{"id":"https://openalex.org/W2088901672","doi":"https://doi.org/10.1186/1471-2105-12-45","title":"Hierarchical graphs for rule-based modeling of biochemical systems","display_name":"Hierarchical graphs for rule-based modeling of biochemical systems","publication_year":2011,"publication_date":"2011-02-02","ids":{"openalex":"https://openalex.org/W2088901672","doi":"https://doi.org/10.1186/1471-2105-12-45","mag":"2088901672","pmid":"https://pubmed.ncbi.nlm.nih.gov/21288338"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-45","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-45","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-45","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/10.1186/1471-2105-12-45","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010255615","display_name":"Nathan Lemons","orcid":"https://orcid.org/0000-0002-5804-6672"},"institutions":[{"id":"https://openalex.org/I198945027","display_name":"Central European University","ror":"https://ror.org/02zx40v98","country_code":"AT","type":"education","lineage":["https://openalex.org/I198945027"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Nathan W Lemons","raw_affiliation_strings":["Department of Mathematics and its Applications, Central European University, H-1051 Budapest, Hungary","Department of Mathematics and Its Applications , Central European University , Budapest , Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and its Applications, Central European University, H-1051 Budapest, Hungary","institution_ids":["https://openalex.org/I198945027"]},{"raw_affiliation_string":"Department of Mathematics and Its Applications , Central European University , Budapest , Hungary","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043402436","display_name":"Bin Hu","orcid":"https://orcid.org/0000-0002-0278-8466"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Hu","raw_affiliation_strings":["Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA","Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Department of Biology, University of New Mexico, Albuquerque, USA","Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory,Los Alamos,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Department of Biology, University of New Mexico, Albuquerque, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory,Los Alamos,USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016126519","display_name":"William S. Hlavacek","orcid":"https://orcid.org/0000-0003-4383-8711"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William S Hlavacek","raw_affiliation_strings":["Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA","Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Department of Biology, University of New Mexico, Albuquerque, USA","Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Department of Biology, University of New Mexico, Albuquerque, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5016126519"],"corresponding_institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I169521973"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9735,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.73937386,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"12","issue":"1","first_page":"45","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6656000018119812,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6656000018119812,"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":0.04960000142455101,"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/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.04100000113248825,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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":0.5722083449363708},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4922899305820465},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.43722572922706604}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5722083449363708},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4922899305820465},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.43722572922706604},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-12-45","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-45","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-45","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:21288338","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21288338","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:osti.gov:1626281","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626281","pdf_url":"https://www.osti.gov/servlets/purl/1626281","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:390bdc341896419e8d51bd53010dca58","is_oa":false,"landing_page_url":"https://doaj.org/article/390bdc341896419e8d51bd53010dca58","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 12, Iss 1, p 45 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3152790","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3152790","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:10.1186/1471-2105-12-45","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-45","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-45","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/G2502972270","display_name":null,"funder_award_id":"GM085273","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G286898171","display_name":null,"funder_award_id":"DE-AC52-06NA2-5396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3055345441","display_name":null,"funder_award_id":"GM085273","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4883031359","display_name":null,"funder_award_id":"GM076570","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5657628048","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5713387433","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G928841278","display_name":null,"funder_award_id":"contract DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2088901672.pdf","grobid_xml":"https://content.openalex.org/works/W2088901672.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W216444324","https://openalex.org/W323766208","https://openalex.org/W1586735752","https://openalex.org/W1607824205","https://openalex.org/W1618519163","https://openalex.org/W1660272337","https://openalex.org/W1859573897","https://openalex.org/W1964538907","https://openalex.org/W1973322735","https://openalex.org/W1974974415","https://openalex.org/W1975507400","https://openalex.org/W1977290213","https://openalex.org/W1977306646","https://openalex.org/W1980843814","https://openalex.org/W1986397618","https://openalex.org/W1986649132","https://openalex.org/W1989305528","https://openalex.org/W1990600049","https://openalex.org/W1996984709","https://openalex.org/W2010152893","https://openalex.org/W2013245328","https://openalex.org/W2013817486","https://openalex.org/W2016291752","https://openalex.org/W2016493782","https://openalex.org/W2028161249","https://openalex.org/W2030205108","https://openalex.org/W2034492556","https://openalex.org/W2035562653","https://openalex.org/W2040860090","https://openalex.org/W2042629507","https://openalex.org/W2047331390","https://openalex.org/W2053799953","https://openalex.org/W2054047789","https://openalex.org/W2069941324","https://openalex.org/W2072499270","https://openalex.org/W2081098704","https://openalex.org/W2082620735","https://openalex.org/W2082874501","https://openalex.org/W2094358340","https://openalex.org/W2099015579","https://openalex.org/W2099693848","https://openalex.org/W2104655345","https://openalex.org/W2105038431","https://openalex.org/W2117633759","https://openalex.org/W2120824302","https://openalex.org/W2121811364","https://openalex.org/W2123121534","https://openalex.org/W2126359798","https://openalex.org/W2135354983","https://openalex.org/W2137561154","https://openalex.org/W2144063122","https://openalex.org/W2144114582","https://openalex.org/W2145006655","https://openalex.org/W2145080853","https://openalex.org/W2151251638","https://openalex.org/W2152529416","https://openalex.org/W2157989234","https://openalex.org/W2159629828","https://openalex.org/W2163493106","https://openalex.org/W2165700291","https://openalex.org/W2165714871","https://openalex.org/W2166987747","https://openalex.org/W2169193349","https://openalex.org/W2175715045","https://openalex.org/W2411943800","https://openalex.org/W2412770081","https://openalex.org/W2416112119","https://openalex.org/W2611943439","https://openalex.org/W3102875255","https://openalex.org/W4251538155"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2350278424","https://openalex.org/W2071432835","https://openalex.org/W4234371507","https://openalex.org/W4299534542","https://openalex.org/W1628824497","https://openalex.org/W4239401009","https://openalex.org/W2053441600","https://openalex.org/W1990401748","https://openalex.org/W2047586841"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,196],"rule-based":[2,291,313],"modeling,":[3],"graphs":[4,134,149,189,231,236,265,285,305],"are":[5,48],"used":[6,49,106,152,224],"to":[7,50,107,135,153,193,225,229,235],"represent":[8,51,136],"molecules:":[9],"a":[10,14,17,19,27,33,39,64,71,75,78,82,92,119,200,204],"colored":[11],"vertex":[12,20,79],"represents":[13,22,32,63,81],"component":[15],"of":[16,26,38,60,66,77,84,91,97,115,125,132,143,159,165,202,214,258,271,286,303,312],"molecule,":[18],"attribute":[21,80],"the":[23,42,88,112,130,156,160,168,174,215,244,259,283,295,300],"internal":[24,89],"state":[25,90],"component,":[28],"and":[29,70,141,163,173,207,246,273,309],"an":[30,61,100,256],"edge":[31,62,239],"bond":[34],"between":[35,243],"components.":[36],"Components":[37],"molecule":[40],"share":[41],"same":[43],"color.":[44],"Furthermore,":[45],"graph-rewriting":[46],"rules":[47,98],"molecular":[52,93,116],"interactions.":[53],"A":[54,95],"rule":[55,72],"that":[56,73,86,103,183],"specifies":[57,74],"addition":[58],"(removal)":[59],"class":[65,83],"association":[67],"(dissociation)":[68],"reactions,":[69],"change":[76],"reactions":[85],"affect":[87],"component.":[94],"set":[96],"comprises":[99],"executable":[101],"model":[102,126],"can":[104,150,190,222],"be":[105,151,191,223],"determine,":[108],"through":[109],"various":[110],"means,":[111],"system-level":[113],"dynamics":[114],"interactions":[117],"in":[118],"biochemical":[120],"system.":[121],"RESULTS:":[122],"For":[123],"purposes":[124],"annotation,":[127],"we":[128,198,219,254],"propose":[129],"use":[131,302],"hierarchical":[133,148,194,230,304],"structural":[137,157],"relationships":[138],"among":[139],"components":[140,162,280],"subcomponents":[142,164],"molecules.":[144],"We":[145,180],"illustrate":[146],"how":[147],"naturally":[154],"document":[155],"organization":[158],"functional":[161,279],"two":[166],"proteins:":[167],"protein":[169],"tyrosine":[170],"kinase":[171],"Lck":[172],"T":[175],"cell":[176],"receptor":[177],"(TCR)":[178],"complex.":[179],"also":[181],"show":[182],"computational":[184],"methods":[185],"developed":[186],"for":[187,252,289],"regular":[188,284],"applied":[192],"graphs.":[195],"particular,":[197],"describe":[199],"generalization":[201],"Nauty,":[203],"graph":[205],"isomorphism":[206],"canonical":[208,227],"labeling":[209],"algorithm.":[210,262],"The":[211,241],"generalized":[212],"version":[213],"Nauty":[216,245],"procedure,":[217],"which":[218],"call":[220],"HNauty,":[221],"assign":[226],"labels":[228],"or":[232],"more":[233,267],"generally":[234],"with":[237,277],"multiple":[238,278],"types.":[240],"difference":[242],"HNauty":[247,261],"procedures":[248],"is":[249],"minor,":[250],"but":[251],"completeness,":[253],"provide":[255,266],"explanation":[257],"entire":[260],"CONCLUSIONS:":[263],"Hierarchical":[264],"intuitive":[268],"formal":[269],"representations":[270],"proteins":[272],"other":[274],"structured":[275],"molecules":[276],"than":[281],"do":[282],"current":[287],"languages":[288],"specifying":[290],"models,":[292],"such":[293],"as":[294],"BioNetGen":[296],"language":[297],"(BNGL).":[298],"Thus,":[299],"proposed":[301],"should":[306],"promote":[307],"clarity":[308],"better":[310],"understanding":[311],"models.":[314]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}