{"id":"https://openalex.org/W4205223779","doi":"https://doi.org/10.1515/jib-2021-0013","title":"Synthetic biology open language visual (SBOL visual) version 3.0","display_name":"Synthetic biology open language visual (SBOL visual) version 3.0","publication_year":2021,"publication_date":"2021-09-01","ids":{"openalex":"https://openalex.org/W4205223779","doi":"https://doi.org/10.1515/jib-2021-0013"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2021-0013","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2021-0013","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0013/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0013/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059658712","display_name":"Hasan Baig","orcid":"https://orcid.org/0000-0002-8765-2604"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hasan Baig","raw_affiliation_strings":["University of Connecticut , Storrs , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut , Storrs , USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112725656","display_name":"Pedro Fontanarossa","orcid":null},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pedro Fontanarossa","raw_affiliation_strings":["University of Utah , Salt Lake City , USA"],"raw_orcid":"https://orcid.org/0000-0002-0535-2684","affiliations":[{"raw_affiliation_string":"University of Utah , Salt Lake City , USA","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060567781","display_name":"J. A. McLaughlin","orcid":"https://orcid.org/0000-0002-7863-624X"},"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"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James McLaughlin","raw_affiliation_strings":["EMBL-EBI , Hinxton , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-EBI , Hinxton , UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021538869","display_name":"James Scott-Brown","orcid":"https://orcid.org/0000-0001-5642-8346"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James Scott-Brown","raw_affiliation_strings":["University of Oxford , Oxford , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Oxford , Oxford , UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037059285","display_name":"Prashant Vaidyanathan","orcid":"https://orcid.org/0000-0002-9722-7089"},"institutions":[{"id":"https://openalex.org/I4210164937","display_name":"Microsoft Research (United Kingdom)","ror":"https://ror.org/05k87vq12","country_code":"GB","type":"company","lineage":["https://openalex.org/I1290206253","https://openalex.org/I4210164937"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Prashant Vaidyanathan","raw_affiliation_strings":["Microsoft Research , Cambridge , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microsoft Research , Cambridge , UK","institution_ids":["https://openalex.org/I4210164937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000195963","display_name":"Thomas E. Gorochowski","orcid":"https://orcid.org/0000-0003-1702-786X"},"institutions":[{"id":"https://openalex.org/I36234482","display_name":"University of Bristol","ror":"https://ror.org/0524sp257","country_code":"GB","type":"education","lineage":["https://openalex.org/I36234482"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thomas Gorochowski","raw_affiliation_strings":["University of Bristol , Bristol , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Bristol , Bristol , UK","institution_ids":["https://openalex.org/I36234482"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028639846","display_name":"G\u00f6ksel M\u0131s\u0131rl\u0131","orcid":"https://orcid.org/0000-0002-2454-7188"},"institutions":[{"id":"https://openalex.org/I56007636","display_name":"Keele University","ror":"https://ror.org/00340yn33","country_code":"GB","type":"education","lineage":["https://openalex.org/I56007636"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Goksel Misirli","raw_affiliation_strings":["Keele University , Newcastle , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Keele University , Newcastle , UK","institution_ids":["https://openalex.org/I56007636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020446837","display_name":"Jacob Beal","orcid":"https://orcid.org/0000-0002-1663-5102"},"institutions":[{"id":"https://openalex.org/I1306686416","display_name":"RTX (United States)","ror":"https://ror.org/0354t7b78","country_code":"US","type":"company","lineage":["https://openalex.org/I1306686416"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jacob Beal","raw_affiliation_strings":["Raytheon BBN Technologies , Cambridge , USA"],"raw_orcid":"https://orcid.org/0000-0002-1663-5102","affiliations":[{"raw_affiliation_string":"Raytheon BBN Technologies , Cambridge , USA","institution_ids":["https://openalex.org/I1306686416"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111386695","display_name":"Chris J. Myers","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Myers","raw_affiliation_strings":["University of Colorado Boulder , Boulder , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado Boulder , Boulder , USA","institution_ids":["https://openalex.org/I188538660"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5020446837"],"corresponding_institution_ids":["https://openalex.org/I1306686416"],"apc_list":null,"apc_paid":null,"fwci":1.3843,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.81550776,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"18","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.989799976348877,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.989799976348877,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.979200005531311,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.975600004196167,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.7262802124023438},{"id":"https://openalex.org/keywords/visual-language","display_name":"Visual language","score":0.4819033443927765},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4167686104774475},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37097039818763733},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3265541195869446},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.16411873698234558},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.06275111436843872}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7262802124023438},{"id":"https://openalex.org/C2780878386","wikidata":"https://www.wikidata.org/wiki/Q1659648","display_name":"Visual language","level":2,"score":0.4819033443927765},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4167686104774475},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37097039818763733},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3265541195869446},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.16411873698234558},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.06275111436843872}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1515/jib-2021-0013","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2021-0013","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0013/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:7466690","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8560346","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:eprints.keele.ac.uk:10132","is_oa":true,"landing_page_url":null,"pdf_url":"https://eprints.keele.ac.uk/10132/1/10.1515_jib-2020-0045.pdf","source":{"id":"https://openalex.org/S4306402149","display_name":"Keele Research Repository (Keele University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56007636","host_organization_name":"Keele University","host_organization_lineage":["https://openalex.org/I56007636"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:7bf5a128a99a4cae82834440fc5bdb18","is_oa":true,"landing_page_url":"https://doaj.org/article/7bf5a128a99a4cae82834440fc5bdb18","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 18, Iss 3 (2021)","raw_type":"article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/135615.2","is_oa":true,"landing_page_url":"https://hdl.handle.net/1721.1/135615.2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"De Gruyter","raw_type":"Article"},{"id":"pmh:oai:eprints.keele.ac.uk:10221","is_oa":true,"landing_page_url":"https://eprints.keele.ac.uk/10221/1/10.1515_jib-2021-0013.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306402149","display_name":"Keele Research Repository (Keele University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56007636","host_organization_name":"Keele University","host_organization_lineage":["https://openalex.org/I56007636"],"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":"","raw_type":"Article"},{"id":"pmh:oai:eprints.keele.ac.uk:8409","is_oa":true,"landing_page_url":"https://eprints.keele.ac.uk/8409/1/%5B16134516%20-%20Journal%20of%20Integrative%20Bioinformatics%5D%20Synthetic%20biology%20open%20language%20visual%20%28SBOL%20visual%29%20version%202.2.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306402149","display_name":"Keele Research Repository (Keele University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56007636","host_organization_name":"Keele University","host_organization_lineage":["https://openalex.org/I56007636"],"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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1515/jib-2021-0013","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2021-0013","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2021-0013/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2958229932","display_name":null,"funder_award_id":"1522074","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4205223779.pdf","grobid_xml":"https://content.openalex.org/works/W4205223779.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2069157810","https://openalex.org/W2123171788","https://openalex.org/W2145435867","https://openalex.org/W4324088634","https://openalex.org/W6779531965"],"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/W2350741829","https://openalex.org/W3204019825","https://openalex.org/W1924502949","https://openalex.org/W4246664336"],"abstract_inverted_index":{"Abstract":[0],"People":[1],"who":[2],"engineer":[3],"biological":[4],"organisms":[5],"often":[6],"find":[7],"it":[8],"useful":[9],"to":[10,15,47,55,63,112,149,194],"draw":[11],"diagrams":[12,105],"in":[13,61,155],"order":[14,62],"communicate":[16],"both":[17],"the":[18,21,30,70,90,113,120,132,156,177,190],"structure":[19,71],"of":[20,74,82,89,127,134,175],"nucleic":[22],"acid":[23],"sequences":[24],"that":[25,104,131],"they":[26],"are":[27,108],"engineering":[28],"and":[29,36,43,57,72,99,106,181],"functional":[31],"relationships":[32],"between":[33,95],"sequence":[34],"features":[35],"other":[37],"molecular":[38],"species.":[39],"Some":[40],"typical":[41],"practices":[42],"conventions":[44,60],"have":[45,185,189],"begun":[46],"emerge":[48],"for":[49,68,138],"such":[50,59],"diagrams.":[51],"SBOL":[52,83,96,100,114,121,152],"Visual":[53,97,101],"aims":[54],"organize":[56],"systematize":[58],"produce":[64],"a":[65,85],"coherent":[66],"language":[67],"expressing":[69],"function":[73],"genetic":[75],"designs.":[76],"This":[77],"document":[78],"details":[79],"version":[80],"3.0":[81],"Visual,":[84],"new":[86],"major":[87,93],"revision":[88],"standard.":[91],"The":[92],"difference":[94],"3":[98,115,153],"2":[102,122],"is":[103,130],"glyphs":[107,184],"defined":[109],"with":[110],"respect":[111],"data":[116,123],"model":[117],"rather":[118],"than":[119],"model.":[124],"A":[125],"byproduct":[126],"this":[128,158],"change":[129],"use":[133],"dashed":[135],"undirected":[136],"lines":[137],"subsystem":[139],"mappings":[140],"has":[141,170],"been":[142,171,186],"removed,":[143,187],"pending":[144],"future":[145],"determination":[146],"on":[147],"how":[148],"represent":[150],"general":[151],"constraints;":[154],"interim,":[157],"annotation":[159],"can":[160],"still":[161],"be":[162],"used":[163],"as":[164,188],"an":[165],"annotation.":[166],"Finally,":[167],"deprecated":[168,178,191],"material":[169],"removed":[172],"from":[173],"collection":[174],"glyphs:":[176],"\u201cinsulator\u201d":[179],"glyph":[180],"\u201cmacromolecule\u201d":[182],"alternative":[183],"BioPAX":[192],"alternatives":[193],"SBO":[195],"terms.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
