From 09949f225a5c394639322d1a3aedaea80753f80e Mon Sep 17 00:00:00 2001
From: bsantan <70932395+bsantan@users.noreply.github.com>
Date: Tue, 20 Aug 2024 12:58:43 -0600
Subject: [PATCH] add madin_etal necessary files

---
 .../madin_etal/chebi_manual_annotation.tsv    |  7 +++++
 .../madin_etal/metabolism_map.yaml            | 27 +++++++++++++++++++
 2 files changed, 34 insertions(+)
 create mode 100644 kg_microbe/transform_utils/madin_etal/chebi_manual_annotation.tsv
 create mode 100644 kg_microbe/transform_utils/madin_etal/metabolism_map.yaml

diff --git a/kg_microbe/transform_utils/madin_etal/chebi_manual_annotation.tsv b/kg_microbe/transform_utils/madin_etal/chebi_manual_annotation.tsv
new file mode 100644
index 00000000..de46fe8a
--- /dev/null
+++ b/kg_microbe/transform_utils/madin_etal/chebi_manual_annotation.tsv
@@ -0,0 +1,7 @@
+object_id	object_label	traits_dataset_term	action
+CHEBI:28885	butan-1-ol	butanol	REPLACE
+CHEBI:51850	Methyl pyruvate	pyruvic acid methyl ester	REPLACE
+CHEBI:16000	ethanolamine	2-aminethanol	REPLACE
+CHEBI:30832	adipic acid	adipate	REPLACE
+CHEBI:18276	dihydrogen	H2_CO2	SUPPLEMENT
+CHEBI:18276	dihydrogen	H2_methanol	SUPPLEMENT
\ No newline at end of file
diff --git a/kg_microbe/transform_utils/madin_etal/metabolism_map.yaml b/kg_microbe/transform_utils/madin_etal/metabolism_map.yaml
new file mode 100644
index 00000000..f4aa3600
--- /dev/null
+++ b/kg_microbe/transform_utils/madin_etal/metabolism_map.yaml
@@ -0,0 +1,27 @@
+- ID: oxygen:anaerobe
+  ActualTerm: anaerobic
+  PreferredTerm: anaerobe
+
+- ID: oxygen:anaerobe
+  ActualTerm: strictly anaerobic
+  PreferredTerm: anaerobe
+
+- ID: oxygen:obligate_anaerobe
+  ActualTerm: obligate anaerobic
+  PreferredTerm: obligate anaerobe
+
+- ID: oxygen:facultative_anaerobe
+  ActualTerm: facultative
+  PreferredTerm: facultative anaerobe
+
+- ID: oxygen:obligate_aerobe
+  ActualTerm: obligate aerobic
+  PreferredTerm: obligate aerobe
+
+- ID: oxygen:aerobe
+  ActualTerm: aerobic
+  PreferredTerm: aerobe
+
+- ID: oxygen:microaerophile
+  ActualTerm: microaerophilic
+  PreferredTerm: microaerophilic