From 506d6e93044c2aa96ea2b9ad4b723aa1f0d9f7c7 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Sat, 25 May 2024 17:18:43 +0300
Subject: [PATCH 1/4] Update pom.xml

---
 pom.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index ab8abdf0b..24d1a1590 100644
--- a/pom.xml
+++ b/pom.xml
@@ -212,9 +212,9 @@
       <version>2.0.13</version>
     </dependency>
     <dependency>
-      <groupId>au.csiro</groupId>
-      <artifactId>elk-owlapi4</artifactId>
-      <version>0.5.0</version>
+      <groupId>io.github.liveontologies</groupId>
+      <artifactId>elk-distribution-owlapi</artifactId>
+      <version>0.6.0</version>
       <exclusions>
         <exclusion>
           <groupId>log4j</groupId>

From e942df9f67ec71c375984933dc556c1b41a984f4 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Sat, 25 May 2024 17:21:44 +0300
Subject: [PATCH 2/4] Update ELK entry in Changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1fe0e6fe2..5bff6de45 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add `--enforce-obo-format`, `--exclude-named-classes` and `--include-subclass-of` features to relax command [#1060, #1183]
 - Updated obographs to [version 0.3.1](https://github.com/geneontology/obographs/releases/tag/v0.3.1)
 - Updated OWL API to 3.5.29. This includes a major update to OBO Format which now supports [IDSPACE declarations](https://github.com/owlcs/owlapi/pull/1102) (non-OBO Foundry prefixes).
+- Updated Elk to version 0.6.0, see [here](https://github.com/liveontologies/elk-reasoner/issues/48#issuecomment-2130090254).
 
 ### Fixed
 - '--annotate-with-source true' does not work with extract --method subset [#1160]

From 5d8c05e002ede4618cc1fb9737f5159c375f9ba3 Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Mon, 27 May 2024 16:24:46 +0300
Subject: [PATCH 3/4] Update pom.xml

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 24d1a1590..0429dda1d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -213,7 +213,7 @@
     </dependency>
     <dependency>
       <groupId>io.github.liveontologies</groupId>
-      <artifactId>elk-distribution-owlapi</artifactId>
+      <artifactId>elk-owlapi</artifactId>
       <version>0.6.0</version>
       <exclusions>
         <exclusion>

From ffddd20778d5df93a57eff2ed5942ceaf3d69552 Mon Sep 17 00:00:00 2001
From: "James A. Overton" <james@overton.ca>
Date: Mon, 27 May 2024 14:11:31 -0400
Subject: [PATCH 4/4] Remove log4j exclusion for elk

---
 pom.xml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 0429dda1d..5fa89645b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -216,10 +216,6 @@
       <artifactId>elk-owlapi</artifactId>
       <version>0.6.0</version>
       <exclusions>
-        <exclusion>
-          <groupId>log4j</groupId>
-          <artifactId>log4j</artifactId>
-        </exclusion>
         <exclusion>
           <groupId>net.sourceforge.owlapi</groupId>
           <artifactId>owlapi-apibinding</artifactId>