{"id":"https://openalex.org/W2121034256","doi":"https://doi.org/10.1038/npre.2009.3724","title":"Systems Biology Graphical Notation: Activity Flow language Level 1","display_name":"Systems Biology Graphical Notation: Activity Flow language Level 1","publication_year":2009,"publication_date":"2009-09-07","ids":{"openalex":"https://openalex.org/W2121034256","doi":"https://doi.org/10.1038/npre.2009.3724","mag":"2121034256"},"language":"en","primary_location":{"id":"doi:10.1038/npre.2009.3724","doi":"https://doi.org/10.1038/npre.2009.3724","is_oa":true,"landing_page_url":"https://doi.org/10.1038/npre.2009.3724","pdf_url":"https://www.nature.com/articles/npre.2009.3724.1.pdf","source":{"id":"https://openalex.org/S48744551","display_name":"Nature Precedings","issn_l":"1756-0357","issn":["1756-0357"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Precedings","raw_type":"journal-article"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.nature.com/articles/npre.2009.3724.1.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060575386","display_name":"Huaiyu Mi","orcid":"https://orcid.org/0000-0001-8721-202X","observed_orcids":["https://orcid.org/0000-0001-8721-202X"]},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Huaiyu Mi","raw_affiliation_strings":["SRI International, USA","SRI International, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SRI International, USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"SRI International, USA#TAB#","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060575386","display_name":"Huaiyu Mi","orcid":"https://orcid.org/0000-0001-8721-202X","observed_orcids":["https://orcid.org/0000-0001-8721-202X"]},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]},{"id":"https://openalex.org/I4210127902","display_name":"Leibniz-Institut f\u00fcr Pflanzengenetik und Kulturpflanzenforschung (IPK)","ror":"https://ror.org/02skbsp27","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127902"]},{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Huaiyu Mi","raw_affiliation_strings":["SRI International, USA","IPK Gatersleben & MLU Halle, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SRI International, USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"IPK Gatersleben & MLU Halle, Germany","institution_ids":["https://openalex.org/I4210127902","https://openalex.org/I68956291"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160415807","display_name":"Falk Schreiber","orcid":null,"observed_orcids":[]},"institutions":[{"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"]},{"id":"https://openalex.org/I4210127902","display_name":"Leibniz-Institut f\u00fcr Pflanzengenetik und Kulturpflanzenforschung (IPK)","ror":"https://ror.org/02skbsp27","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210127902"]},{"id":"https://openalex.org/I68956291","display_name":"Martin Luther University Halle-Wittenberg","ror":"https://ror.org/05gqaka33","country_code":"DE","type":"education","lineage":["https://openalex.org/I68956291"]}],"countries":["DE","GB"],"is_corresponding":false,"raw_author_name":"Falk Schreiber","raw_affiliation_strings":["IPK Gatersleben & MLU Halle, Germany","EMBL European Bioinformatics Institute, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IPK Gatersleben & MLU Halle, Germany","institution_ids":["https://openalex.org/I4210127902","https://openalex.org/I68956291"]},{"raw_affiliation_string":"EMBL European Bioinformatics Institute, UK,","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160449316","display_name":"Nicolas Le Nov\u00e9re","orcid":null,"observed_orcids":[]},"institutions":[{"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"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicolas Le Nov\u00e9re","raw_affiliation_strings":["EMBL European Bioinformatics Institute, UK","CSBE, University of Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL European Bioinformatics Institute, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"CSBE, University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160409738","display_name":"Stuart Moodie","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stuart Moodie","raw_affiliation_strings":["CSBE, University of Edinburgh, UK","University of Edinburgh (UK)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSBE, University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Edinburgh (UK)","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020746275","display_name":"Anatoly Sorokin","orcid":"https://orcid.org/0000-0002-0047-0606","observed_orcids":["https://orcid.org/0000-0002-0047-0606"]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anatoly Sorokin","raw_affiliation_strings":["University of Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060575386"],"corresponding_institution_ids":["https://openalex.org/I1298353152","https://openalex.org/I4210127902","https://openalex.org/I68956291"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8978999853134155,"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":0.8978999853134155,"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":0.07699999958276749,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.006599999964237213,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/systems-biology-graphical-notation","display_name":"SBGN","score":0.9959999918937683},{"id":"https://openalex.org/keywords/graphical-notation","display_name":"graphical notation","score":0.597000002861023},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"synthetic biology","score":0.6349999904632568},{"id":"https://openalex.org/keywords/standardization","display_name":"standardization","score":0.5049999952316284},{"id":"https://openalex.org/keywords/process-description","display_name":"process description","score":0.5759999752044678},{"id":"https://openalex.org/keywords/entity-relationships","display_name":"entity relationships","score":0.996999979019165},{"id":"https://openalex.org/keywords/signaling-pathways","display_name":"signaling pathways","score":0.7480000257492065},{"id":"https://openalex.org/keywords/metabolic-networks","display_name":"metabolic networks","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C45357846","wikidata":"https://www.wikidata.org/wiki/Q2001982","display_name":"Notation","level":2,"score":0.7388098835945129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7195322513580322},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5072609782218933},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4883853793144226},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4272938072681427},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.42232781648635864},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3757272958755493},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.21465444564819336},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.20896857976913452},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1513138711452484},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.12145444750785828},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09204629063606262},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1038/npre.2009.3724","doi":"https://doi.org/10.1038/npre.2009.3724","is_oa":true,"landing_page_url":"https://doi.org/10.1038/npre.2009.3724","pdf_url":"https://www.nature.com/articles/npre.2009.3724.1.pdf","source":{"id":"https://openalex.org/S48744551","display_name":"Nature Precedings","issn_l":"1756-0357","issn":["1756-0357"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Precedings","raw_type":"journal-article"},{"id":"doi:10.1038/npre.2009.3724.1","doi":"https://doi.org/10.1038/npre.2009.3724.1","is_oa":true,"landing_page_url":"https://doi.org/10.1038/npre.2009.3724.1","pdf_url":null,"source":{"id":"https://openalex.org/S48744551","display_name":"Nature Precedings","issn_l":"1756-0357","issn":["1756-0357"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Precedings","raw_type":"journal-article"},{"id":"pmh:oai:nature.com:10.1038/npre.2009.3724.1","doi":null,"is_oa":true,"landing_page_url":"http://precedings.nature.com/documents/3724/version/1","pdf_url":null,"source":{"id":"https://openalex.org/S48744551","display_name":"Nature Precedings","issn_l":"1756-0357","issn":["1756-0357"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nature Precedings","raw_type":"Manuscript"}],"best_oa_location":{"id":"doi:10.1038/npre.2009.3724","doi":"https://doi.org/10.1038/npre.2009.3724","is_oa":true,"landing_page_url":"https://doi.org/10.1038/npre.2009.3724","pdf_url":"https://www.nature.com/articles/npre.2009.3724.1.pdf","source":{"id":"https://openalex.org/S48744551","display_name":"Nature Precedings","issn_l":"1756-0357","issn":["1756-0357"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Precedings","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3199835447","display_name":null,"funder_award_id":"BB/G530441/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320311508","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2121034256.pdf","grobid_xml":"https://content.openalex.org/works/W2121034256.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W36358301","https://openalex.org/W1565561072","https://openalex.org/W1702766678","https://openalex.org/W1931404780","https://openalex.org/W2041396547","https://openalex.org/W2045478141","https://openalex.org/W2051923386","https://openalex.org/W2064885721","https://openalex.org/W2099007946","https://openalex.org/W2099987999","https://openalex.org/W2102664288","https://openalex.org/W2103031848","https://openalex.org/W2112651905","https://openalex.org/W2121905803","https://openalex.org/W2133429395","https://openalex.org/W2144192824","https://openalex.org/W2150908245","https://openalex.org/W4249884416","https://openalex.org/W4285719527","https://openalex.org/W4301353258"],"related_works":["https://openalex.org/W2091050840","https://openalex.org/W4235521279","https://openalex.org/W2153216922","https://openalex.org/W2145272885","https://openalex.org/W4254464710","https://openalex.org/W2069157810","https://openalex.org/W7223122452","https://openalex.org/W4242519561","https://openalex.org/W3002962092","https://openalex.org/W2950329335"],"abstract_inverted_index":{"Abstract":[0],"Standard":[1],"graphical":[2,116],"representations":[3],"have":[4,30,90,136],"played":[5],"a":[6,50,98,115,123,153],"crucial":[7],"role":[8],"in":[9,57,167,192,199],"science":[10],"and":[11,67,77,128,133,145,178,190,224,234,243],"engineering":[12],"throughout":[13],"the":[14,33,41,45,53,62,73,94,139,142,146,179,206,217],"last":[15,95],"century.":[16],"Without":[17],"electrical":[18],"symbolism,":[19],"it":[20],"is":[21,114,176],"very":[22],"likely":[23],"that":[24],"our":[25],"industrial":[26],"society":[27],"would":[28],"not":[29],"evolved":[31],"at":[32],"same":[34],"pace.":[35],"Similarly,":[36],"specialized":[37],"notations":[38],"such":[39],"as":[40],"Feynmann":[42],"notation":[43],"or":[44],"process":[46],"flow":[47],"diagrams":[48],"did":[49],"lot":[51],"for":[52,75],"adoption":[54],"of":[55,64,70,80,125,159,173,205,219,236],"concepts":[56],"their":[58],"own":[59],"fields.":[60],"With":[61],"advent":[63],"Systems":[65,109],"Biology,":[66,72],"more":[68,85],"recently":[69],"Synthetic":[71],"need":[74],"precise":[76],"unambiguous":[78,169],"descriptions":[79],"biochemical":[81,160],"interactions":[82],"has":[83,106,211],"become":[84],"pressing.":[86],"While":[87],"some":[88],"ideas":[89],"been":[91,137,212],"advanced":[92],"over":[93,119],"decade,":[96],"with":[97],"few":[99],"detailed":[100],"proposals,":[101],"no":[102],"actual":[103],"community":[104,124],"standard":[105],"emerged.":[107],"The":[108,171,202],"Biology":[110],"Graphical":[111],"Notation":[112],"(SBGN)":[113],"representation":[117],"crafted":[118],"several":[120],"years":[121],"by":[122,216],"biochemists,":[126,220],"modellers":[127],"computer":[129],"scientists.":[130],"Three":[131],"orthogonal":[132],"complementary":[134],"languages":[135,228],"created,":[138],"Process":[140],"Descriptions,":[141],"Entity":[143],"Relationships":[144],"Activity":[147,208],"Flows.":[148],"Using":[149],"these":[150],"three":[151],"idioms":[152],"scientist":[154],"can":[155,163],"represent":[156],"any":[157],"network":[158],"interactions,":[161],"which":[162],"then":[164],"be":[165],"interpreted":[166],"an":[168],"way.":[170],"set":[172],"symbols":[174],"used":[175],"limited,":[177],"grammar":[180],"quite":[181],"simple,":[182],"to":[183,195],"allow":[184],"its":[185],"usage":[186],"ranging":[187],"from":[188],"textbooks":[189],"teaching":[191],"high":[193],"schools":[194],"peer":[196],"reviewed":[197],"articles":[198],"scientific":[200],"journals.":[201],"first":[203],"level":[204],"SBGN":[207,227],"Flow":[209],"language":[210],"publicly":[213],"released.":[214],"Shared":[215],"communities":[218],"genomic":[221],"scientists,":[222],"theoreticians":[223],"computational":[225],"biologists,":[226],"will":[229],"foster":[230],"efficient":[231],"storage,":[232],"exchange":[233],"reuse":[235],"information":[237],"on":[238],"signaling":[239],"pathways,":[240],"metabolic":[241],"networks":[242],"gene":[244],"regulatory":[245],"maps.":[246]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
