synbiodex/sbol-specification issues and pull requests

#104 - Implementation

Pull Request - State: closed - Opened by cjmyers over 7 years ago

#103 - Combo

Pull Request - State: closed - Opened by nroehner over 7 years ago

#102 - Added Attachment class.

Pull Request - State: closed - Opened by ckmadsen over 7 years ago

#101 - Expand the definition of SBOL-compliant URI

Issue - State: closed - Opened by bbartley almost 8 years ago - 3 comments
Labels: question, Needs SEP

#100 - Updates for provenance for SBOL 2.2.0

Pull Request - State: closed - Opened by cjmyers almost 8 years ago - 1 comment

#99 - wasGeneratedBy variable in prov-o UML Figure 29 should be 0..*

Issue - State: closed - Opened by cjmyers almost 8 years ago - 2 comments
Labels: bug, Non-SEP change

#98 - 2.1.0 Specification has contradicting examples of the PROVO-O namespace

Issue - State: closed - Opened by bbartley over 8 years ago - 2 comments
Labels: bug, Non-SEP change

#96 - displayId is not meaningfully optional

Issue - State: closed - Opened by chrismacklin over 8 years ago - 15 comments
Labels: presentation issues, Non-SEP change

#95 - Authors field for ComponentDefinitions (and other things?)

Issue - State: closed - Opened by graik over 8 years ago - 1 comment
Labels: presentation issues, Non-SEP change

#93 - Fix examples

Pull Request - State: closed - Opened by cjmyers over 8 years ago - 2 comments

#92 - Problem with URIs in Example B.1.7

Issue - State: closed - Opened by cjmyers over 8 years ago - 1 comment
Labels: bug, Non-SEP change

#91 - Specify deletion mutations

Issue - State: closed - Opened by jakebeal over 8 years ago - 3 comments
Labels: enhancement, Needs SEP

#89 - Best practice needed to add extra rdf:type to distinguish GenericTopLevels

Issue - State: closed - Opened by cjmyers over 8 years ago - 3 comments
Labels: enhancement, Needs SEP

#88 - Need a validation rule for namespace to end with delimiter

Issue - State: closed - Opened by cjmyers over 8 years ago - 4 comments
Labels: Non-SEP change, validation rules

#87 - Implementation of SEP12 into specification

Pull Request - State: closed - Opened by jakebeal over 8 years ago - 4 comments

#86 - Vertical Orientation Option

Issue - State: closed - Opened by jfarlow over 8 years ago - 2 comments

#85 - Typo in Prov-o figure (Figure 29)

Issue - State: closed - Opened by cjmyers over 8 years ago - 1 comment

#84 - wasDerivedFrom should be 0..n

Issue - State: closed - Opened by jakebeal over 8 years ago - 1 comment
Labels: enhancement, Needs SEP

#83 - Sequence by reference

Issue - State: closed - Opened by jakebeal over 8 years ago - 2 comments
Labels: enhancement, Needs SEP

#81 - Sep011

Pull Request - State: closed - Opened by cjmyers almost 9 years ago

#80 - New authors

Pull Request - State: closed - Opened by tramyn almost 9 years ago

#79 - Updated the provenance examples using libSBOLj

Pull Request - State: closed - Opened by goksel almost 9 years ago

#78 - Changing 2.0 to 2.1, 2.x or just 2 as appropriate

Pull Request - State: closed - Opened by jakebeal almost 9 years ago - 5 comments

#77 - Extended the best practices with the provenance section

Pull Request - State: closed - Opened by goksel almost 9 years ago

#76 - SBOL 2.0 to SBOL 2.x

Issue - State: closed - Opened by jakebeal almost 9 years ago
Labels: presentation issues

#75 - Update SequenceAnnotation UML

Pull Request - State: closed - Opened by cjmyers almost 9 years ago

#74 - Mentioned GenBank feature

Pull Request - State: closed - Opened by cjmyers almost 9 years ago

#73 - Best practices using colons in URIs

Issue - State: closed - Opened by cjmyers almost 9 years ago - 1 comment
Labels: Non-SEP change

#72 - Add Provenance recommendations to best practices

Issue - State: closed - Opened by cjmyers almost 9 years ago - 1 comment
Labels: Non-SEP change

#71 - Removed role integration from SA

Pull Request - State: closed - Opened by cjmyers almost 9 years ago

#70 - Sequence annotation cannot have both a role and a component

Issue - State: closed - Opened by jakebeal almost 9 years ago - 2 comments
Labels: enhancement, Needs SEP, Non-SEP change

#69 - Add interaction sbo terms

Pull Request - State: closed - Opened by tramyn almost 9 years ago - 2 comments

#68 - Need to add discussion about using Roles on SequenceAnnotations

Issue - State: closed - Opened by cjmyers almost 9 years ago - 2 comments

#67 - Completed edits for new roles/roleIntegration fields.

Pull Request - State: closed - Opened by cjmyers almost 9 years ago

#66 - Integrate the substance of SEP 004 into SBOL-specification.

Pull Request - State: closed - Opened by mikebissell about 9 years ago - 3 comments

#65 - Representation of combinatorial assemblies

Issue - State: closed - Opened by jakebeal about 9 years ago - 1 comment
Labels: duplicate

#64 - Update link for URI syntax in rules 10201 and 10203

Issue - State: closed - Opened by zgzn about 9 years ago - 1 comment

#63 - refer to W3C recommendation for "cool URIs" in RDF

Issue - State: closed - Opened by graik about 9 years ago - 1 comment
Labels: question, presentation issues, Non-SEP change

#62 - Version 2.1 SEP 4 UML Update

Pull Request - State: closed - Opened by nroehner about 9 years ago

#61 - rule-10601 has been removed

Issue - State: closed - Opened by jakebeal over 9 years ago - 2 comments
Labels: bug

#60 - SBOL 2.0.1 Edits

Pull Request - State: closed - Opened by nroehner over 9 years ago - 1 comment

#59 - Representing circular elements

Issue - State: closed - Opened by jakebeal over 9 years ago - 5 comments
Labels: enhancement, Needs SEP

#58 - New rule 10527

Issue - State: closed - Opened by cjmyers over 9 years ago - 5 comments
Labels: question, ready-for-pull

#57 - Revise rule 10511

Issue - State: closed - Opened by cjmyers over 9 years ago - 9 comments
Labels: question, ready-for-pull

#56 - wasDerivedFrom checks only for TopLevel

Issue - State: closed - Opened by cjmyers over 9 years ago - 3 comments
Labels: Non-SEP change, ready-for-pull

#55 - Better describe the purpose of displayId

Issue - State: closed - Opened by graik over 9 years ago - 5 comments
Labels: presentation issues, Non-SEP change

#54 - displayId should be renamed

Issue - State: closed - Opened by 3ach over 9 years ago - 7 comments
Labels: Needs SEP

#53 - SBOL 2 needs clear semantics to distinguish whether certain classes / properties indicate a designer's intent versus an empirical observation after the design is actualized into a real biological construct

Issue - State: closed - Opened by bbartley over 9 years ago - 2 comments
Labels: question

#52 - Implement InteractionDefinition

Issue - State: closed - Opened by jamesamcl over 9 years ago
Labels: enhancement, Needs SEP

#51 - Quick grammar fixes

Issue - State: closed - Opened by michael13162 over 9 years ago - 2 comments
Labels: Non-SEP change, ready-for-pull

#50 - Rules sbol-10517 and sbol-10516 overlap

Issue - State: closed - Opened by cjmyers over 9 years ago - 1 comment
Labels: Non-SEP change, ready-for-pull

#49 - Validation rules for Annotations and Generic Top Levels

Issue - State: closed - Opened by cjmyers over 9 years ago - 1 comment
Labels: Non-SEP change, ready-for-pull

#48 - Make a new category for weak required rules that are impossible to check

Issue - State: closed - Opened by zgzn over 9 years ago - 1 comment
Labels: Non-SEP change, ready-for-pull

#47 - Mention Maven semantic versioning in rule 10211

Issue - State: closed - Opened by zgzn over 9 years ago - 3 comments
Labels: Non-SEP change, ready-for-pull

#46 - Rule 10806 can be more specific

Issue - State: closed - Opened by cjmyers over 9 years ago - 3 comments
Labels: Non-SEP change, ready-for-pull

#45 - Remove rule 10205

Issue - State: closed - Opened by cjmyers over 9 years ago - 7 comments
Labels: Needs SEP

#44 - Rules for inherited, required, and optional properties should be revised

Issue - State: closed - Opened by cjmyers over 9 years ago - 5 comments
Labels: Non-SEP change, ready-for-pull

#43 - Add more requirement to sbol-10207 to allow it to be checked.

Issue - State: closed - Opened by zgzn over 9 years ago - 2 comments
Labels: Non-SEP change, ready-for-pull

#42 - Define precise meaning of "locally unique" for sbol-10205

Issue - State: closed - Opened by zgzn over 9 years ago - 10 comments
Labels: Non-SEP change, ready-for-pull

#41 - Need a rule to disallow annotations in SBOL namespace

Issue - State: closed - Opened by cjmyers over 9 years ago - 11 comments
Labels: Non-SEP change, ready-for-pull

#40 - Need validation rule that there should only be one SBOL namespace

Issue - State: closed - Opened by cjmyers over 9 years ago - 5 comments
Labels: Non-SEP change, ready-for-pull

#39 - Need validation rule on uniqueness of persistent identities

Issue - State: closed - Opened by cjmyers over 9 years ago - 2 comments
Labels: Non-SEP change, ready-for-pull

#38 - Change strong required to weak required for validation rule sbol-11703.

Issue - State: closed - Opened by zgzn over 9 years ago - 3 comments
Labels: Non-SEP change, ready-for-pull

#37 - ordering of serialized elements

Issue - State: closed - Opened by chrismacklin over 9 years ago - 2 comments

#36 - Contradictory mappings

Issue - State: closed - Opened by cjmyers over 9 years ago - 1 comment
Labels: Non-SEP change, ready-for-pull

#35 - Required namespaces

Issue - State: closed - Opened by cjmyers almost 10 years ago - 1 comment

#34 - Best practices on interaction types and participant roles

Issue - State: closed - Opened by cjmyers almost 10 years ago - 3 comments
Labels: Non-SEP change, ready-for-pull

#33 - Require role on participation

Issue - State: closed - Opened by cjmyers almost 10 years ago - 5 comments
Labels: Non-SEP change, ready-for-pull

#32 - Locations fail to unambiguously specify their related Sequence (if multiple Sequences in a ComponentDefinition).

Issue - State: closed - Opened by mikebissell almost 10 years ago - 9 comments
Labels: Needs SEP

#31 - Expand ComponentInstance:definition cardinality to support libraries

Issue - State: closed - Opened by jakebeal almost 10 years ago - 11 comments
Labels: enhancement, question, Needs SEP

#30 - Explicitly specify whether collections are expected to be ordered.

Issue - State: closed - Opened by mikebissell about 10 years ago - 5 comments
Labels: duplicate

#29 - Create cover page with authors and abstracts

Issue - State: closed - Opened by cjmyers about 10 years ago - 3 comments
Labels: presentation issues

#28 - Provide application use case examples

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: invalid, presentation issues

#27 - Ensure that users can ignore features they do not need

Issue - State: closed - Opened by jakebeal about 10 years ago - 4 comments
Labels: presentation issues, ready-for-pull

#26 - Definition / Instance distinction needs to be better explained

Issue - State: closed - Opened by jakebeal about 10 years ago - 3 comments
Labels: bug, presentation issues

#25 - Should ComponentDefinition be allowed to have multiple Sequences?

Issue - State: closed - Opened by jakebeal about 10 years ago - 5 comments
Labels: question, Needs SEP

#24 - Is Module / ModuleDefinition more complexity than necessary?

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: question, Needs SEP

#23 - Should ComponentInstance and ComponentDefinition be separate?

Issue - State: closed - Opened by jakebeal about 10 years ago - 8 comments
Labels: question, Needs SEP

#22 - Specification needs better examples

Issue - State: closed - Opened by jakebeal about 10 years ago - 3 comments
Labels: enhancement, presentation issues, Non-SEP change

#21 - Figure needs clarification

Issue - State: closed - Opened by jakebeal about 10 years ago
Labels: presentation issues

#20 - Best practice file extension

Issue - State: closed - Opened by jakebeal about 10 years ago - 3 comments
Labels: Non-SEP change, ready-for-pull

#19 - SEP 004: Add contextual role properties to SequenceAnnotation and Component

Issue - State: closed - Opened by mikebissell about 10 years ago - 13 comments
Labels: enhancement

#18 - Confirm that BioPax terms in data model example match model specification

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: bug

#17 - Get a BBF RFC number

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: bug

#16 - Have enough people looked at this history?

Issue - State: closed - Opened by jakebeal about 10 years ago - 4 comments
Labels: help wanted, question

#15 - Serialization example runs off right margin

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: bug, presentation issues

#14 - Check sanity of mapping section location

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: presentation issues

#13 - More types of relationships for SequenceConstraint

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: enhancement, Needs SEP

#12 - What URIs are allowed for SequenceConstraint restriction property?

Issue - State: closed - Opened by jakebeal about 10 years ago - 8 comments
Labels: question, Needs SEP

#11 - Better recommended role for Transcription Factor

Issue - State: closed - Opened by jakebeal about 10 years ago - 8 comments
Labels: bug, Non-SEP change

#10 - Consolidate recommended sequence encodings?

Issue - State: closed - Opened by jakebeal about 10 years ago - 6 comments
Labels: bug, enhancement, Non-SEP change

#9 - Add examples of use of each class

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: Non-SEP change, examples

#8 - Ensure that no UML figures have labels conflicting with their arrows

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: presentation issues

#7 - Which ontology should be used for protein roles?

Issue - State: closed - Opened by jakebeal about 10 years ago - 5 comments
Labels: enhancement, Needs SEP

#6 - Create an XSD for SBOL2

Issue - State: closed - Opened by jakebeal about 10 years ago - 6 comments
Labels: enhancement, Non-SEP change

#5 - Versioning of linked compliant objects

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: Needs SEP

#4 - Best practices for creation and modification dates

Issue - State: closed - Opened by jakebeal about 10 years ago - 1 comment
Labels: enhancement, Non-SEP change, ready-for-pull

#3 - Pre-release final pass on 2.0 spec

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: presentation issues

#2 - Improve "format comparison" figure

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: presentation issues

#1 - First paragraph of "purpose" is too detailed

Issue - State: closed - Opened by jakebeal about 10 years ago - 2 comments
Labels: presentation issues

GitHub / synbiodex/sbol-specification issues and pull requests