{"id":"https://openalex.org/W2171567979","doi":"https://doi.org/10.1186/1751-0473-6-5","title":"Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format","display_name":"Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format","publication_year":2011,"publication_date":"2011-03-21","ids":{"openalex":"https://openalex.org/W2171567979","doi":"https://doi.org/10.1186/1751-0473-6-5","mag":"2171567979","pmid":"https://pubmed.ncbi.nlm.nih.gov/21418653"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-6-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-6-5","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-6-5","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-6-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057153002","display_name":"Ryan L Webb","orcid":null},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ryan L Webb","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York NY 10029, USA. avi.maayan@mssm.edu","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York, NY, 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York NY 10029, USA. avi.maayan@mssm.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032951414","display_name":"Avi Ma\u2019ayan","orcid":"https://orcid.org/0000-0002-6904-1017"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Avi Ma'ayan","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York, NY, 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5057153002"],"corresponding_institution_ids":["https://openalex.org/I98704320"],"apc_list":null,"apc_paid":null,"fwci":0.6651,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.69751329,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"6","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6543999910354614,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6543999910354614,"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":0.2897000014781952,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.013000000268220901,"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/computer-science","display_name":"Computer science","score":0.8015201091766357},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.7896704077720642},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.46452176570892334},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35730141401290894},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2981811761856079}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8015201091766357},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.7896704077720642},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.46452176570892334},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35730141401290894},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2981811761856079}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1751-0473-6-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-6-5","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-6-5","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:21418653","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21418653","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:doaj.org/article:ecfad9f0e1014230b497415dedae45b2","is_oa":false,"landing_page_url":"https://doaj.org/article/ecfad9f0e1014230b497415dedae45b2","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":"Source Code for Biology and Medicine, Vol 6, Iss 1, p 5 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2082390","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3071313","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-6-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-6-5","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/1751-0473-6-5","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1936110908","display_name":null,"funder_award_id":"P50GM071558","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8370264171","display_name":null,"funder_award_id":"KL2RR029885","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309468","display_name":"Memorial Sloan-Kettering Cancer Center","ror":"https://ror.org/02yrq0923"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171567979.pdf","grobid_xml":"https://content.openalex.org/works/W2171567979.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1597403892","https://openalex.org/W1599207601","https://openalex.org/W1969709265","https://openalex.org/W1982428412","https://openalex.org/W2006933206","https://openalex.org/W2012129116","https://openalex.org/W2091119718","https://openalex.org/W2098023402","https://openalex.org/W2132992030","https://openalex.org/W2135857985","https://openalex.org/W2137531873","https://openalex.org/W2149248356","https://openalex.org/W2150908245","https://openalex.org/W2164298117","https://openalex.org/W2171030481","https://openalex.org/W2915108429","https://openalex.org/W2917375902"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,39,201,253],"World":[2],"Wide":[3],"Web":[4,67],"plays":[5],"a":[6,84,119,244,258],"critical":[7],"role":[8],"in":[9,96,137],"enabling":[10],"molecular,":[11],"cell,":[12],"systems":[13,142,178,265],"and":[14,22,65,80,115,128,149,221,230,248,263,272,279],"computational":[15,177,264],"biologists":[16,266],"to":[17,44,47,121,155,217,267],"exchange,":[18],"search,":[19],"visualize,":[20],"integrate,":[21],"analyze":[23],"experimental":[24,262],"data.":[25],"Such":[26],"efforts":[27],"can":[28],"be":[29],"further":[30],"enhanced":[31],"through":[32,50],"the":[33,51,66,89,138,159,166,171,176,207,215,282,285],"development":[34,52],"of":[35,53,76,91,135,140,161,197,225,237,274,284],"semantic":[36,40],"web":[37,41],"concepts.":[38],"idea":[42],"is":[43,110,133,170,257],"enable":[45],"machines":[46],"understand":[48],"data":[49,56,97,123,193],"protocol":[54],"free":[55],"exchange":[57,124],"formats":[58,109],"such":[59,99,117,204],"as":[60,100,116,190],"Resource":[61],"Description":[62],"Framework":[63],"(RDF)":[64],"Ontology":[68],"Language":[69],"(OWL).":[70],"These":[71],"standards":[72],"provide":[73],"formal":[74],"descriptors":[75],"objects,":[77],"object":[78],"properties":[79],"their":[81,150,269],"relationships":[82],"within":[83],"specific":[85],"knowledge":[86],"domain.":[87],"However,":[88],"overhead":[90],"converting":[92,162],"datasets":[93],"typically":[94],"stored":[95],"tables":[98],"Excel,":[101],"text":[102],"or":[103,107],"PDF":[104],"into":[105,165,206,234,242],"RDF":[106],"OWL":[108,211],"not":[111],"trivial":[112],"for":[113,246,277],"non-specialists":[114],"produces":[118],"barrier":[120],"seamless":[122],"between":[125,147],"researchers,":[126],"databases":[127],"analysis":[129],"tools.":[130],"This":[131],"problem":[132],"particularly":[134],"importance":[136],"field":[139],"network":[141],"biology":[143,179],"where":[144],"biochemical":[145,163,199,250],"interactions":[146,164,205,276],"genes":[148],"protein":[151,226],"products":[152],"are":[153],"abstracted":[154],"networks.":[156,251],"RESULTS:":[157],"For":[158],"purpose":[160],"BioPAX":[167,208],"format,":[168],"which":[169],"leading":[172],"standard":[173],"developed":[174,182],"by":[175],"community,":[180],"we":[181],"an":[183],"open-source":[184],"command":[185],"line":[186],"tool":[187,202,216,255],"that":[188,260],"takes":[189],"input":[191],"tabular":[192],"describing":[194],"different":[195],"types":[196],"molecular":[198,275],"interactions.":[200],"converts":[203],"level":[209],"3":[210],"format.":[212],"We":[213],"used":[214],"convert":[218],"several":[219],"existing":[220],"new":[222],"mammalian":[223],"networks":[224,233,239,271],"interactions,":[227],"signalling":[228],"pathways,":[229],"transcriptional":[231],"regulatory":[232],"BioPAX.":[235],"Some":[236],"these":[238],"were":[240],"deposited":[241],"PathwayCommons,":[243],"repository":[245],"consolidating":[247],"organizing":[249],"CONCLUSIONS:":[252],"software":[254],"Sig2BioPAX":[256],"resource":[259],"enables":[261],"contribute":[268],"identified":[270],"pathways":[273],"integration":[278],"reuse":[280],"with":[281],"rest":[283],"research":[286],"community.":[287]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
