Releases: SynBioDex/SBOL-specification
Releases · SynBioDex/SBOL-specification
Release list
v3.1.0
SBOL Specification version 3.1.0
What's Changed
- Change obsolete GO:0005623 to CL:0000000 by @tcmitchell in #479
- Changed figure 9 resolving #482 by @Fontanapink in #483
- Fix NCIT terminology in practices by @jakebeal in #486
- Add URI comparison reminder, resolving #476 by @jakebeal in #481
- Clarify rule sbol3-10902 by @tcmitchell in #484
- Fixed Typos (Issue #487) by @LukasBuecherl in #490
- Update sbol3.tex by @LukasBuecherl in #494
- Proposed fix for #489 by @PrashantVaidyanathan in #495
- Change all URIs to IRIs or URLs, depending on context. Resolves #369 by @jakebeal in #466
- Change
CompenentDefinitiontoComponentDefinitionby @tcmitchell in #506 - 3.1 by @Gonza10V in #511
New Contributors
- @LukasBuecherl made their first contribution in #490
- @Gonza10V made their first contribution in #511
Full Changelog: v3.0.1...v3.1.0
Contributors
tcmitchell, PrashantVaidyanathan, and 4 other contributors
Assets 3
v3.0.1
SBOL Specification version 3.0.1
What's Changed
- Fixed another set of wrong edge names in the two cell figure. by @jakebeal in #367
- Move declaration of SBOL namespace from serialization to identifiers by @jakebeal in #378
- Change constants with v2 to v3, which will fix #375 by @jakebeal in #377
- Implementation of SEP 047 by @jakebeal in #383
- Draft implementation of SEP 048 by @jakebeal in #384
- proposed fix for issue #374 by @jakebeal in #386
- proposed fix for issue #381 by @jakebeal in #385
- change all identifiers.org URLs to short form by @jakebeal in #393
- add serialization recommendation by @jakebeal in #394
- Use best practices in URI examples by @jakebeal in #398
- added version commands by @Fontanapink in #401
- Implemented issue #390 by @IsabelMarleen in #407
- Changed: "https://www.w3.org/TR/prov-o/" namespace to "http://www.w3.… by @lmnh in #408
- Serialization example for RDF updated and XML example altered to match by @chofski in #406
- Remove draft watermark by @tcmitchell in #405
- Implemented issue #387 by @IsabelMarleen in #409
- Enable building with docker image by @tcmitchell in #403
- Changed: Engineered Gene to Engineered Region in the recommended SO r… by @lmnh in #404
- Update vocabulary.tex by @JMante1 in #414
- Fix OM figure by @cjmyers in #413
- Change versioning tagsin document by @Fontanapink in #415
- Change SBOL3 logos by @Fontanapink in #416
- Add PubChem as a recommended alternative for small molecules in best practices by @jakebeal in #419
- Fix Issue 202 by @jakebeal in #425
- Implement SEP 050, removing Namespace object by @jakebeal in #426
- Draft update based on SEP 049 by @jakebeal in #427
- Correct a bad pluralization and an obsolete reference to the 'current' spec. by @mikebissell in #428
- Compact validation rules and other updates by @jakebeal in #424
- Fix #429 by @bbartley in #430
- making sure validation3 can be safely deleted by @jakebeal in #432
- Fix #435 by @jakebeal in #442
- Fix #437 by @jakebeal in #443
- Add Tom Mitchell as author by @jakebeal in #444
- Add extension of SBOL classes to extension options by @jakebeal in #445
- Improve complementary standards section by @jakebeal in #447
- Fix primitive URL encoding problem by @jakebeal in #446
- Explain closure assumptions and document composition implications by @jakebeal in #448
- Partial resolution of #431: Feature and Location are declared abstract in prose by @jakebeal in #449
- Use RDF cardinality terminology by @jakebeal in #450
- Remove all embedded redlines from text, per issue #441 by @jakebeal in #451
- Remove italics for abstract classes, due to umlet export problem by @jakebeal in #452
- Combinatorial derivation & validation rules by @jakebeal in #440
- Location issue patches by @jakebeal in #456
- Change ComponentReference property hasFeature to refersTo by @jakebeal in #463
- Resolve issue #464 by explaining how to set a missing sequence property by @jakebeal in #467
- Add a line making dual-typing of PROV-O and OM explicit. by @jakebeal in #470
- update GitHub actions workflow by @jamesscottbrown in #471
- recommend use of existing SO terms for feature orientation by @jamesscottbrown in #472
- Release 3.0.1 by @tcmitchell in #473
New Contributors
- @IsabelMarleen made their first contribution in #407
- @lmnh made their first contribution in #408
- @tcmitchell made their first contribution in #405
- @JMante1 made their first contribution in #414
Full Changelog: v3.0.0...v3.0.1
Contributors
jamesscottbrown, tcmitchell, and 9 other contributors
Assets 3
v3.0.0
Major update to version 3.0.0
Summary of changes implemented can be found in SEP 46: Changes in the new SBOL 3.0 specification
v2.3.0
Backwards-compatible release extending data model. In addition to minor textual and graphical updates and corrections, the key changes are:
- SEP 013 -- Sequence insertion and replacement
- SEP 021 -- Experiments and Experimental Data
- SEP 026 -- Add a link from Location to Sequence
- SEP 027 -- Adding a type field to Activity class
- SEP 028 -- Measurements/Parameters and Unit
Additional Changes:
- Separate "Complementary Standards" into its own section
v2.2.1
v2.2.0
Backwards-compatible release extending data model and updating ontology terms and best practices. In addition to minor textual updates and corrections, the key changes are:
- SEP 07 - Support for Combinatorial Design
- SEP 12 - Cardinality for Identified.wasDerivedFrom
- SEP 18 - The Inclusion of the Attachment Class for Attaching Data to Designs
- SEP 19 - Support for Using SBOL to Model the Design-Build-Test-Learn Cycle
Differences from v2.1.0 are marked by colored text and change-bars.
v2.1.0
Backwards-compatible release extending data model and updating ontology terms and best practices. In addition to minor textual updates and corrections, the key changes are:
- "role" is added to Component and SequenceAnnotation, "roleIntegration" allows a Component role to override a ComponentDefinition role in context. SequenceAnnotation roles are used for marking features that should not have their own ComponentDefinition (e.g., restriction sites, imported GenBank features)
- SBO terms added to fill out recommended Interaction and Participation tables
- Best practices for representing topology (e.g., circular vs. linear DNA) using SequenceOntology types
- Best practices for tracking provenance
- Best practices for dealing with RDF compliance issues on identifiers.org by alternative use of equivalent compliant purl.org URIs
Differences from v2.0 are marked by colored text and change-bars.