From 106349f2d82a0755798c7dc150630c50b03bae9e Mon Sep 17 00:00:00 2001
From: viktorwichern <135847866+viktorwichern@users.noreply.github.com>
Date: Sat, 3 Feb 2024 00:05:11 +0100
Subject: [PATCH] attempt to create import structure

---
 oeo-imports/envo/envo-n-hierarchy.txt   |  1 +
 oeo-imports/envo/envo-w-hierarchy.txt   |  3 +++
 oeo-imports/envo/extract-envo-module.sh | 20 ++++++++++++++++++++
 3 files changed, 24 insertions(+)
 create mode 100644 oeo-imports/envo/envo-n-hierarchy.txt
 create mode 100644 oeo-imports/envo/envo-w-hierarchy.txt
 create mode 100644 oeo-imports/envo/extract-envo-module.sh

diff --git a/oeo-imports/envo/envo-n-hierarchy.txt b/oeo-imports/envo/envo-n-hierarchy.txt
new file mode 100644
index 0000000..553d59f
--- /dev/null
+++ b/oeo-imports/envo/envo-n-hierarchy.txt
@@ -0,0 +1 @@
+http://purl.obolibrary.org/obo/ENVO_01000254 # environmental system 
\ No newline at end of file
diff --git a/oeo-imports/envo/envo-w-hierarchy.txt b/oeo-imports/envo/envo-w-hierarchy.txt
new file mode 100644
index 0000000..53102b4
--- /dev/null
+++ b/oeo-imports/envo/envo-w-hierarchy.txt
@@ -0,0 +1,3 @@
+http://purl.obolibrary.org/obo/ENVO_02500000 # environmental system process 
+http://purl.obolibrary.org/obo/ENVO_01000629 # climate change 
+http://purl.obolibrary.org/obo/ENVO_02500004 # greenhouse effect
\ No newline at end of file
diff --git a/oeo-imports/envo/extract-envo-module.sh b/oeo-imports/envo/extract-envo-module.sh
new file mode 100644
index 0000000..931751b
--- /dev/null
+++ b/oeo-imports/envo/extract-envo-module.sh
@@ -0,0 +1,20 @@
+# Note: For consistent results run with ROBOT v1.91 or higher
+# Download the ENVO release from 2023-13-02
+curl -L https://raw.githubusercontent.com/EnvironmentOntology/envo/v2023-02-13/envo.owl > envo-full-download.owl
+# Extract the terms we want with hierarchy until the upper term "entity" (IAO_0000030). 
+#  -- tbd in oeo-import-edits
+# Classification:  tbd in oeo-import-edits
+robot merge --input envo-full-download.owl extract --method MIREOT --lower-terms envo-w-hierarchy.txt --intermediates all --upper-term http://purl.obolibrary.org/obo/BFO_0000001 --output envo-extracted-w-hierarchy.owl
+# Extract the terms we want without hierarchy
+robot merge --input envo-full-download.owl extract --method MIREOT --lower-terms envo-n-hierarchy.txt --upper-term owl:topObjectProperty --intermediates none --output envo-extracted-n-hierarchy.owl
+# Create Extracted module and annotate with new ontology information
+robot merge --input envo-extracted-w-hierarchy.owl --input envo-extracted-n-hierarchy.owl annotate --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/envo-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/envo-extracted.owl --output envo-extracted.owl
+# Annotates the output module with a commentary to the origin of the content
+robot annotate --input envo-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the The Environment Ontology (ENVO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT from the list of selected terms (envo-extract-w-hierarchy.txt, envo-extract-n-hierarchy.txt) located in the OEO-tools repository." --output envo-extracted.owl
+# Annotates each axiom with the ontology IRI, using prov:wasDerivedFrom
+robot annotate --input envo-extracted.owl --annotate-derived-from true --annotate-defined-by true --output envo-extracted.owl
+## Annotate with new ontology information
+#robot annotate --input envo-extracted.owl  --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/envo-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/envo-extracted.owl --output envo-extracted.owl
+rm envo-full-download.owl
+rm envo-extracted-w-hierarchy.owl
+rm envo-extracted-n-hierarchy.owl
\ No newline at end of file