From 8048d87cd3cfdc4b9966884fc9f37d1f03c01ced Mon Sep 17 00:00:00 2001
From: goksel <gokselmisirli@yahoo.com>
Date: Sun, 20 Sep 2020 19:39:44 +0100
Subject: [PATCH 1/2] Added Maven instructions in the README file

---
 README.md                                     |  64 ++++++----
 .../component_urn_uri.jsonld                  |   2 +-
 .../component_urn_uri/component_urn_uri.nt    |   6 +-
 .../component_urn_uri/component_urn_uri.rdf   |   2 +-
 .../component_urn_uri/component_urn_uri.rj    |   2 +-
 .../component_urn_uri/component_urn_uri.ttl   |   2 +-
 .../activity/activity.jsonld                  |  12 +-
 .../provenance_entity/activity/activity.nt    |   4 +-
 .../provenance_entity/activity/activity.rdf   |   4 +-
 .../provenance_entity/activity/activity.rj    |  12 +-
 .../provenance_entity/activity/activity.ttl   |   4 +-
 libSBOLj3/pom.xml                             | 117 ++++++++++++------
 12 files changed, 145 insertions(+), 86 deletions(-)

diff --git a/README.md b/README.md
index 4077fc3..7715e37 100644
--- a/README.md
+++ b/README.md
@@ -1,30 +1,42 @@
-# libSBOLj
-XML
-```
-<rdf:RDF
-    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:sbol="http://sbols.org/v3#">
-   <sbol:Sequence rdf:about="http://myseq.org/seqabc">
-      <sbol:encoding rdf:resource="http://sbols.org/v3#iupacNucleicAcid"/>
-      <sbol:elements>aaaatttggg</sbol:elements>
-      <sbol:description>pTetR promoter</sbol:description>
-      <sbol:name>pTetR</sbol:name>
-      <sbol:displayId>pTetR</sbol:displayId>
-   </sbol:Sequence>
-</rdf:RDF>
-```
+# libSBOLj3 - A Java library for the Synthetic Biology Open Language 3
+The libSBOLj Java library has been developed for the Synthetic Biology Open Language 3.0. The library is  under development and is currently available as an alpha release. 
 
-Turtle:
-```
+SBOL represents data using RDF graphs, which can be serialised in different formats. The libSBOLj3 library supports the following RDF formats.
+* RDF/XML
+* Turtle
+* N3
+* JSON-LD
+* RDF/JSON
 
-@base          <http://testbase.org> .
-@prefix sbol:  <http://sbols.org/v3#> .
+## How to use libSBOLj3
 
-<http://myseq.org/seqabc>
-        a                 sbol:Sequence ;
-        sbol:description  "pTetR promoter" ;
-        sbol:displayId    "pTetR" ;
-        sbol:elements     "aaaatttggg" ;
-        sbol:encoding     sbol:iupacNucleicAcid ;
-        sbol:name         "pTetR" .
+### As a Maven dependency in a Maven project
+Use this option if you are developing a Java application using Maven. Add the following libSBOLj dependency to your Maven applications's POM file (pom.xml. Please also make sure that you include the Nexus's Snapshots repository in the POM file. 
+``` 
+</dependencies>
+	...
+   <dependency>
+		<groupId>org.sbolstandard</groupId>
+		<artifactId>libSBOLj3</artifactId>
+		<version>1.0-SNAPSHOT</version>
+	</dependency>
+   ...
+</dependencies>
+
+<repositories>
+   <repository>
+      <id>oss-sonatype</id>
+      <name>oss-sonatype</name>
+      <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
+      <snapshots>
+         <enabled>true</enabled>
+      </snapshots>
+   </repository>
+</repositories>
 ```
+
+### As a Java dependency in a non-Maven project
+The libSBOLj3 library is available as a JAR file. Please download the file from . A single JAR file (with the "withDepencencies" suffix), which includes all the required libSBOLj3 related dependencies is also available.
+
+## SBOL Examples
+Several SBOL3 examples are available as part of the libSBOLj3 library. These examples can be found at . These examples have also been made available as part of the SBOLTestSuite at https://github.com/SynBioDex/SBOLTestSuite/tree/master/SBOL3. Some of these examples have beeen explained in the recent SBOL3 paper. Please see  https://doi.org/10.3389/fbioe.2020.01009 for more details.
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld
index 30057df..21f2f70 100644
--- a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld
+++ b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld
@@ -1,5 +1,5 @@
 {
-  "@id" : "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122",
+  "@id" : "urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122",
   "@type" : "sbol:Component",
   "name" : "TetR",
   "type" : "SBO:0000252",
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt
index d372a36..a81d65c 100644
--- a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt
+++ b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt
@@ -1,3 +1,3 @@
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://sbols.org/v3#name> "TetR" .
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122> <http://sbols.org/v3#name> "TetR" .
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf
index 72f2947..bf537cd 100644
--- a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf
+++ b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf
@@ -10,7 +10,7 @@
     xmlns="https://sbolstandard.org/examples/"
     xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
    xml:base="https://sbolstandard.org/examples/">
-   <sbol:Component rdf:about="urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122">
+   <sbol:Component rdf:about="urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122">
       <sbol:name>TetR</sbol:name>
       <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
    </sbol:Component>
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj
index 79b62a9..9fc709d 100644
--- a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj
+++ b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj
@@ -1,5 +1,5 @@
 { 
-  "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122" : { 
+  "urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122" : { 
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
       "type" : "uri" ,
       "value" : "http://sbols.org/v3#Component"
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl
index ae4038b..f874e8a 100644
--- a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl
+++ b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl
@@ -9,7 +9,7 @@
 @prefix prov:  <http://www.w3.org/ns/prov#> .
 @prefix om:    <http://www.ontology-of-units-of-measure.org/resource/om-2/> .
 
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122>
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122>
         a          sbol:Component ;
         sbol:name  "TetR" ;
         sbol:type  SBO:0000252 .
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.jsonld b/libSBOLj3/output/provenance_entity/activity/activity.jsonld
index 67049bc..00412b0 100644
--- a/libSBOLj3/output/provenance_entity/activity/activity.jsonld
+++ b/libSBOLj3/output/provenance_entity/activity/activity.jsonld
@@ -26,10 +26,10 @@
     "displayId" : "codon_optimization_activity",
     "name" : "Codon optimization activity",
     "type" : "sbol:design",
-    "endedAtTime" : "2020-08-30T17:16:29.495Z",
+    "endedAtTime" : "2020-08-30T17:48:04.765Z",
     "qualifiedAssociation" : "codon_optimization_activity/association",
     "qualifiedUsage" : [ "codon_optimization_activity/optimised_usage", "codon_optimization_activity/source_usage" ],
-    "startedAtTime" : "2019-07-29T17:16:29.495Z"
+    "startedAtTime" : "2019-07-29T17:48:04.765Z"
   }, {
     "@id" : "codon_optimization_activity/association",
     "@type" : "prov:Association",
@@ -112,15 +112,15 @@
       "@id" : "http://www.w3.org/ns/prov#qualifiedAssociation",
       "@type" : "@id"
     },
-    "endedAtTime" : {
-      "@id" : "http://www.w3.org/ns/prov#endedAtTime"
+    "startedAtTime" : {
+      "@id" : "http://www.w3.org/ns/prov#startedAtTime"
     },
     "qualifiedUsage" : {
       "@id" : "http://www.w3.org/ns/prov#qualifiedUsage",
       "@type" : "@id"
     },
-    "startedAtTime" : {
-      "@id" : "http://www.w3.org/ns/prov#startedAtTime"
+    "endedAtTime" : {
+      "@id" : "http://www.w3.org/ns/prov#endedAtTime"
     },
     "@vocab" : "https://sbolstandard.org/examples/",
     "SBO" : "https://identifiers.org/SBO:",
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.nt b/libSBOLj3/output/provenance_entity/activity/activity.nt
index e175070..7222192 100644
--- a/libSBOLj3/output/provenance_entity/activity/activity.nt
+++ b/libSBOLj3/output/provenance_entity/activity/activity.nt
@@ -39,11 +39,11 @@
 <https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Plan> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#type> <http://sbols.org/v3#design> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedAssociation> <https://sbolstandard.org/examples/codon_optimization_activity/association> .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#endedAtTime> "2020-08-30T17:16:29.495Z" .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#startedAtTime> "2019-07-29T17:48:04.765Z" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedUsage> <https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#name> "Codon optimization activity" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#description> "An activity that is used to optimise codons" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#displayId> "codon_optimization_activity" .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#startedAtTime> "2019-07-29T17:16:29.495Z" .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#endedAtTime> "2020-08-30T17:48:04.765Z" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedUsage> <https://sbolstandard.org/examples/codon_optimization_activity/source_usage> .
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.rdf b/libSBOLj3/output/provenance_entity/activity/activity.rdf
index 497e862..783301f 100644
--- a/libSBOLj3/output/provenance_entity/activity/activity.rdf
+++ b/libSBOLj3/output/provenance_entity/activity/activity.rdf
@@ -55,7 +55,7 @@
             <sbol:displayId>association</sbol:displayId>
          </prov:Association>
       </prov:qualifiedAssociation>
-      <prov:endedAtTime>2020-08-30T17:16:29.495Z</prov:endedAtTime>
+      <prov:startedAtTime>2019-07-29T17:48:04.765Z</prov:startedAtTime>
       <prov:qualifiedUsage>
          <prov:Usage rdf:about="codon_optimization_activity/optimised_usage">
             <prov:hadRole rdf:resource="https://identifiers.org/SBO:0000011"/>
@@ -66,7 +66,7 @@
       <sbol:name>Codon optimization activity</sbol:name>
       <sbol:description>An activity that is used to optimise codons</sbol:description>
       <sbol:displayId>codon_optimization_activity</sbol:displayId>
-      <prov:startedAtTime>2019-07-29T17:16:29.495Z</prov:startedAtTime>
+      <prov:endedAtTime>2020-08-30T17:48:04.765Z</prov:endedAtTime>
       <prov:qualifiedUsage>
          <prov:Usage rdf:about="codon_optimization_activity/source_usage">
             <prov:hadRole rdf:resource="https://identifiers.org/SBO:0000645"/>
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.rj b/libSBOLj3/output/provenance_entity/activity/activity.rj
index f0dac56..62b9002 100644
--- a/libSBOLj3/output/provenance_entity/activity/activity.rj
+++ b/libSBOLj3/output/provenance_entity/activity/activity.rj
@@ -165,7 +165,12 @@
      ] ,
     "http://www.w3.org/ns/prov#endedAtTime" : [ { 
       "type" : "literal" ,
-      "value" : "2020-08-30T17:16:29.495Z"
+      "value" : "2020-08-30T17:48:04.765Z"
+    }
+     ] ,
+    "http://www.w3.org/ns/prov#startedAtTime" : [ { 
+      "type" : "literal" ,
+      "value" : "2019-07-29T17:48:04.765Z"
     }
      ] ,
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
@@ -173,11 +178,6 @@
       "value" : "http://www.w3.org/ns/prov#Activity"
     }
      ] ,
-    "http://www.w3.org/ns/prov#startedAtTime" : [ { 
-      "type" : "literal" ,
-      "value" : "2019-07-29T17:16:29.495Z"
-    }
-     ] ,
     "http://sbols.org/v3#name" : [ { 
       "type" : "literal" ,
       "value" : "Codon optimization activity"
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.ttl b/libSBOLj3/output/provenance_entity/activity/activity.ttl
index e495e6f..91ebfea 100644
--- a/libSBOLj3/output/provenance_entity/activity/activity.ttl
+++ b/libSBOLj3/output/provenance_entity/activity/activity.ttl
@@ -69,7 +69,7 @@
         sbol:displayId             "codon_optimization_activity" ;
         sbol:name                  "Codon optimization activity" ;
         sbol:type                  sbol:design ;
-        prov:endedAtTime           "2020-08-30T17:16:29.495Z" ;
+        prov:endedAtTime           "2020-08-30T17:48:04.765Z" ;
         prov:qualifiedAssociation  <codon_optimization_activity/association> ;
         prov:qualifiedUsage        <codon_optimization_activity/optimised_usage> , <codon_optimization_activity/source_usage> ;
-        prov:startedAtTime         "2019-07-29T17:16:29.495Z" .
+        prov:startedAtTime         "2019-07-29T17:48:04.765Z" .
diff --git a/libSBOLj3/pom.xml b/libSBOLj3/pom.xml
index 27eff2a..c1b5dd1 100644
--- a/libSBOLj3/pom.xml
+++ b/libSBOLj3/pom.xml
@@ -1,20 +1,25 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>org.sbolstandard</groupId>
-  <artifactId>libSBOLj3</artifactId>
-  <packaging>jar</packaging>
-  <version>1.0-SNAPSHOT</version>
-  <name>libSBOLj3</name>
-  <url>http://maven.apache.org</url>
-  <dependencies>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13</version>
-      <scope>test</scope>
-    </dependency>
-    		<dependency>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>org.sbolstandard</groupId>
+	<artifactId>libSBOLj3</artifactId>
+	<packaging>jar</packaging>
+	<version>1.0-SNAPSHOT</version>
+	<name>libSBOLj3</name>
+	<url>https://github.com/goksel/libSBOLj3</url>
+	<issueManagement>
+		<system>GitHub Issues</system>
+		<url>https://github.com/goksel/libSBOLj3/issues</url>
+	</issueManagement>
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.13</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-base</artifactId>
 			<version>3.14.0</version>
@@ -23,25 +28,67 @@
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-arq</artifactId>
 			<version>3.14.0</version>
-		</dependency>  
+		</dependency>
 		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
-<dependency>
-    <groupId>commons-io</groupId>
-    <artifactId>commons-io</artifactId>
-    <version>2.6</version>
-</dependency>
-		
-  </dependencies>
-<build>
-  <plugins>
-    <plugin>
-      <groupId>org.apache.maven.plugins</groupId>
-      <artifactId>maven-compiler-plugin</artifactId>
-      <version>3.3</version>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.6</version>
+		</dependency>
+
+	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.3</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+			
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>3.2.4</version>
+				<configuration>
+					<shadedArtifactAttached>true</shadedArtifactAttached>
+					<shadedClassifierName>withDependencies</shadedClassifierName>
+				</configuration>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+
+				
+				    <plugin>
+      <groupId>org.sonatype.plugins</groupId>
+      <artifactId>nexus-staging-maven-plugin</artifactId>
+      <version>1.6.7</version>
+      <extensions>true</extensions>
       <configuration>
-        <source>1.8</source>
-        <target>1.8</target>
+        <serverId>ossrh</serverId>
+        <nexusUrl>https://oss.sonatype.org/</nexusUrl>
+        <autoReleaseAfterClose>false</autoReleaseAfterClose>
       </configuration>
     </plugin>
-  </plugins>
-</build></project>
+    
+
+		</plugins>
+	</build>
+	
+		<distributionManagement>
+		<snapshotRepository>
+			<id>ossrh</id>
+			<url>https://oss.sonatype.org/content/repositories/snapshots</url>
+		</snapshotRepository>
+	</distributionManagement>
+	
+</project>

From a43f75a15a3fac5644073861508a0313af838259 Mon Sep 17 00:00:00 2001
From: goksel <gokselmisirli@yahoo.com>
Date: Sun, 20 Sep 2020 20:04:50 +0100
Subject: [PATCH 2/2] Updated the README with links to the examples and the
 recent SBOL paper

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 7715e37..8b8991e 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # libSBOLj3 - A Java library for the Synthetic Biology Open Language 3
-The libSBOLj Java library has been developed for the Synthetic Biology Open Language 3.0. The library is  under development and is currently available as an alpha release. 
+The libSBOLj Java library has been developed for the [Synthetic Biology Open Language 3.0](https://sbolstandard.org/data-model-specification). The library is  under development and is currently available as an alpha release. 
 
 SBOL represents data using RDF graphs, which can be serialised in different formats. The libSBOLj3 library supports the following RDF formats.
 * RDF/XML
@@ -11,7 +11,7 @@ SBOL represents data using RDF graphs, which can be serialised in different form
 ## How to use libSBOLj3
 
 ### As a Maven dependency in a Maven project
-Use this option if you are developing a Java application using Maven. Add the following libSBOLj dependency to your Maven applications's POM file (pom.xml. Please also make sure that you include the Nexus's Snapshots repository in the POM file. 
+Use this option if you are developing a Java application using [Maven](https://maven.apache.org/). Add the following libSBOLj3 dependency to your Maven applications's POM file (pom.xml). Please also make sure that you include the Nexus' Snapshots repository URL in the POM file. 
 ``` 
 </dependencies>
 	...
@@ -36,7 +36,7 @@ Use this option if you are developing a Java application using Maven. Add the fo
 ```
 
 ### As a Java dependency in a non-Maven project
-The libSBOLj3 library is available as a JAR file. Please download the file from . A single JAR file (with the "withDepencencies" suffix), which includes all the required libSBOLj3 related dependencies is also available.
+The libSBOLj3 library is available as a JAR file. Please download the file from the [releases page](https://github.com/goksel/libSBOLj3/tags). A single JAR file (with the "withDepencencies" suffix), which includes all the required libSBOLj3 related dependencies, is also available.
 
 ## SBOL Examples
-Several SBOL3 examples are available as part of the libSBOLj3 library. These examples can be found at . These examples have also been made available as part of the SBOLTestSuite at https://github.com/SynBioDex/SBOLTestSuite/tree/master/SBOL3. Some of these examples have beeen explained in the recent SBOL3 paper. Please see  https://doi.org/10.3389/fbioe.2020.01009 for more details.
+[Several SBOL3 examples](https://github.com/goksel/libSBOLj3/tree/master/libSBOLj3/output) are available as part of the libSBOLj3 library. These examples have also been made available as part of the [SBOLTestSuite](https://github.com/SynBioDex/SBOLTestSuite/tree/master/SBOL3). Some of these examples have beeen explained in the recent SBOL3 paper, titled "[The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering]"(https://doi.org/10.3389/fbioe.2020.01009).