{"id":"https://openalex.org/W2041956905","doi":"https://doi.org/10.1186/1752-0509-3-34","title":"Version control of pathway models using XML patches","display_name":"Version control of pathway models using XML patches","publication_year":2009,"publication_date":"2009-03-17","ids":{"openalex":"https://openalex.org/W2041956905","doi":"https://doi.org/10.1186/1752-0509-3-34","mag":"2041956905","pmid":"https://pubmed.ncbi.nlm.nih.gov/19292901"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-3-34","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-3-34","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-34","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-34","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004158727","display_name":"Peter Saffrey","orcid":null},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Peter Saffrey","raw_affiliation_strings":["Department of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK. pzs@dcs.gla.ac.uk","Department of Computing Science University of Glasgow, Glasgow, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK. pzs@dcs.gla.ac.uk","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Department of Computing Science University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080204187","display_name":"Richard Orton","orcid":"https://orcid.org/0000-0002-3389-4325"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard Orton","raw_affiliation_strings":["Department of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK","Department of Computing Science University of Glasgow, Glasgow, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Department of Computing Science University of Glasgow, Glasgow, UK","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5004158727"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":null,"apc_paid":null,"fwci":1.8946,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.85348562,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"3","issue":"1","first_page":"34","last_page":"34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.4641999900341034,"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"}},"topics":[{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.4641999900341034,"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"}},{"id":"https://openalex.org/T10142","display_name":"Formal Methods in Verification","score":0.15219999849796295,"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/T10639","display_name":"Advanced Software Engineering Methodologies","score":0.14249999821186066,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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":0.6329761147499084},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.584082841873169},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5162591934204102},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.452446848154068},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31495869159698486},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2648521661758423}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6329761147499084},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.584082841873169},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5162591934204102},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.452446848154068},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31495869159698486},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2648521661758423}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004815","descriptor_name":"Epidermal Growth Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-3-34","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-3-34","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-34","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:19292901","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19292901","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:eprints.gla.ac.uk:59697","is_oa":false,"landing_page_url":"http://eprints.gla.ac.uk/view/author/9984.html>","pdf_url":null,"source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":false,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:2674044","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2674044","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 Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-3-34","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-3-34","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-3-34","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2041956905.pdf","grobid_xml":"https://content.openalex.org/works/W2041956905.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W101679455","https://openalex.org/W1569192135","https://openalex.org/W1667204010","https://openalex.org/W1795056021","https://openalex.org/W1965853004","https://openalex.org/W1967412917","https://openalex.org/W1990736894","https://openalex.org/W1994481836","https://openalex.org/W1996405087","https://openalex.org/W2010489503","https://openalex.org/W2024797550","https://openalex.org/W2024985960","https://openalex.org/W2052380264","https://openalex.org/W2070564840","https://openalex.org/W2089562567","https://openalex.org/W2095670464","https://openalex.org/W2098719212","https://openalex.org/W2102653059","https://openalex.org/W2103017472","https://openalex.org/W2105437542","https://openalex.org/W2107062718","https://openalex.org/W2139937771","https://openalex.org/W2150908245","https://openalex.org/W2159594827","https://openalex.org/W2163188200","https://openalex.org/W2164354034","https://openalex.org/W2483101662","https://openalex.org/W2561675875","https://openalex.org/W4243013071","https://openalex.org/W4285719527","https://openalex.org/W6602499392"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2393259792","https://openalex.org/W5284979","https://openalex.org/W4245853730"],"abstract_inverted_index":{"BACKGROUND:":[0],"Computational":[1],"modelling":[2],"has":[3,55],"become":[4],"an":[5,17],"important":[6],"tool":[7],"in":[8,19,122],"understanding":[9],"biological":[10],"systems":[11],"such":[12,119],"as":[13],"signalling":[14],"pathways.":[15],"With":[16],"increase":[18],"size":[20],"complexity":[21],"of":[22,47,50,58,98,102,110],"models":[23,44],"comes":[24],"a":[25,56,62,68,75,99,107],"need":[26],"for":[27,42],"techniques":[28],"to":[29,36,86,114,130],"manage":[30],"model":[31,69,103],"versions":[32],"and":[33,95,105,124,132],"their":[34],"relationship":[35],"one":[37],"another.":[38],"Model":[39],"version":[40,52,70],"control":[41,53,71],"pathway":[43],"shares":[45],"some":[46],"the":[48,87],"features":[49],"software":[51],"but":[54],"number":[57],"differences":[59],"that":[60,127],"warrant":[61],"specific":[63],"solution.":[64],"RESULTS:":[65],"We":[66,82],"present":[67],"method,":[72],"along":[73],"with":[74],"prototype":[76],"implementation,":[77],"based":[78],"on":[79],"XML":[80],"patches.":[81],"show":[83],"its":[84],"application":[85],"EGF/RAS/RAF":[88],"pathway.":[89],"CONCLUSION:":[90],"Our":[91],"method":[92],"allows":[93],"quick":[94],"convenient":[96],"storage":[97],"wide":[100],"range":[101],"variations":[104],"enables":[106],"thorough":[108],"explanation":[109],"these":[111,116],"variations.":[112],"Trying":[113],"produce":[115],"results":[117,121],"without":[118],"methods":[120],"slow":[123],"cumbersome":[125],"development":[126],"is":[128],"prone":[129],"frustration":[131],"human":[133],"error.":[134]},"counts_by_year":[{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
