{"id":"https://openalex.org/W2133429395","doi":"https://doi.org/10.2390/biecoll-jib-2006-36","title":"A Graphical Notation to describe the Logical Interactions of Biological Pathways","display_name":"A Graphical Notation to describe the Logical Interactions of Biological Pathways","publication_year":2007,"publication_date":"2007-01-01","ids":{"openalex":"https://openalex.org/W2133429395","doi":"https://doi.org/10.2390/biecoll-jib-2006-36","mag":"2133429395"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.324.525","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.525","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.sbgn.org/images/a/aa/Moodie_2006.pdf","raw_type":"text"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2390/biecoll-jib-2006-36","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053863175","display_name":"Stuart Moodie","orcid":"https://orcid.org/0000-0001-6191-5595"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Moodie, Stuart L.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020746275","display_name":"Anatoly Sorokin","orcid":"https://orcid.org/0000-0002-0047-0606"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sorokin, Anatoly","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082079518","display_name":"Igor Goryanin","orcid":"https://orcid.org/0000-0002-8293-774X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Goryanin, Igor","raw_affiliation_strings":["School of Informatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Informatics","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065696246","display_name":"Peter Ghazal","orcid":"https://orcid.org/0000-0003-0035-2228"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ghazal, Peter","raw_affiliation_strings":["Deanery of Biomedical Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deanery of Biomedical Sciences","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.5573,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.8967562,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"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":0.9997000098228455,"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":0.9997000098228455,"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":0.9997000098228455,"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":0.9986000061035156,"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/notation","display_name":"Notation","score":0.8860361576080322},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7632327675819397},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.7070838212966919},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.5485495328903198},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5121698379516602},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4654797911643982},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.45174479484558105},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37349215149879456},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19962778687477112},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12205418944358826},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11555790901184082},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10156574845314026}],"concepts":[{"id":"https://openalex.org/C45357846","wikidata":"https://www.wikidata.org/wiki/Q2001982","display_name":"Notation","level":2,"score":0.8860361576080322},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7632327675819397},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7070838212966919},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.5485495328903198},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5121698379516602},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4654797911643982},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.45174479484558105},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37349215149879456},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19962778687477112},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12205418944358826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11555790901184082},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10156574845314026},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.324.525","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.525","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.sbgn.org/images/a/aa/Moodie_2006.pdf","raw_type":"text"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:217","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2007/217/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/index.php?paper_id=36","raw_type":"Journal Article"},{"id":"doi:10.2390/biecoll-jib-2006-36","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2006-36","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2006-36","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2006-36","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1586879504","https://openalex.org/W1702766678","https://openalex.org/W1974018903","https://openalex.org/W1980558594","https://openalex.org/W2022431825","https://openalex.org/W2041396547","https://openalex.org/W2045478141","https://openalex.org/W2059000558","https://openalex.org/W2064885721","https://openalex.org/W2108723074","https://openalex.org/W2112651905","https://openalex.org/W2117364474","https://openalex.org/W2117391818","https://openalex.org/W2125637396","https://openalex.org/W2139439234","https://openalex.org/W2143784594","https://openalex.org/W2149665940","https://openalex.org/W2149991291","https://openalex.org/W2150908245","https://openalex.org/W2164727176","https://openalex.org/W2168846334","https://openalex.org/W2984707384"],"related_works":["https://openalex.org/W2045478141","https://openalex.org/W2150908245","https://openalex.org/W2149991291","https://openalex.org/W2112651905","https://openalex.org/W2069157810","https://openalex.org/W2138280093","https://openalex.org/W2147714160","https://openalex.org/W2121905803","https://openalex.org/W2102653059","https://openalex.org/W2041396547","https://openalex.org/W2172102555","https://openalex.org/W2161682775","https://openalex.org/W2153258203","https://openalex.org/W2121650210","https://openalex.org/W2117364474","https://openalex.org/W2064885721","https://openalex.org/W2042880070","https://openalex.org/W1702766678","https://openalex.org/W2054779024","https://openalex.org/W2010502047"],"abstract_inverted_index":{"The":[0,23,87],"modelling":[1],"of":[2,12,34,92,96],"biological":[3,57],"intra-cellular":[4],"pathways":[5,36,103],"requires":[6],"the":[7,67,74,90],"systematic":[8],"capture":[9],"and":[10,20,30,44,54],"representation":[11,95],"interactions":[13],"between":[14],"components":[15],"that":[16,47],"are":[17,50,107],"biologically":[18,76],"correct":[19],"computationally":[21],"rigorous.":[22],"challenge":[24],"is":[25,99],"two":[26],"fold,":[27],"to":[28,42,45,102],"verify":[29],"extend":[31],"our":[32],"understanding":[33],"such":[35,48],"by":[37,52],"comparing":[38],"in":[39,110],"silico":[40],"models":[41,49],"experiments;":[43],"ensure":[46],"understandable":[51],"biologists":[53],"for":[55,85],"checking":[56],"validity.":[58],"In":[59],"this":[60],"report":[61],"we":[62],"present":[63],"a":[64,81,93],"graphical":[65],"notation,":[66],"Edinburgh":[68],"Pathway":[69],"Notation":[70],"(EPN),":[71],"which":[72,98],"satisfies":[73],"central":[75],"driven":[77],"requirements":[78],"while":[79],"providing":[80],"strict":[82],"formal":[83],"framework":[84],"analysis.":[86],"EPN":[88],"emphasises":[89],"use":[91],"logical":[94],"pathways,":[97],"particularly":[100],"suited":[101],"were":[104],"some":[105],"mechanisms":[106],"not":[108],"known":[109],"detail.":[111],"1":[112]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
