{"id":"https://openalex.org/W1989258321","doi":"https://doi.org/10.1109/bibe.2007.4375678","title":"XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes","display_name":"XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes","publication_year":2007,"publication_date":"2007-10-01","ids":{"openalex":"https://openalex.org/W1989258321","doi":"https://doi.org/10.1109/bibe.2007.4375678","mag":"1989258321","pmid":"https://pubmed.ncbi.nlm.nih.gov/21464833"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2007.4375678","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375678","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3039882","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107139754","display_name":"Michael L. Blinov","orcid":"https://orcid.org/0000-0002-9363-9705"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael L. Blinov","raw_affiliation_strings":["Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, USA","University of Connecticut Health Center, Farmington,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, USA","institution_ids":["https://openalex.org/I75929689"]},{"raw_affiliation_string":"University of Connecticut Health Center, Farmington,","institution_ids":["https://openalex.org/I75929689"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066544731","display_name":"Ion I. Moraru","orcid":"https://orcid.org/0000-0002-3746-9676"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75929689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ion I. Moraru","raw_affiliation_strings":["Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, USA","University of Connecticut Health Center, Farmington,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, USA","institution_ids":["https://openalex.org/I75929689"]},{"raw_affiliation_string":"University of Connecticut Health Center, Farmington,","institution_ids":["https://openalex.org/I75929689"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I75929689"],"apc_list":null,"apc_paid":null,"fwci":0.8338,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.72888955,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"4230","issue":null,"first_page":"987","last_page":"994"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9976000189781189,"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":0.9965999722480774,"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/sbml","display_name":"SBML","score":0.9057901501655579},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.766954779624939},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.7433412075042725},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7328568696975708},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.698138952255249},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5698655247688293},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5374006032943726},{"id":"https://openalex.org/keywords/combinatorial-explosion","display_name":"Combinatorial explosion","score":0.4187326729297638},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3477133810520172},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.32485443353652954},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15410128235816956},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10690239071846008},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.09134683012962341}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9057901501655579},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.766954779624939},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.7433412075042725},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7328568696975708},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.698138952255249},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5698655247688293},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5374006032943726},{"id":"https://openalex.org/C115908005","wikidata":"https://www.wikidata.org/wiki/Q2668364","display_name":"Combinatorial explosion","level":2,"score":0.4187326729297638},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3477133810520172},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.32485443353652954},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15410128235816956},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10690239071846008},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09134683012962341},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"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/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1109/bibe.2007.4375678","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375678","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmid:21464833","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21464833","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":"Proceedings. IEEE International Symposium on Bioinformatics and Bioengineering","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3039882","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3039882","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Int Symp Bioinformatics Bioeng","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.373.2478","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.373.2478","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.ccam.uchc.edu/mblinov/library/blinov-XML.pdf","raw_type":"text"},{"id":"pmh:oai:digitalcommons.lib.uconn.edu:uchcres_articles-1069","is_oa":false,"landing_page_url":"https://digitalcommons.lib.uconn.edu/uchcres_articles/70","pdf_url":null,"source":{"id":"https://openalex.org/S4377196438","display_name":"OpenCommons - UConn (University of Connecticut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I140172145","host_organization_name":"University of Connecticut","host_organization_lineage":["https://openalex.org/I140172145"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"UCHC Articles - Research","raw_type":"text"},{"id":"pmh:oai:opencommons.uconn.edu:uchcres_articles-1069","is_oa":false,"landing_page_url":"https://opencommons.uconn.edu/uchcres_articles/70","pdf_url":null,"source":{"id":"https://openalex.org/S4377196438","display_name":"OpenCommons - UConn (University of Connecticut)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I140172145","host_organization_name":"University of Connecticut","host_organization_lineage":["https://openalex.org/I140172145"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"UCHC Articles - Research","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:3039882","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3039882","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Int Symp Bioinformatics Bioeng","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1610795535","display_name":null,"funder_award_id":"P41 RR013186","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G224078746","display_name":null,"funder_award_id":"U54-RR022232","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G4798651605","display_name":null,"funder_award_id":"R01GM076570","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W323766208","https://openalex.org/W1607824205","https://openalex.org/W1660272337","https://openalex.org/W1977290213","https://openalex.org/W1984886691","https://openalex.org/W2034492556","https://openalex.org/W2034994414","https://openalex.org/W2040890820","https://openalex.org/W2069941324","https://openalex.org/W2082874501","https://openalex.org/W2097468167","https://openalex.org/W2111682035","https://openalex.org/W2139941949","https://openalex.org/W2145080853","https://openalex.org/W2149999958","https://openalex.org/W2150908245","https://openalex.org/W2151251638","https://openalex.org/W2163493106","https://openalex.org/W2165700291","https://openalex.org/W3150331393","https://openalex.org/W4251538155","https://openalex.org/W6636466610"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W3041939341"],"abstract_inverted_index":{"Multi-state":[0],"molecules":[1,13,31,53],"and":[2,30,87],"multi-component":[3],"complexes":[4,37],"are":[5,66,81],"commonly":[6],"involved":[7],"in":[8],"cellular":[9],"signaling.":[10],"Accounting":[11],"for":[12,98,113],"that":[14,23,32,94],"have":[15],"multiple":[16,28,40],"potential":[17],"states,":[18],"such":[19],"as":[20],"a":[21,111],"protein":[22],"may":[24],"be":[25,83,96],"phosphorylated":[26],"on":[27],"residues,":[29],"combine":[33],"to":[34,69,82],"form":[35,110],"heterogeneous":[36],"located":[38],"among":[39],"compartments,":[41],"generates":[42],"an":[43],"effect":[44],"of":[45,57,117],"combinatorial":[46,72],"complexity.":[47,73],"Models":[48],"involving":[49],"relatively":[50],"few":[51],"signaling":[52],"can":[54,95],"include":[55],"thousands":[56],"distinct":[58],"chemical":[59],"species.":[60],"Several":[61],"software":[62],"tools":[63,75],"(StochSim,":[64],"BioNetGen)":[65],"already":[67],"available":[68],"deal":[70],"with":[71],"Such":[74],"need":[76],"information":[77],"standards":[78],"if":[79],"models":[80],"shared,":[84],"jointly":[85],"evaluated":[86],"developed.":[88],"Here":[89],"we":[90],"discuss":[91],"XML":[92],"conventions":[93],"adopted":[97],"modeling":[99],"biochemical":[100],"reaction":[101,106],"networks":[102],"described":[103],"by":[104],"user-specified":[105],"rules.":[107],"These":[108],"could":[109],"basis":[112],"possible":[114],"future":[115],"extensions":[116],"the":[118],"Systems":[119],"Biology":[120],"Markup":[121],"Language":[122],"(SBML).":[123]},"counts_by_year":[],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}