which":[50],"is":[51,64,76,95],"largely":[52],"unaccounted":[53],"in":[55,121,137],"available":[56],"but":[58],"absence":[60],"standardized":[62],"vocabularies":[63],"an":[65],"additional":[66],"confounding":[67],"factor.":[68],"As":[69],"result":[71],"discrepant":[73],"it":[75,94],"very":[77],"difficult":[78],"identify":[80],"biologically":[81],"meaningful":[82],"pathways":[83,134],"interactome":[85],"networks":[86,116],"priori.":[88],"However,":[89],"by":[90],"incorporating":[91],"prior":[92],"knowledge,":[93],"possible":[96],"successively":[98],"build":[99],"out":[100],"complexity":[102,115],"high":[104],"confidence":[105],"simple":[108,132],"linear":[109,133],"transduction":[111],"scaffold.":[112],"Such":[113],"reduced":[114],"appear":[117],"suitable":[118],"use":[120],"models":[123],"while":[124],"being":[125],"richer":[126],"better":[128],"justified":[129],"than":[130],"usually":[135],"depicted":[136],"diagrams":[138],"transduction.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":22},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}