Synthetic biology open language visual (SBOL visual) version 3.0
People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and convent...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2021-10-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2021-0013 |
| _version_ | 1818307229056499712 |
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| author | Baig Hasan Fontanarossa Pedro McLaughlin James Scott-Brown James Vaidyanathan Prashant Gorochowski Thomas Misirli Goksel Beal Jacob Myers Chris |
| author_facet | Baig Hasan Fontanarossa Pedro McLaughlin James Scott-Brown James Vaidyanathan Prashant Gorochowski Thomas Misirli Goksel Beal Jacob Myers Chris |
| author_sort | Baig Hasan |
| collection | DOAJ |
| description | People who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 3.0 of SBOL Visual, a new major revision of the standard. The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model. A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed, pending future determination on how to represent general SBOL 3 constraints; in the interim, this annotation can still be used as an annotation. Finally, deprecated material has been removed from collection of glyphs: the deprecated “insulator” glyph and “macromolecule” alternative glyphs have been removed, as have the deprecated BioPAX alternatives to SBO terms. |
| first_indexed | 2024-12-13T06:55:03Z |
| format | Article |
| id | doaj.art-7bf5a128a99a4cae82834440fc5bdb18 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-13T06:55:03Z |
| publishDate | 2021-10-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-7bf5a128a99a4cae82834440fc5bdb182022-12-21T23:56:03ZengDe GruyterJournal of Integrative Bioinformatics1613-45162021-10-0118310.1515/jib-2021-0013Synthetic biology open language visual (SBOL visual) version 3.0Baig Hasan0Fontanarossa Pedro1McLaughlin James2Scott-Brown James3Vaidyanathan Prashant4Gorochowski Thomas5Misirli Goksel6Beal Jacob7Myers Chris8University of Connecticut, Storrs, USAUniversity of Utah, Salt Lake City, USAEMBL-EBI, Hinxton, UKUniversity of Oxford, Oxford, UKMicrosoft Research, Cambridge, UKUniversity of Bristol, Bristol, UKKeele University, Newcastle, UKRaytheon BBN Technologies, Cambridge, USAUniversity of Colorado Boulder, Boulder, USAPeople who engineer biological organisms often find it useful to draw diagrams in order to communicate both the structure of the nucleic acid sequences that they are engineering and the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 3.0 of SBOL Visual, a new major revision of the standard. The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model. A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed, pending future determination on how to represent general SBOL 3 constraints; in the interim, this annotation can still be used as an annotation. Finally, deprecated material has been removed from collection of glyphs: the deprecated “insulator” glyph and “macromolecule” alternative glyphs have been removed, as have the deprecated BioPAX alternatives to SBO terms.https://doi.org/10.1515/jib-2021-0013diagramssbol visualstandards |
| spellingShingle | Baig Hasan Fontanarossa Pedro McLaughlin James Scott-Brown James Vaidyanathan Prashant Gorochowski Thomas Misirli Goksel Beal Jacob Myers Chris Synthetic biology open language visual (SBOL visual) version 3.0 Journal of Integrative Bioinformatics diagrams sbol visual standards |
| title | Synthetic biology open language visual (SBOL visual) version 3.0 |
| title_full | Synthetic biology open language visual (SBOL visual) version 3.0 |
| title_fullStr | Synthetic biology open language visual (SBOL visual) version 3.0 |
| title_full_unstemmed | Synthetic biology open language visual (SBOL visual) version 3.0 |
| title_short | Synthetic biology open language visual (SBOL visual) version 3.0 |
| title_sort | synthetic biology open language visual sbol visual version 3 0 |
| topic | diagrams sbol visual standards |
| url | https://doi.org/10.1515/jib-2021-0013 |
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