From d74b57062098f6c3c3b80af5c849ec0944e6e6d7 Mon Sep 17 00:00:00 2001
From: Jeremy Zucker <djinnome@gmail.com>
Date: Mon, 8 Jun 2020 10:23:44 -0700
Subject: [PATCH 01/10] Added IL6-AMP pathway

---
 Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn       | 224 ++++++++++++++
 .../IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt | 291 ++++++++++++++++++
 .../SARS_CoV2_ARDS_JT_compartment.sbgn        | 228 ++++++++++++++
 .../SARS_CoV2_ARDS_JT_compartments (1).sbgn   | 228 ++++++++++++++
 4 files changed, 971 insertions(+)
 create mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn
 create mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt
 create mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.sbgn
 create mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn

diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn
new file mode 100644
index 0000000..21240cb
--- /dev/null
+++ b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn
@@ -0,0 +1,224 @@
+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.3">
+  <map id="SARS_CoV2_ARDS_JT.sbgn" language="activity flow">
+    <glyph id="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" class="biological activity">
+      <label text="SARS_CoV2"/>
+      <bbox x="116" y="-63" w="60" h="30"/>
+      <glyph id="nwtUOI_de6e5917-8277-459a-8601-e5b41b119c84" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="121" y="-69" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" class="biological activity">
+      <label text="ACE-2"/>
+      <bbox x="312.2633792654036" y="6.65178780532252" w="60" h="30"/>
+      <glyph id="nwtUOI_882f5a09-1f69-46a2-803a-e6415f5518af" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="317.2633792654036" y="0.6517878053225203" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d" class="biological activity">
+      <label text="Angiotensin II"/>
+      <bbox x="411" y="-72" w="60" h="30"/>
+      <glyph id="nwtUOI_9734954e-ce38-4d6b-b174-b755296e6f87" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="416" y="-78" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" class="biological activity">
+      <label text="AT1R"/>
+      <bbox x="533" y="8" w="60" h="30"/>
+      <glyph id="nwtUOI_7c40f9a3-b5f6-4e67-a3a5-608719594329" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="538" y="2" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" class="biological activity">
+      <label text="ADAM17"/>
+      <bbox x="686" y="7" w="60" h="30"/>
+      <glyph id="nwtUOI_a8b0dcc8-2044-4029-84ff-697eb9d373e4" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="691" y="1" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f" class="biological activity">
+      <label text="IL-6R\alpha"/>
+      <bbox x="849" y="7" w="60" h="30"/>
+      <glyph id="nwtUOI_85205377-9d0f-4cb7-92f4-a1cf052cb945" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="854" y="1" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" class="biological activity">
+      <label text="EGF"/>
+      <bbox x="410.51226998555603" y="127.68998759161451" w="60" h="30"/>
+      <glyph id="nwtUOI_926f93af-5744-41be-a87a-73a1cc889e48" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="415.51226998555603" y="121.68998759161451" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_467f7364-10c5-41d7-9889-917373e41162" class="biological activity">
+      <label text="STAT3"/>
+      <bbox x="856.7409483445673" y="246.81094072322628" w="60" h="30"/>
+      <glyph id="nwtUOI_b3625151-50da-4b9b-a5de-af47ac3aeda2" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="861.7409483445673" y="240.81094072322628" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_be369f32-cb2f-4328-a094-c15c356a4505" class="biological activity">
+      <label text="EGFR"/>
+      <bbox x="404.7674680886842" y="179.6276103540774" w="60" h="30"/>
+      <glyph id="nwtUOI_2e7f77b0-71f8-42d1-8956-7bd84baf82ca" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="409.7674680886842" y="173.6276103540774" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b" class="biological activity">
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+      <bbox x="533.1417767239601" y="189.51229259058277" w="60" h="30"/>
+      <glyph id="nwtUOI_4faac32f-98d6-4aac-a3c2-9e91dcb2275e" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="538.1417767239601" y="183.51229259058277" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" class="biological activity">
+      <label text="sIL-6R\alpha"/>
+      <bbox x="683.5457773386427" y="190.02019484784927" w="112.87201056629073" h="30"/>
+      <glyph id="nwtUOI_448c20d5-d229-41d9-a4b3-cc1e914bd115" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="698.2389792757959" y="184.02019484784927" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_1418e98a-456b-42a9-a723-d243855cc770" class="biological activity">
+      <label text="IL-6"/>
+      <bbox x="854.3724122509493" y="139.4328931041598" w="60" h="30"/>
+      <glyph id="nwtUOI_39d57e2a-c30f-407f-9d13-cf62ca40e4ad" class="unit of information">
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+        <entity name="macromolecule"/>
+        <bbox x="859.3724122509493" y="133.4328931041598" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" class="biological activity">
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+      <bbox x="303.9854717001037" y="282.26898539337884" w="60" h="30"/>
+      <glyph id="nwtUOI_fc07e3f8-0664-4442-a493-b2a8a57362c5" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="308.9854717001037" y="276.26898539337884" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_70505ee2-f32e-4d66-88e7-36087274966b" class="biological activity">
+      <label text="FCN1(PRR)"/>
+      <bbox x="303" y="119" w="60" h="30"/>
+      <glyph id="nwtUOI_5199d973-277f-403a-91c8-34d75b03ace1" class="unit of information">
+        <label text=""/>
+        <entity name="complex"/>
+        <bbox x="308" y="113" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" class="biological activity">
+      <label text="IL6/STAT3"/>
+      <bbox x="520" y="295" w="60" h="30"/>
+      <glyph id="nwtUOI_069526b5-ed15-4f88-b0ac-681c4d84aed1" class="unit of information">
+        <label text=""/>
+        <entity name="complex"/>
+        <bbox x="525" y="289" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d" class="phenotype">
+      <label text="ARDS"/>
+      <bbox x="400.0958725001" y="444.20433679745116" w="60" h="30"/>
+    </glyph>
+    <glyph id="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314" class="biological activity">
+      <label text="IL6-AMP"/>
+      <bbox x="398" y="382" w="60" h="30"/>
+    </glyph>
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\ No newline at end of file
diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt
new file mode 100644
index 0000000..6c0aad6
--- /dev/null
+++ b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt
@@ -0,0 +1,291 @@
+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
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diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.sbgn b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.sbgn
new file mode 100644
index 0000000..f0b0f59
--- /dev/null
+++ b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.sbgn
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diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn
new file mode 100644
index 0000000..205c787
--- /dev/null
+++ b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn	
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\ No newline at end of file
-- 
GitLab


From 0efb56fd6550b4eb6287969b19b54e2bec3e9800 Mon Sep 17 00:00:00 2001
From: Jeremy Zucker <djinnome@gmail.com>
Date: Mon, 8 Jun 2020 10:26:40 -0700
Subject: [PATCH 02/10] removed multiple names for the files

---
 .../{SARS_CoV2_ARDS_JT.sbgn => IL6-AMP.sbgn}  |   0
 .../IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt | 291 ------------------
 .../SARS_CoV2_ARDS_JT_compartment.sbgn        | 228 --------------
 .../SARS_CoV2_ARDS_JT_compartments (1).sbgn   | 228 --------------
 4 files changed, 747 deletions(-)
 rename Curation/IL6-AMP/{SARS_CoV2_ARDS_JT.sbgn => IL6-AMP.sbgn} (100%)
 delete mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt
 delete mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.sbgn
 delete mode 100644 Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn

diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
similarity index 100%
rename from Curation/IL6-AMP/SARS_CoV2_ARDS_JT.sbgn
rename to Curation/IL6-AMP/IL6-AMP.sbgn
diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt
deleted file mode 100644
index 6c0aad6..0000000
--- a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartment.nwt
+++ /dev/null
@@ -1,291 +0,0 @@
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deleted file mode 100644
index f0b0f59..0000000
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diff --git a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn b/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn
deleted file mode 100644
index 205c787..0000000
--- a/Curation/IL6-AMP/SARS_CoV2_ARDS_JT_compartments (1).sbgn	
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\ No newline at end of file
-- 
GitLab


From c4292ab92c477e484fc2a4d7931af56e31e10a2b Mon Sep 17 00:00:00 2001
From: Jeremy Zucker <djinnome@gmail.com>
Date: Mon, 8 Jun 2020 10:27:01 -0700
Subject: [PATCH 03/10] With compartments now

---
 Curation/IL6-AMP/IL6-AMP.sbgn | 146 +++++++++++++++++-----------------
 1 file changed, 75 insertions(+), 71 deletions(-)

diff --git a/Curation/IL6-AMP/IL6-AMP.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
index 21240cb..f0b0f59 100644
--- a/Curation/IL6-AMP/IL6-AMP.sbgn
+++ b/Curation/IL6-AMP/IL6-AMP.sbgn
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
 <sbgn xmlns="http://sbgn.org/libsbgn/0.3">
-  <map id="SARS_CoV2_ARDS_JT.sbgn" language="activity flow">
+  <map id="SARS_CoV2_ARDS_JT_compartment.sbgn" language="activity flow">
     <glyph id="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" class="biological activity">
       <label text="SARS_CoV2"/>
       <bbox x="116" y="-63" w="60" h="30"/>
@@ -55,7 +55,11 @@
         <bbox x="854" y="1" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" class="biological activity">
+    <glyph id="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74" class="compartment">
+      <label text="Cytosol"/>
+      <bbox x="287.37499999999994" y="96.75" w="644.9909483445673" h="285.875"/>
+    </glyph>
+    <glyph id="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="EGF"/>
       <bbox x="410.51226998555603" y="127.68998759161451" w="60" h="30"/>
       <glyph id="nwtUOI_926f93af-5744-41be-a87a-73a1cc889e48" class="unit of information">
@@ -64,16 +68,16 @@
         <bbox x="415.51226998555603" y="121.68998759161451" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_467f7364-10c5-41d7-9889-917373e41162" class="biological activity">
+    <glyph id="nwtN_467f7364-10c5-41d7-9889-917373e41162" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="STAT3"/>
-      <bbox x="856.7409483445673" y="246.81094072322628" w="60" h="30"/>
+      <bbox x="856.7409483445673" y="237.81094072322628" w="60" h="30"/>
       <glyph id="nwtUOI_b3625151-50da-4b9b-a5de-af47ac3aeda2" class="unit of information">
         <label text=""/>
         <entity name="macromolecule"/>
-        <bbox x="861.7409483445673" y="240.81094072322628" w="12" h="12"/>
+        <bbox x="861.7409483445673" y="231.81094072322628" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_be369f32-cb2f-4328-a094-c15c356a4505" class="biological activity">
+    <glyph id="nwtN_be369f32-cb2f-4328-a094-c15c356a4505" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="EGFR"/>
       <bbox x="404.7674680886842" y="179.6276103540774" w="60" h="30"/>
       <glyph id="nwtUOI_2e7f77b0-71f8-42d1-8956-7bd84baf82ca" class="unit of information">
@@ -82,7 +86,7 @@
         <bbox x="409.7674680886842" y="173.6276103540774" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b" class="biological activity">
+    <glyph id="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="TNF\alpha"/>
       <bbox x="533.1417767239601" y="189.51229259058277" w="60" h="30"/>
       <glyph id="nwtUOI_4faac32f-98d6-4aac-a3c2-9e91dcb2275e" class="unit of information">
@@ -91,34 +95,34 @@
         <bbox x="538.1417767239601" y="183.51229259058277" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" class="biological activity">
+    <glyph id="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="sIL-6R\alpha"/>
-      <bbox x="683.5457773386427" y="190.02019484784927" w="112.87201056629073" h="30"/>
+      <bbox x="683.5457773386427" y="181.02019484784927" w="112.87201056629073" h="30"/>
       <glyph id="nwtUOI_448c20d5-d229-41d9-a4b3-cc1e914bd115" class="unit of information">
         <label text=""/>
         <entity name="macromolecule"/>
-        <bbox x="698.2389792757959" y="184.02019484784927" w="12" h="12"/>
+        <bbox x="698.2389792757959" y="175.02019484784927" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_1418e98a-456b-42a9-a723-d243855cc770" class="biological activity">
+    <glyph id="nwtN_1418e98a-456b-42a9-a723-d243855cc770" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="IL-6"/>
-      <bbox x="854.3724122509493" y="139.4328931041598" w="60" h="30"/>
+      <bbox x="854.3724122509493" y="130.4328931041598" w="60" h="30"/>
       <glyph id="nwtUOI_39d57e2a-c30f-407f-9d13-cf62ca40e4ad" class="unit of information">
         <label text=""/>
         <entity name="macromolecule"/>
-        <bbox x="859.3724122509493" y="133.4328931041598" w="12" h="12"/>
+        <bbox x="859.3724122509493" y="124.4328931041598" w="12" h="12"/>
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     </glyph>
-    <glyph id="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" class="biological activity">
+    <glyph id="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="NF-\kappaB"/>
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@@ -127,46 +131,46 @@
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@@ -176,49 +180,49 @@
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+      <end x="855.1833390624676" y="240.59923210286314"/>
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-      <end x="333.8722993285338" y="278.51904231655"/>
+    <arc id="nwtE_570ccd33-6874-49ff-931e-1a3a381a22c4" class="positive influence" source="nwtN_be369f32-cb2f-4328-a094-c15c356a4505" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
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+    <arc id="nwtE_d5d9617e-c684-4687-a168-80f4055fdbfc" class="positive influence" source="nwtN_70505ee2-f32e-4d66-88e7-36087274966b" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
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 </sbgn>
\ No newline at end of file
-- 
GitLab


From 3e1bf21f0d1172f7f7ce3b1a6367752394459c21 Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Mon, 8 Jun 2020 11:09:06 -0700
Subject: [PATCH 04/10] Added membrane and extracellular compartments

---
 Curation/IL6-AMP/IL6-AMP.sbgn | 202 ++++++++++++++++++----------------
 1 file changed, 105 insertions(+), 97 deletions(-)

diff --git a/Curation/IL6-AMP/IL6-AMP.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
index f0b0f59..718b35f 100644
--- a/Curation/IL6-AMP/IL6-AMP.sbgn
+++ b/Curation/IL6-AMP/IL6-AMP.sbgn
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
 <sbgn xmlns="http://sbgn.org/libsbgn/0.3">
-  <map id="SARS_CoV2_ARDS_JT_compartment.sbgn" language="activity flow">
+  <map id="IL6-AMP.sbgn" language="activity flow">
     <glyph id="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" class="biological activity">
       <label text="SARS_CoV2"/>
       <bbox x="116" y="-63" w="60" h="30"/>
@@ -10,53 +10,8 @@
         <bbox x="121" y="-69" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" class="biological activity">
-      <label text="ACE-2"/>
-      <bbox x="312.2633792654036" y="6.65178780532252" w="60" h="30"/>
-      <glyph id="nwtUOI_882f5a09-1f69-46a2-803a-e6415f5518af" class="unit of information">
-        <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="317.2633792654036" y="0.6517878053225203" w="12" h="12"/>
-      </glyph>
-    </glyph>
-    <glyph id="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d" class="biological activity">
-      <label text="Angiotensin II"/>
-      <bbox x="411" y="-72" w="60" h="30"/>
-      <glyph id="nwtUOI_9734954e-ce38-4d6b-b174-b755296e6f87" class="unit of information">
-        <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="416" y="-78" w="12" h="12"/>
-      </glyph>
-    </glyph>
-    <glyph id="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" class="biological activity">
-      <label text="AT1R"/>
-      <bbox x="533" y="8" w="60" h="30"/>
-      <glyph id="nwtUOI_7c40f9a3-b5f6-4e67-a3a5-608719594329" class="unit of information">
-        <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="538" y="2" w="12" h="12"/>
-      </glyph>
-    </glyph>
-    <glyph id="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" class="biological activity">
-      <label text="ADAM17"/>
-      <bbox x="686" y="7" w="60" h="30"/>
-      <glyph id="nwtUOI_a8b0dcc8-2044-4029-84ff-697eb9d373e4" class="unit of information">
-        <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="691" y="1" w="12" h="12"/>
-      </glyph>
-    </glyph>
-    <glyph id="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f" class="biological activity">
-      <label text="IL-6R\alpha"/>
-      <bbox x="849" y="7" w="60" h="30"/>
-      <glyph id="nwtUOI_85205377-9d0f-4cb7-92f4-a1cf052cb945" class="unit of information">
-        <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="854" y="1" w="12" h="12"/>
-      </glyph>
-    </glyph>
     <glyph id="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74" class="compartment">
-      <label text="Cytosol"/>
+      <label text="CELL/Cytosol"/>
       <bbox x="287.37499999999994" y="96.75" w="644.9909483445673" h="285.875"/>
     </glyph>
     <glyph id="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
@@ -148,53 +103,78 @@
       <label text="ARDS"/>
       <bbox x="397.0958725001" y="480.20433679745116" w="60" h="30"/>
     </glyph>
-    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
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-      <end x="682.2500667456936" y="22.220587799047756"/>
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+        <entity name="macromolecule"/>
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+      <end x="367.56975172101636" y="270.87325903831595"/>
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+    <arc id="nwtE_0bd7e68e-ee47-4055-b173-b6abf352a638" class="positive influence" source="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
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+      <end x="461.4562291531453" y="336.3688109694321"/>
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-      <start x="532.5167767239601" y="214.9038841151438"/>
-      <end x="367.56975172101636" y="270.87325903831595"/>
+    <arc id="nwtE_42d1090c-7bfb-4ad7-84c2-38533b33c193" class="negative influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_467f7364-10c5-41d7-9889-917373e41162">
+      <start x="780.3600507546012" y="211.64519484784927"/>
+      <end x="855.1833390624676" y="240.59923210286314"/>
     </arc>
     <arc id="nwtE_70b85473-5868-4fbb-bd4a-2a0c954ce1e5" class="negative influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_1418e98a-456b-42a9-a723-d243855cc770">
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@@ -204,25 +184,53 @@
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-      <start x="718.1532865986793" y="37.625"/>
-      <end x="737.4018708161891" y="177.29945326741642"/>
+    <arc id="nwtE_d8973b07-21e9-4df1-9376-ef8ee15854c9" class="positive influence" source="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
+      <start x="355.05180800645076" y="297.89398539337884"/>
+      <end x="404.4237051576331" y="334.51335203449713"/>
     </arc>
     <arc id="nwtE_d5d9617e-c684-4687-a168-80f4055fdbfc" class="positive influence" source="nwtN_70505ee2-f32e-4d66-88e7-36087274966b" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
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       <end x="333.8608500450233" y="263.51905441629754"/>
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-      <end x="404.4237051576331" y="334.51335203449713"/>
+    <arc id="nwtE_58ff4874-8208-49a7-a486-08e19f5ee06b" class="positive influence" source="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314" target="nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d">
+      <start x="427.9013508075114" y="367.625"/>
+      <end x="427.2142511378736" y="476.45439907823356"/>
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-      <end x="461.4562291531453" y="336.3688109694321"/>
+    <arc id="nwtE_dd9a675e-fe26-4bb6-9748-543db794baa5" class="positive influence" source="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" target="nwtN_be369f32-cb2f-4328-a094-c15c356a4505">
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+      <end x="436.8393036380696" y="175.89655310936462"/>
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+    <arc id="nwtE_2ab1c268-177f-4543-90d8-7091286f166f" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7">
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+      <end x="737.4018708161891" y="177.29945326741642"/>
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+    <arc id="nwtE_3c904923-4811-42a7-aaee-b64306ea656c" class="negative influence" source="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" target="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab">
+      <start x="176.62499999999997" y="-37.131512921453044"/>
+      <end x="310.6959665685871" y="10.448848474758933"/>
+    </arc>
+    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
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+      <end x="682.2500667456936" y="22.220587799047756"/>
+    </arc>
+    <arc id="nwtE_9001073a-2f98-406c-9e44-e4a7fad79b4a" class="negative influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f">
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+      <end x="847.375" y="22"/>
+    </arc>
+    <arc id="nwtE_d10e76c2-5656-4d79-b225-284809044acb" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d">
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+      <end x="473.99963516921434" y="128.01931718360873"/>
+    </arc>
+    <arc id="nwtE_b7fcee90-e854-4f44-af7f-a500a28df9c8" class="negative influence" source="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" target="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d">
+      <start x="361.8784413259976" y="6.026787805322513"/>
+      <end x="420.60276659980286" y="-40.75193660394518"/>
+    </arc>
+    <arc id="nwtE_8b87d142-d93c-47da-83fc-9d8833e4a47e" class="positive influence" source="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d" target="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7">
+      <start x="464.828125" y="-41.375"/>
+      <end x="534.9305193965648" y="4.59378321086222"/>
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 </sbgn>
\ No newline at end of file
-- 
GitLab


From 34a673540269c43be7c544138b9f5d318ab789d1 Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Mon, 8 Jun 2020 13:47:29 -0700
Subject: [PATCH 05/10] Cell membrane and cytosol now inside compartment CELL

---
 Curation/IL6-AMP/IL6-AMP.sbgn | 152 +++++++++++++++++-----------------
 1 file changed, 78 insertions(+), 74 deletions(-)

diff --git a/Curation/IL6-AMP/IL6-AMP.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
index 718b35f..85a472b 100644
--- a/Curation/IL6-AMP/IL6-AMP.sbgn
+++ b/Curation/IL6-AMP/IL6-AMP.sbgn
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
 <sbgn xmlns="http://sbgn.org/libsbgn/0.3">
-  <map id="IL6-AMP.sbgn" language="activity flow">
+  <map id="IL6-AMP-cellmodel.sbgn" language="activity flow">
     <glyph id="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" class="biological activity">
       <label text="SARS_CoV2"/>
       <bbox x="116" y="-63" w="60" h="30"/>
@@ -10,100 +10,100 @@
         <bbox x="121" y="-69" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74" class="compartment">
-      <label text="CELL/Cytosol"/>
-      <bbox x="287.37499999999994" y="96.75" w="644.9909483445673" h="285.875"/>
+    <glyph id="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4" class="compartment">
+      <label text="CELL "/>
+      <bbox x="270.7499999999998" y="-32.2232121946775" w="678.2409483445676" h="431.4732121946775"/>
+    </glyph>
+    <glyph id="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74" class="compartment" compartmentRef="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4">
+      <label text="Cytosol"/>
+      <bbox x="287.37499999999983" y="96.75" w="644.9909483445675" h="285.875"/>
     </glyph>
     <glyph id="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="EGF"/>
-      <bbox x="410.51226998555603" y="127.68998759161451" w="60" h="30"/>
+      <bbox x="410.5122699855559" y="127.68998759161451" w="60" h="30"/>
       <glyph id="nwtUOI_926f93af-5744-41be-a87a-73a1cc889e48" class="unit of information">
         <label text=""/>
         <entity name="macromolecule"/>
-        <bbox x="415.51226998555603" y="121.68998759161451" w="12" h="12"/>
+        <bbox x="415.5122699855559" y="121.68998759161451" w="12" h="12"/>
       </glyph>
     </glyph>
     <glyph id="nwtN_467f7364-10c5-41d7-9889-917373e41162" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="STAT3"/>
-      <bbox x="856.7409483445673" y="237.81094072322628" w="60" h="30"/>
+      <bbox x="856.7409483445674" y="237.8109407232263" w="60" h="30"/>
       <glyph id="nwtUOI_b3625151-50da-4b9b-a5de-af47ac3aeda2" class="unit of information">
         <label text=""/>
         <entity name="macromolecule"/>
-        <bbox x="861.7409483445673" y="231.81094072322628" w="12" h="12"/>
+        <bbox x="861.7409483445674" y="231.8109407232263" w="12" h="12"/>
       </glyph>
     </glyph>
     <glyph id="nwtN_be369f32-cb2f-4328-a094-c15c356a4505" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="EGFR"/>
-      <bbox x="404.7674680886842" y="179.6276103540774" w="60" h="30"/>
+      <bbox x="404.7674680886841" y="179.6276103540774" w="60" h="30"/>
       <glyph id="nwtUOI_2e7f77b0-71f8-42d1-8956-7bd84baf82ca" class="unit of information">
         <label text=""/>
         <entity name="macromolecule"/>
-        <bbox x="409.7674680886842" y="173.6276103540774" w="12" h="12"/>
+        <bbox x="409.7674680886841" y="173.6276103540774" w="12" h="12"/>
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       <end x="534.9305193965648" y="4.59378321086222"/>
     </arc>
+    <arc id="nwtE_9001073a-2f98-406c-9e44-e4a7fad79b4a" class="negative influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f">
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   </map>
 </sbgn>
\ No newline at end of file
-- 
GitLab


From 441834e4060cfdb8192c4fe45df6642a7451eced Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Mon, 8 Jun 2020 23:31:33 -0700
Subject: [PATCH 06/10] Virus changed to UNSPECIFIED, AngiotensinII changed to
 compound, And functionality is next

---
 Curation/IL6-AMP/IL6-AMP.sbgn | 64 +++++++++++++++++------------------
 1 file changed, 32 insertions(+), 32 deletions(-)

diff --git a/Curation/IL6-AMP/IL6-AMP.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
index 85a472b..94397a3 100644
--- a/Curation/IL6-AMP/IL6-AMP.sbgn
+++ b/Curation/IL6-AMP/IL6-AMP.sbgn
@@ -1,13 +1,13 @@
 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
 <sbgn xmlns="http://sbgn.org/libsbgn/0.3">
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-    <glyph id="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" class="biological activity">
+  <map id="IL6-AMP-cellmodelC.sbgn" language="activity flow">
+    <glyph id="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" class="biological activity">
       <label text="SARS_CoV2"/>
-      <bbox x="116" y="-63" w="60" h="30"/>
-      <glyph id="nwtUOI_de6e5917-8277-459a-8601-e5b41b119c84" class="unit of information">
+      <bbox x="125.79106820047997" y="-35.54789659909564" w="73.58837890625" h="25"/>
+      <glyph id="nwtUOI_bf758fc0-3196-43b9-81d7-42fb4f03bd23" class="unit of information">
         <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="121" y="-69" w="12" h="12"/>
+        <entity name="unspecified entity"/>
+        <bbox x="130.79106820047997" y="-41.54789659909564" w="12" h="12"/>
       </glyph>
     </glyph>
     <glyph id="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4" class="compartment">
@@ -147,19 +147,23 @@
       <label text="ARDS"/>
       <bbox x="397.0958725001" y="480.20433679745116" w="60" h="30"/>
     </glyph>
-    <glyph id="nwtN_e7b7aa5b-894b-43ea-8597-41b50bea1981" class="compartment">
-      <label text="Bloodstream/extracellular space"/>
-      <bbox x="322.39697265625" y="-94.3125" w="237.2060546875" h="68"/>
+    <glyph id="nwtN_60d92d6f-04f2-4fc4-a19a-05e93c8e25b3" class="compartment">
+      <label text="Bloodstream/Extracellular Space"/>
+      <bbox x="334.3098317141568" y="-101.78609133925286" w="241.095703125" h="68"/>
     </glyph>
-    <glyph id="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d" class="biological activity" compartmentRef="nwtN_e7b7aa5b-894b-43ea-8597-41b50bea1981">
+    <glyph id="nwtN_6ea56ed0-cf8b-4466-86b8-2bd7aa99e46a" class="biological activity" compartmentRef="nwtN_60d92d6f-04f2-4fc4-a19a-05e93c8e25b3">
       <label text="Angiotensin II"/>
-      <bbox x="411" y="-72" w="60" h="30"/>
-      <glyph id="nwtUOI_9734954e-ce38-4d6b-b174-b755296e6f87" class="unit of information">
+      <bbox x="413.2573827908133" y="-79.47359133925286" w="83.20060097168694" h="30"/>
+      <glyph id="nwtUOI_2886bf8e-1c60-4045-86b0-33afb4b4dd30" class="unit of information">
         <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="416" y="-78" w="12" h="12"/>
+        <entity name="complex"/>
+        <bbox x="422.5108263022893" y="-85.47359133925286" w="12" h="12"/>
       </glyph>
     </glyph>
+    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
+      <start x="593.625" y="22.799836601307188"/>
+      <end x="682.2500667456936" y="22.220587799047756"/>
+    </arc>
     <arc id="nwtE_dd9a675e-fe26-4bb6-9748-543db794baa5" class="positive influence" source="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" target="nwtN_be369f32-cb2f-4328-a094-c15c356a4505">
       <start x="438.78399431823954" y="158.3149875916145"/>
       <end x="436.8393036380695" y="175.89655310936462"/>
@@ -204,9 +208,9 @@
       <start x="355.05180800645064" y="297.8939853933789"/>
       <end x="404.423705157633" y="334.51335203449713"/>
     </arc>
-    <arc id="nwtE_dbc43495-12f8-42d8-a29f-b2baefe9a4d2" class="positive influence" source="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" target="nwtN_70505ee2-f32e-4d66-88e7-36087274966b">
-      <start x="162.05425824175825" y="-32.375"/>
-      <end x="308.9757280981638" y="110.6180883094429"/>
+    <arc id="nwtE_c57bd8b9-fae4-48b0-a3ab-cd34ff2d7154" class="negative influence" source="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" target="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab">
+      <start x="200.00444710672994" y="-13.738883658512975"/>
+      <end x="310.66795802927595" y="13.79159122039329"/>
     </arc>
     <arc id="nwtE_0bd7e68e-ee47-4055-b173-b6abf352a638" class="positive influence" source="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
       <start x="519.3750000000002" y="309.3084016393442"/>
@@ -216,25 +220,21 @@
       <start x="427.9013508075113" y="367.625"/>
       <end x="427.2142511378736" y="476.45439907823356"/>
     </arc>
-    <arc id="nwtE_3c904923-4811-42a7-aaee-b64306ea656c" class="negative influence" source="nwtN_3c1c0998-5973-4c3b-a640-e69a10b2ce88" target="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab">
-      <start x="176.62499999999997" y="-37.131512921453044"/>
-      <end x="310.6959665685871" y="10.448848474758933"/>
-    </arc>
-    <arc id="nwtE_b7fcee90-e854-4f44-af7f-a500a28df9c8" class="negative influence" source="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" target="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d">
-      <start x="361.8784413259976" y="6.026787805322513"/>
-      <end x="420.60276659980286" y="-40.75193660394518"/>
-    </arc>
-    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
-      <start x="593.625" y="22.799836601307188"/>
-      <end x="682.2500667456936" y="22.220587799047756"/>
-    </arc>
-    <arc id="nwtE_8b87d142-d93c-47da-83fc-9d8833e4a47e" class="positive influence" source="nwtN_be420794-d2e8-45f0-ba81-2bcc0b4bd89d" target="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7">
-      <start x="464.828125" y="-41.375"/>
-      <end x="534.9305193965648" y="4.59378321086222"/>
+    <arc id="nwtE_4251c614-168a-49d5-9ae4-0eed8db066a8" class="positive influence" source="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" target="nwtN_70505ee2-f32e-4d66-88e7-36087274966b">
+      <start x="176.82736812902354" y="-9.922896599095651"/>
+      <end x="308.0887656748262" y="111.04273175789312"/>
     </arc>
     <arc id="nwtE_9001073a-2f98-406c-9e44-e4a7fad79b4a" class="negative influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f">
       <start x="746.625" y="22"/>
       <end x="847.375" y="22"/>
     </arc>
+    <arc id="nwtE_d614ac0f-49c7-410d-9456-6c93fb26ecb7" class="negative influence" source="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" target="nwtN_6ea56ed0-cf8b-4466-86b8-2bd7aa99e46a">
+      <start x="362.6904127095477" y="6.0267878053225274"/>
+      <end x="433.6363731993221" y="-48.241035062050976"/>
+    </arc>
+    <arc id="nwtE_f7fbd377-fe55-486e-8651-b874f679ada1" class="negative influence" source="nwtN_6ea56ed0-cf8b-4466-86b8-2bd7aa99e46a" target="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7">
+      <start x="474.1746413771754" y="-48.84859133925288"/>
+      <end x="538.0344389319522" y="2.8059875857071717"/>
+    </arc>
   </map>
 </sbgn>
\ No newline at end of file
-- 
GitLab


From a7507d095f1f90cbeb2eae233041de287441e9f0 Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Tue, 9 Jun 2020 15:44:06 -0700
Subject: [PATCH 07/10] and added, I don't like the way it represents, please
 check the logic works

---
 Curation/IL6-AMP/IL6-AMP.sbgn | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/Curation/IL6-AMP/IL6-AMP.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
index 94397a3..0964092 100644
--- a/Curation/IL6-AMP/IL6-AMP.sbgn
+++ b/Curation/IL6-AMP/IL6-AMP.sbgn
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
 <sbgn xmlns="http://sbgn.org/libsbgn/0.3">
-  <map id="IL6-AMP-cellmodelC.sbgn" language="activity flow">
+  <map id="IL6-AMP-cellmodelANDC.sbgn" language="activity flow">
     <glyph id="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" class="biological activity">
       <label text="SARS_CoV2"/>
       <bbox x="125.79106820047997" y="-35.54789659909564" w="73.58837890625" h="25"/>
@@ -103,6 +103,11 @@
       <label text="IL6-AMP"/>
       <bbox x="397.9999999999999" y="337" w="60" h="30"/>
     </glyph>
+    <glyph id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2" class="and" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
+      <bbox x="411.64882589519726" y="282.1607204892606" w="21.42857142857143" h="21.42857142857143"/>
+      <port id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1" x="407.363111609483" y="292.8750062035463"/>
+      <port id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.2" x="437.363111609483" y="292.8750062035463"/>
+    </glyph>
     <glyph id="nwtN_20b011b8-d72a-49ab-979a-275adb620b95" class="compartment" compartmentRef="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4">
       <label text="Cell Membrane"/>
       <bbox x="296.63837926540367" y="-15.598212194677476" w="627.9866207345964" h="69.22321219467747"/>
@@ -204,17 +209,17 @@
       <start x="333.10385176153494" y="149.62499999999997"/>
       <end x="333.8608500450232" y="263.51905441629765"/>
     </arc>
-    <arc id="nwtE_d8973b07-21e9-4df1-9376-ef8ee15854c9" class="positive influence" source="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
-      <start x="355.05180800645064" y="297.8939853933789"/>
-      <end x="404.423705157633" y="334.51335203449713"/>
+    <arc id="nwtE_94c637ff-b04b-4946-b01c-fb6f5b7c67ac" class="positive influence" source="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.2" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
+      <start x="437.988111609483" y="292.8750062035463"/>
+      <end x="426.2137479299574" y="333.2641061444747"/>
     </arc>
     <arc id="nwtE_c57bd8b9-fae4-48b0-a3ab-cd34ff2d7154" class="negative influence" source="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" target="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab">
       <start x="200.00444710672994" y="-13.738883658512975"/>
       <end x="310.66795802927595" y="13.79159122039329"/>
     </arc>
-    <arc id="nwtE_0bd7e68e-ee47-4055-b173-b6abf352a638" class="positive influence" source="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
-      <start x="519.3750000000002" y="309.3084016393442"/>
-      <end x="461.45622915314516" y="336.36881096943216"/>
+    <arc id="nwtE_b746acb3-0e28-449f-90c5-ad367a441ba2" class="logic arc" source="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" target="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1">
+      <start x="364.6104717001036" y="285.9442293537792"/>
+      <end x="406.738111609483" y="292.8750062035463"/>
     </arc>
     <arc id="nwtE_58ff4874-8208-49a7-a486-08e19f5ee06b" class="positive influence" source="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314" target="nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d">
       <start x="427.9013508075113" y="367.625"/>
@@ -236,5 +241,9 @@
       <start x="474.1746413771754" y="-48.84859133925288"/>
       <end x="538.0344389319522" y="2.8059875857071717"/>
     </arc>
+    <arc id="nwtE_34c1db2e-165c-4027-97f3-6aebfdac932b" class="logic arc" source="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" target="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1">
+      <start x="519.3750000000002" y="294.4901322349909"/>
+      <end x="406.738111609483" y="292.8750062035463"/>
+    </arc>
   </map>
 </sbgn>
\ No newline at end of file
-- 
GitLab


From c612e9eafaeabd650d9eeedfbb1e8bddb468367d Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Tue, 9 Jun 2020 22:30:59 -0700
Subject: [PATCH 08/10] all nodes labeled, most with HGNC ID, sIL-6r is an
 exception it is PUBMED labeled

---
 Curation/IL6-AMP/IL6-AMP.sbgn | 96 +++++++++++++++++------------------
 1 file changed, 48 insertions(+), 48 deletions(-)

diff --git a/Curation/IL6-AMP/IL6-AMP.sbgn b/Curation/IL6-AMP/IL6-AMP.sbgn
index 0964092..667dcd4 100644
--- a/Curation/IL6-AMP/IL6-AMP.sbgn
+++ b/Curation/IL6-AMP/IL6-AMP.sbgn
@@ -1,6 +1,6 @@
 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
 <sbgn xmlns="http://sbgn.org/libsbgn/0.3">
-  <map id="IL6-AMP-cellmodelANDC.sbgn" language="activity flow">
+  <map id="IL6-AMPLABELED.sbgn" language="activity flow">
     <glyph id="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" class="biological activity">
       <label text="SARS_CoV2"/>
       <bbox x="125.79106820047997" y="-35.54789659909564" w="73.58837890625" h="25"/>
@@ -92,11 +92,11 @@
     </glyph>
     <glyph id="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <label text="IL6/STAT3"/>
-      <bbox x="520.0000000000002" y="280" w="60" h="30"/>
+      <bbox x="529.0000000000002" y="280" w="60" h="30"/>
       <glyph id="nwtUOI_069526b5-ed15-4f88-b0ac-681c4d84aed1" class="unit of information">
         <label text=""/>
         <entity name="complex"/>
-        <bbox x="525.0000000000002" y="274" w="12" h="12"/>
+        <bbox x="534.0000000000002" y="274" w="12" h="12"/>
       </glyph>
     </glyph>
     <glyph id="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314" class="biological activity" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
@@ -105,8 +105,8 @@
     </glyph>
     <glyph id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2" class="and" compartmentRef="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74">
       <bbox x="411.64882589519726" y="282.1607204892606" w="21.42857142857143" h="21.42857142857143"/>
-      <port id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1" x="407.363111609483" y="292.8750062035463"/>
-      <port id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.2" x="437.363111609483" y="292.8750062035463"/>
+      <port id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1" x="422.363111609483" y="277.8750062035463"/>
+      <port id="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.2" x="422.363111609483" y="307.8750062035463"/>
     </glyph>
     <glyph id="nwtN_20b011b8-d72a-49ab-979a-275adb620b95" class="compartment" compartmentRef="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4">
       <label text="Cell Membrane"/>
@@ -130,15 +130,6 @@
         <bbox x="538" y="2" w="12" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" class="biological activity" compartmentRef="nwtN_20b011b8-d72a-49ab-979a-275adb620b95">
-      <label text="ADAM17"/>
-      <bbox x="686" y="7" w="60" h="30"/>
-      <glyph id="nwtUOI_a8b0dcc8-2044-4029-84ff-697eb9d373e4" class="unit of information">
-        <label text=""/>
-        <entity name="macromolecule"/>
-        <bbox x="691" y="1" w="12" h="12"/>
-      </glyph>
-    </glyph>
     <glyph id="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f" class="biological activity" compartmentRef="nwtN_20b011b8-d72a-49ab-979a-275adb620b95">
       <label text="IL-6R\alpha"/>
       <bbox x="849" y="7" w="60" h="30"/>
@@ -148,35 +139,40 @@
         <bbox x="854" y="1" w="12" h="12"/>
       </glyph>
     </glyph>
+    <glyph id="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" class="biological activity" compartmentRef="nwtN_20b011b8-d72a-49ab-979a-275adb620b95">
+      <label text="ADAM17"/>
+      <bbox x="686" y="7" w="60" h="30"/>
+      <glyph id="nwtUOI_a8b0dcc8-2044-4029-84ff-697eb9d373e4" class="unit of information">
+        <label text=""/>
+        <entity name="macromolecule"/>
+        <bbox x="691" y="1" w="12" h="12"/>
+      </glyph>
+    </glyph>
     <glyph id="nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d" class="phenotype">
-      <label text="ARDS"/>
+      <label text="CRS"/>
       <bbox x="397.0958725001" y="480.20433679745116" w="60" h="30"/>
     </glyph>
-    <glyph id="nwtN_60d92d6f-04f2-4fc4-a19a-05e93c8e25b3" class="compartment">
+    <glyph id="nwtN_d27ebed2-a890-4ee2-b9c4-043e11a8ea6f" class="compartment">
       <label text="Bloodstream/Extracellular Space"/>
-      <bbox x="334.3098317141568" y="-101.78609133925286" w="241.095703125" h="68"/>
+      <bbox x="342.6555342969351" y="-135.9263289380632" w="241.095703125" h="68"/>
     </glyph>
-    <glyph id="nwtN_6ea56ed0-cf8b-4466-86b8-2bd7aa99e46a" class="biological activity" compartmentRef="nwtN_60d92d6f-04f2-4fc4-a19a-05e93c8e25b3">
+    <glyph id="nwtN_7c625c3a-58c8-4eb3-86ea-611f3327cbaa" class="biological activity" compartmentRef="nwtN_d27ebed2-a890-4ee2-b9c4-043e11a8ea6f">
       <label text="Angiotensin II"/>
-      <bbox x="413.2573827908133" y="-79.47359133925286" w="83.20060097168694" h="30"/>
-      <glyph id="nwtUOI_2886bf8e-1c60-4045-86b0-33afb4b4dd30" class="unit of information">
+      <bbox x="424.8757491406851" y="-111.11382893806321" w="76.6552734375" h="25"/>
+      <glyph id="nwtUOI_5491e1df-2d5c-4525-a37d-78b0eb2dfa9d" class="unit of information">
         <label text=""/>
-        <entity name="complex"/>
-        <bbox x="422.5108263022893" y="-85.47359133925286" w="12" h="12"/>
+        <entity name="simple chemical"/>
+        <bbox x="429.8757491406851" y="-117.11382893806321" w="12" h="12"/>
       </glyph>
     </glyph>
-    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
-      <start x="593.625" y="22.799836601307188"/>
-      <end x="682.2500667456936" y="22.220587799047756"/>
+    <arc id="nwtE_34c1db2e-165c-4027-97f3-6aebfdac932b" class="logic arc" source="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" target="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1">
+      <start x="528.3750000000002" y="294.5237162102931"/>
+      <end x="422.363111609483" y="277.2500062035463"/>
     </arc>
     <arc id="nwtE_dd9a675e-fe26-4bb6-9748-543db794baa5" class="positive influence" source="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d" target="nwtN_be369f32-cb2f-4328-a094-c15c356a4505">
       <start x="438.78399431823954" y="158.3149875916145"/>
       <end x="436.8393036380695" y="175.89655310936462"/>
     </arc>
-    <arc id="nwtE_d10e76c2-5656-4d79-b225-284809044acb" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d">
-      <start x="685.375" y="35.41668055342936"/>
-      <end x="473.99963516921423" y="128.01931718360873"/>
-    </arc>
     <arc id="nwtE_42d1090c-7bfb-4ad7-84c2-38533b33c193" class="negative influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_467f7364-10c5-41d7-9889-917373e41162">
       <start x="780.3600507546014" y="211.6451948478493"/>
       <end x="855.1833390624677" y="240.59923210286317"/>
@@ -189,28 +185,28 @@
       <start x="532.5167767239602" y="214.90388411514385"/>
       <end x="367.56975172101625" y="270.873259038316"/>
     </arc>
-    <arc id="nwtE_9297fd64-05c7-476f-becd-afa13fa15866" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b">
-      <start x="702.9137047988002" y="37.62499999999997"/>
-      <end x="578.2345656353388" y="186.49154469253233"/>
+    <arc id="nwtE_bc89972d-ed8b-4908-aa34-5470c7607f70" class="negative influence" source="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" target="nwtN_7c625c3a-58c8-4eb3-86ea-611f3327cbaa">
+      <start x="357.97599650549" y="6.0267878053225274"/>
+      <end x="449.295706359273" y="-84.78370192169109"/>
     </arc>
     <arc id="nwtE_70b85473-5868-4fbb-bd4a-2a0c954ce1e5" class="negative influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_1418e98a-456b-42a9-a723-d243855cc770">
       <start x="784.5800021391414" y="180.3951948478493"/>
       <end x="852.803657024871" y="156.49301626032187"/>
     </arc>
     <arc id="nwtE_96001b84-bfca-46c4-9824-5b2f61ed2fe0" class="positive influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87">
-      <start x="709.9911663652463" y="211.6451948478493"/>
-      <end x="582.7620377117639" y="277.93109968573435"/>
+      <start x="711.411910726016" y="211.6451948478493"/>
+      <end x="590.3116223139024" y="277.8755235431378"/>
     </arc>
-    <arc id="nwtE_2ab1c268-177f-4543-90d8-7091286f166f" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7">
-      <start x="718.1532865986793" y="37.62499999999997"/>
-      <end x="737.4018708161892" y="177.29945326741648"/>
+    <arc id="nwtE_e08fbef7-ff65-4ca0-b359-11e6eb6d9723" class="negative influence" source="nwtN_7c625c3a-58c8-4eb3-86ea-611f3327cbaa" target="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7">
+      <start x="473.97379389635336" y="-85.48882893806321"/>
+      <end x="544.7226878316909" y="0.7269606326170361"/>
     </arc>
     <arc id="nwtE_d5d9617e-c684-4687-a168-80f4055fdbfc" class="positive influence" source="nwtN_70505ee2-f32e-4d66-88e7-36087274966b" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
       <start x="333.10385176153494" y="149.62499999999997"/>
       <end x="333.8608500450232" y="263.51905441629765"/>
     </arc>
     <arc id="nwtE_94c637ff-b04b-4946-b01c-fb6f5b7c67ac" class="positive influence" source="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.2" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
-      <start x="437.988111609483" y="292.8750062035463"/>
+      <start x="422.363111609483" y="308.5000062035463"/>
       <end x="426.2137479299574" y="333.2641061444747"/>
     </arc>
     <arc id="nwtE_c57bd8b9-fae4-48b0-a3ab-cd34ff2d7154" class="negative influence" source="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" target="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab">
@@ -219,7 +215,7 @@
     </arc>
     <arc id="nwtE_b746acb3-0e28-449f-90c5-ad367a441ba2" class="logic arc" source="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" target="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1">
       <start x="364.6104717001036" y="285.9442293537792"/>
-      <end x="406.738111609483" y="292.8750062035463"/>
+      <end x="422.363111609483" y="277.2500062035463"/>
     </arc>
     <arc id="nwtE_58ff4874-8208-49a7-a486-08e19f5ee06b" class="positive influence" source="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314" target="nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d">
       <start x="427.9013508075113" y="367.625"/>
@@ -233,17 +229,21 @@
       <start x="746.625" y="22"/>
       <end x="847.375" y="22"/>
     </arc>
-    <arc id="nwtE_d614ac0f-49c7-410d-9456-6c93fb26ecb7" class="negative influence" source="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" target="nwtN_6ea56ed0-cf8b-4466-86b8-2bd7aa99e46a">
-      <start x="362.6904127095477" y="6.0267878053225274"/>
-      <end x="433.6363731993221" y="-48.241035062050976"/>
+    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
+      <start x="593.625" y="22.799836601307188"/>
+      <end x="682.2500667456936" y="22.220587799047756"/>
     </arc>
-    <arc id="nwtE_f7fbd377-fe55-486e-8651-b874f679ada1" class="negative influence" source="nwtN_6ea56ed0-cf8b-4466-86b8-2bd7aa99e46a" target="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7">
-      <start x="474.1746413771754" y="-48.84859133925288"/>
-      <end x="538.0344389319522" y="2.8059875857071717"/>
+    <arc id="nwtE_2ab1c268-177f-4543-90d8-7091286f166f" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7">
+      <start x="718.1532865986793" y="37.62499999999997"/>
+      <end x="737.4018708161892" y="177.29945326741648"/>
     </arc>
-    <arc id="nwtE_34c1db2e-165c-4027-97f3-6aebfdac932b" class="logic arc" source="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87" target="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1">
-      <start x="519.3750000000002" y="294.4901322349909"/>
-      <end x="406.738111609483" y="292.8750062035463"/>
+    <arc id="nwtE_9297fd64-05c7-476f-becd-afa13fa15866" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b">
+      <start x="702.9137047988002" y="37.62499999999997"/>
+      <end x="578.2345656353388" y="186.49154469253233"/>
+    </arc>
+    <arc id="nwtE_d10e76c2-5656-4d79-b225-284809044acb" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d">
+      <start x="685.375" y="35.41668055342936"/>
+      <end x="473.99963516921423" y="128.01931718360873"/>
     </arc>
   </map>
 </sbgn>
\ No newline at end of file
-- 
GitLab


From 2dbede86a2332980786a8d81fd5f96578238e22d Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Wed, 10 Jun 2020 12:31:19 -0700
Subject: [PATCH 09/10] .nwt output of the most recent file, hopefully with
 annotations included

---
 Curation/IL6-AMP/IL6-AMPLABELED.nwt | 578 ++++++++++++++++++++++++++++
 1 file changed, 578 insertions(+)
 create mode 100644 Curation/IL6-AMP/IL6-AMPLABELED.nwt

diff --git a/Curation/IL6-AMP/IL6-AMPLABELED.nwt b/Curation/IL6-AMP/IL6-AMPLABELED.nwt
new file mode 100644
index 0000000..89a6bc2
--- /dev/null
+++ b/Curation/IL6-AMP/IL6-AMPLABELED.nwt
@@ -0,0 +1,578 @@
+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="activity flow">
+    <extension>
+      <renderInformation 
+        xmlns="http://www.sbml.org/sbml/level3/version1/render/version1" id="renderInformation" program-name="sbgnviz" program-version="6.0.1" background-color="#00000000">
+        <listOfColorDefinitions>
+          <colorDefinition id="color_1" value="#ffffffff"/>
+          <colorDefinition id="color_2" value="#555555"/>
+          <colorDefinition id="color_3" value="#ffffff"/>
+          <colorDefinition id="color_4" value="#ffffff7f"/>
+        </listOfColorDefinitions>
+        <listOfBackgroundImages/>
+        <listOfStyles>
+          <style id="nodeffffff15555551.2511normalnormalHelvetica0001" idList="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d nwtN_7c625c3a-58c8-4eb3-86ea-611f3327cbaa nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d nwtN_467f7364-10c5-41d7-9889-917373e41162 nwtN_be369f32-cb2f-4328-a094-c15c356a4505 nwtN_79ff928c-e6ed-435a-86d4-3911524a875b nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7 nwtN_1418e98a-456b-42a9-a723-d243855cc770 nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37 nwtN_70505ee2-f32e-4d66-88e7-36087274966b nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87 nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314 nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7 nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
+            <g font-size="11" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="1.25" fill="color_1" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="infoboxffffff55555519normalnormalArial0f0f0fellipse" idList="nwtUOI_bf758fc0-3196-43b9-81d7-42fb4f03bd23">
+            <g font-size="9" font-family="Arial" font-weight="normal" font-style="normal" font-color="#0f0f0f" stroke="color_2" stroke-width="1" fill="color_3"/>
+          </style>
+          <style id="nodeffffff0.55555553.2514normalnormalHelvetica0001" idList="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4 nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74 nwtN_20b011b8-d72a-49ab-979a-275adb620b95 nwtN_d27ebed2-a890-4ee2-b9c4-043e11a8ea6f">
+            <g font-size="14" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="3.25" fill="color_4" background-image-opacity="1" background-opacity="0.5"/>
+          </style>
+          <style id="infoboxffffff55555519normalnormalArial0f0f0fstadium" idList="nwtUOI_5491e1df-2d5c-4525-a37d-78b0eb2dfa9d">
+            <g font-size="9" font-family="Arial" font-weight="normal" font-style="normal" font-color="#0f0f0f" stroke="color_2" stroke-width="1" fill="color_3"/>
+          </style>
+          <style id="nodeffffff15555551.251" idList="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2">
+            <g stroke="color_2" stroke-width="1.25" fill="color_1" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="infoboxffffff55555519normalnormalArial0f0f0froundrectangle" idList="nwtUOI_926f93af-5744-41be-a87a-73a1cc889e48 nwtUOI_b3625151-50da-4b9b-a5de-af47ac3aeda2 nwtUOI_2e7f77b0-71f8-42d1-8956-7bd84baf82ca nwtUOI_4faac32f-98d6-4aac-a3c2-9e91dcb2275e nwtUOI_448c20d5-d229-41d9-a4b3-cc1e914bd115 nwtUOI_39d57e2a-c30f-407f-9d13-cf62ca40e4ad nwtUOI_fc07e3f8-0664-4442-a493-b2a8a57362c5 nwtUOI_882f5a09-1f69-46a2-803a-e6415f5518af nwtUOI_7c40f9a3-b5f6-4e67-a3a5-608719594329 nwtUOI_85205377-9d0f-4cb7-92f4-a1cf052cb945 nwtUOI_a8b0dcc8-2044-4029-84ff-697eb9d373e4">
+            <g font-size="9" font-family="Arial" font-weight="normal" font-style="normal" font-color="#0f0f0f" stroke="color_2" stroke-width="1" fill="color_3"/>
+          </style>
+          <style id="infoboxffffff55555519normalnormalArial0f0f0fcomplex" idList="nwtUOI_5199d973-277f-403a-91c8-34d75b03ace1 nwtUOI_069526b5-ed15-4f88-b0ac-681c4d84aed1">
+            <g font-size="9" font-family="Arial" font-weight="normal" font-style="normal" font-color="#0f0f0f" stroke="color_2" stroke-width="1" fill="color_3"/>
+          </style>
+          <style id="edge5555551.25" idList="nwtE_34c1db2e-165c-4027-97f3-6aebfdac932b nwtE_dd9a675e-fe26-4bb6-9748-543db794baa5 nwtE_42d1090c-7bfb-4ad7-84c2-38533b33c193 nwtE_570ccd33-6874-49ff-931e-1a3a381a22c4 nwtE_33980085-ebbf-479c-a6d1-6c4bbf835f2d nwtE_bc89972d-ed8b-4908-aa34-5470c7607f70 nwtE_70b85473-5868-4fbb-bd4a-2a0c954ce1e5 nwtE_96001b84-bfca-46c4-9824-5b2f61ed2fe0 nwtE_e08fbef7-ff65-4ca0-b359-11e6eb6d9723 nwtE_d5d9617e-c684-4687-a168-80f4055fdbfc nwtE_94c637ff-b04b-4946-b01c-fb6f5b7c67ac nwtE_c57bd8b9-fae4-48b0-a3ab-cd34ff2d7154 nwtE_b746acb3-0e28-449f-90c5-ad367a441ba2 nwtE_58ff4874-8208-49a7-a486-08e19f5ee06b nwtE_4251c614-168a-49d5-9ae4-0eed8db066a8 nwtE_9001073a-2f98-406c-9e44-e4a7fad79b4a nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5 nwtE_2ab1c268-177f-4543-90d8-7091286f166f nwtE_9297fd64-05c7-476f-becd-afa13fa15866 nwtE_d10e76c2-5656-4d79-b225-284809044acb">
+            <g stroke="color_2" stroke-width="1.25"/>
+          </style>
+        </listOfStyles>
+      </renderInformation>
+      <mapProperties>
+        <compoundPadding>0</compoundPadding>
+        <extraCompartmentPadding>14</extraCompartmentPadding>
+        <extraComplexPadding>10</extraComplexPadding>
+        <arrowScale>1.25</arrowScale>
+        <showComplexName>true</showComplexName>
+        <dynamicLabelSize>regular</dynamicLabelSize>
+        <inferNestingOnLoad>false</inferNestingOnLoad>
+        <fitLabelsToNodes>false</fitLabelsToNodes>
+        <fitLabelsToInfoboxes>false</fitLabelsToInfoboxes>
+        <recalculateLayoutOnComplexityManagement>true</recalculateLayoutOnComplexityManagement>
+        <rearrangeOnComplexityManagement>true</rearrangeOnComplexityManagement>
+        <animateOnDrawingChanges>true</animateOnDrawingChanges>
+        <adjustNodeLabelFontSizeAutomatically>false</adjustNodeLabelFontSizeAutomatically>
+        <enablePorts>true</enablePorts>
+        <enableSIFTopologyGrouping>false</enableSIFTopologyGrouping>
+        <allowCompoundNodeResize>true</allowCompoundNodeResize>
+        <mapColorScheme>black_white</mapColorScheme>
+        <mapColorSchemeStyle>solid</mapColorSchemeStyle>
+        <mapName>Pathway #sbgn-network-container-0</mapName>
+        <mapDescription/>
+      </mapProperties>
+    </extension>
+    <glyph id="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" class="biological activity">
+      <extension>
+        <annotation>
+          <rdf:RDF 
+            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
+            xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+            <rdf:Description rdf:about="#nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee">
+              <bqmodel:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/mesh:C000656484"/>
+                </rdf:Bag>
+              </bqmodel:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </extension>
+      <label text="SARS_CoV2"/>
+      <bbox x="125.79106820047997" y="-35.54789659909564" w="73.58837890625" h="25"/>
+      <glyph id="nwtUOI_bf758fc0-3196-43b9-81d7-42fb4f03bd23" class="unit of information">
+        <label text=""/>
+        <entity name="unspecified entity"/>
+        <bbox x="130.79106820047997" y="-41.54789659909564" w="12" h="12"/>
+      </glyph>
+    </glyph>
+    <glyph id="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4" class="compartment">
+      <extension>
+        <extraInfo>
+          <w>650.2409483445676</w>
+          <h>403.4732121946775</h>
+          <minW>0</minW>
+          <minH>0</minH>
+          <WLBias>0</WLBias>
+          <WRBias>0</WRBias>
+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
+        </extraInfo>
+      </extension>
+      <label text="CELL "/>
+      <bbox x="270.7499999999998" y="-32.2232121946775" w="678.2409483445676" h="431.4732121946775"/>
+    </glyph>
+    <glyph id="nwtN_a1d16e15-5e7f-4da5-b45d-ae4b0a0f8e74" class="compartment" compartmentRef="nwtN_ba8b9d12-cdf2-4353-b101-d3ff935bc8e4">
+      <extension>
+        <extraInfo>
+          <w>616.9909483445675</w>
+          <h>257.875</h>
+          <minW>0</minW>
+          <minH>257.875</minH>
+          <WLBias>0</WLBias>
+          <WRBias>0</WRBias>
+          <HTBias>1</HTBias>
+          <HBBias>0</HBBias>
+        </extraInfo>
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+    <arc id="nwtE_570ccd33-6874-49ff-931e-1a3a381a22c4" class="positive influence" source="nwtN_be369f32-cb2f-4328-a094-c15c356a4505" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
+      <start x="416.7997137846763" y="210.2526103540774"/>
+      <end x="354.3113119951723" y="264.59336220547675"/>
+    </arc>
+    <arc id="nwtE_33980085-ebbf-479c-a6d1-6c4bbf835f2d" class="positive influence" source="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
+      <start x="532.5167767239602" y="214.90388411514385"/>
+      <end x="367.56975172101625" y="270.873259038316"/>
+    </arc>
+    <arc id="nwtE_bc89972d-ed8b-4908-aa34-5470c7607f70" class="negative influence" source="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab" target="nwtN_7c625c3a-58c8-4eb3-86ea-611f3327cbaa">
+      <start x="357.97599650549" y="6.0267878053225274"/>
+      <end x="449.295706359273" y="-84.78370192169109"/>
+    </arc>
+    <arc id="nwtE_70b85473-5868-4fbb-bd4a-2a0c954ce1e5" class="negative influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_1418e98a-456b-42a9-a723-d243855cc770">
+      <start x="784.5800021391414" y="180.3951948478493"/>
+      <end x="852.803657024871" y="156.49301626032187"/>
+    </arc>
+    <arc id="nwtE_96001b84-bfca-46c4-9824-5b2f61ed2fe0" class="positive influence" source="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7" target="nwtN_76e68f4e-6318-403b-bcce-4e3c0aa68d87">
+      <start x="711.411910726016" y="211.6451948478493"/>
+      <end x="590.3116223139024" y="277.8755235431378"/>
+    </arc>
+    <arc id="nwtE_e08fbef7-ff65-4ca0-b359-11e6eb6d9723" class="negative influence" source="nwtN_7c625c3a-58c8-4eb3-86ea-611f3327cbaa" target="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7">
+      <start x="473.97379389635336" y="-85.48882893806321"/>
+      <end x="544.7226878316909" y="0.7269606326170361"/>
+    </arc>
+    <arc id="nwtE_d5d9617e-c684-4687-a168-80f4055fdbfc" class="positive influence" source="nwtN_70505ee2-f32e-4d66-88e7-36087274966b" target="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37">
+      <start x="333.10385176153494" y="149.62499999999997"/>
+      <end x="333.8608500450232" y="263.51905441629765"/>
+    </arc>
+    <arc id="nwtE_94c637ff-b04b-4946-b01c-fb6f5b7c67ac" class="positive influence" source="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.2" target="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314">
+      <start x="422.363111609483" y="308.5000062035463"/>
+      <end x="426.2137479299574" y="333.2641061444747"/>
+    </arc>
+    <arc id="nwtE_c57bd8b9-fae4-48b0-a3ab-cd34ff2d7154" class="negative influence" source="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" target="nwtN_2262df82-a1b2-4001-9c22-ea738e4f23ab">
+      <start x="200.00444710672994" y="-13.738883658512975"/>
+      <end x="310.66795802927595" y="13.79159122039329"/>
+    </arc>
+    <arc id="nwtE_b746acb3-0e28-449f-90c5-ad367a441ba2" class="logic arc" source="nwtN_06347d12-c2a1-47d1-89c2-b71c6a222f37" target="nwtN_df7dfd0c-7f17-4723-9bb0-2f6d0bdeb5a2.1">
+      <start x="364.6104717001036" y="285.9442293537792"/>
+      <end x="422.363111609483" y="277.2500062035463"/>
+    </arc>
+    <arc id="nwtE_58ff4874-8208-49a7-a486-08e19f5ee06b" class="positive influence" source="nwtN_72669a7a-c2ca-4b8c-9073-60d844cb7314" target="nwtN_a67c1260-780c-4ec6-a0b1-ff23cb0a957d">
+      <start x="427.9013508075113" y="367.625"/>
+      <end x="427.2142511378736" y="476.45439907823356"/>
+    </arc>
+    <arc id="nwtE_4251c614-168a-49d5-9ae4-0eed8db066a8" class="positive influence" source="nwtN_4fb08269-3595-4f06-9210-7d6a439d88ee" target="nwtN_70505ee2-f32e-4d66-88e7-36087274966b">
+      <start x="176.82736812902354" y="-9.922896599095651"/>
+      <end x="308.0887656748262" y="111.04273175789312"/>
+    </arc>
+    <arc id="nwtE_9001073a-2f98-406c-9e44-e4a7fad79b4a" class="negative influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_64e4f43f-638e-4dd2-a4df-95c8df8f967f">
+      <start x="746.625" y="22"/>
+      <end x="847.375" y="22"/>
+    </arc>
+    <arc id="nwtE_18fa78ab-43e6-40ab-a572-708cf413c8c5" class="positive influence" source="nwtN_ba8484a1-bad5-44d1-8f74-ed8eacc26fb7" target="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38">
+      <start x="593.625" y="22.799836601307188"/>
+      <end x="682.2500667456936" y="22.220587799047756"/>
+    </arc>
+    <arc id="nwtE_2ab1c268-177f-4543-90d8-7091286f166f" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_eefe0301-0922-41f6-9b8c-4b3e5ee2f3c7">
+      <start x="718.1532865986793" y="37.62499999999997"/>
+      <end x="737.4018708161892" y="177.29945326741648"/>
+    </arc>
+    <arc id="nwtE_9297fd64-05c7-476f-becd-afa13fa15866" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_79ff928c-e6ed-435a-86d4-3911524a875b">
+      <start x="702.9137047988002" y="37.62499999999997"/>
+      <end x="578.2345656353388" y="186.49154469253233"/>
+    </arc>
+    <arc id="nwtE_d10e76c2-5656-4d79-b225-284809044acb" class="positive influence" source="nwtN_622deede-99f6-4ce4-aa85-c9b289c8cd38" target="nwtN_dda74e6c-4a74-447b-b965-af67ed4e591d">
+      <start x="685.375" y="35.41668055342936"/>
+      <end x="473.99963516921423" y="128.01931718360873"/>
+    </arc>
+  </map>
+</sbgn>
\ No newline at end of file
-- 
GitLab


From 2716e1968ba207d6afcfde38cc8ad6cb33f29db7 Mon Sep 17 00:00:00 2001
From: Jeremy Teuton <jeremy.teuton@pnnl.gov>
Date: Wed, 10 Jun 2020 12:35:40 -0700
Subject: [PATCH 10/10] same as other same file name but .sbml export

---
 Curation/IL6-AMP/IL6-AMPLABELED.sbml | 269 +++++++++++++++++++++++++++
 1 file changed, 269 insertions(+)
 create mode 100644 Curation/IL6-AMP/IL6-AMPLABELED.sbml

diff --git a/Curation/IL6-AMP/IL6-AMPLABELED.sbml b/Curation/IL6-AMP/IL6-AMPLABELED.sbml
new file mode 100644
index 0000000..09754c6
--- /dev/null
+++ b/Curation/IL6-AMP/IL6-AMPLABELED.sbml
@@ -0,0 +1,269 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<!-- Created by minerva version 14.0.13 on 2020-06-10 at 21:33:25 CEST with JSBML version 1.4. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" layout:required="false" level="3" multi:required="true" render:required="false" version="2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+  <model areaUnits="area_unit" extentUnits="mole" lengthUnits="metre" substanceUnits="mole" timeUnits="second" volumeUnits="litre">
+    <notes>
+      <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+    </notes>
+    <annotation>
+      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#unknown">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+    </annotation>
+      <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="minerva_layout">
+        <render:listOfRenderInformation xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+          <render:renderInformation render:id="minerva_definitions">
+            <render:listOfColorDefinitions>
+              <render:colorDefinition render:id="color_FF8080FF" render:value="#8080FFFF"/>
+              <render:colorDefinition render:id="color_FFFFFFFF" render:value="#FFFFFFFF"/>
+              <render:colorDefinition render:id="color_FF000000" render:value="#000000FF"/>
+            </render:listOfColorDefinitions>
+            <render:listOfStyles>
+              <render:style render:idList="SbmlCompartmentExporter_0">
+                <render:g render:font-size="12" render:stroke="color_FF8080FF" render:stroke-width="1.0">
+                  <render:rectangle render:height="100%" render:rx="0%" render:ry="0%" render:width="100%" render:x="0%" render:y="0%"/>
+                </render:g>
+              </render:style>
+              <render:style render:idList="text_SbmlCompartmentExporter_0">
+                <render:g render:text-anchor="start" render:vtext-anchor="top"/>
+              </render:style>
+              <render:style render:idList="SbmlCompartmentExporter_1">
+                <render:g render:font-size="12" render:stroke="color_FF8080FF" render:stroke-width="1.0">
+                  <render:rectangle render:height="100%" render:rx="0%" render:ry="0%" render:width="100%" render:x="0%" render:y="0%"/>
+                </render:g>
+              </render:style>
+              <render:style render:idList="text_SbmlCompartmentExporter_1">
+                <render:g render:text-anchor="start" render:vtext-anchor="top"/>
+              </render:style>
+              <render:style render:idList="SbmlCompartmentExporter_2">
+                <render:g render:font-size="12" render:stroke="color_FF8080FF" render:stroke-width="1.0">
+                  <render:rectangle render:height="100%" render:rx="0%" render:ry="0%" render:width="100%" render:x="0%" render:y="0%"/>
+                </render:g>
+              </render:style>
+              <render:style render:idList="text_SbmlCompartmentExporter_2">
+                <render:g render:text-anchor="start" render:vtext-anchor="top"/>
+              </render:style>
+              <render:style render:idList="SbmlCompartmentExporter_3">
+                <render:g render:font-size="12" render:stroke="color_FF8080FF" render:stroke-width="1.0">
+                  <render:rectangle render:height="100%" render:rx="0%" render:ry="0%" render:width="100%" render:x="0%" render:y="0%"/>
+                </render:g>
+              </render:style>
+              <render:style render:idList="text_SbmlCompartmentExporter_3">
+                <render:g render:text-anchor="start" render:vtext-anchor="top"/>
+              </render:style>
+              <render:style render:idList="SbmlSpeciesExporter_1">
+                <render:g render:fill="color_FFFFFFFF" render:font-size="12" render:stroke-width="1.0">
+                  <render:rectangle render:height="100%" render:rx="0%" render:ry="0%" render:stroke="color_FF000000" render:width="100%" render:x="0%" render:y="0%"/>
+                </render:g>
+              </render:style>
+              <render:style render:idList="text_SbmlSpeciesExporter_1">
+                <render:g render:text-anchor="middle" render:vtext-anchor="middle"/>
+              </render:style>
+            </render:listOfStyles>
+          </render:renderInformation>
+        </render:listOfRenderInformation>
+        <layout:dimensions layout:height="374.27801513671875" layout:width="1074.7820358276367"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="comp_4" layout:id="SbmlCompartmentExporter_0">
+            <layout:boundingBox>
+              <layout:position layout:x="287.375" layout:y="96.75" layout:z="2"/>
+              <layout:dimensions layout:height="285.875" layout:width="644.990966796875"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+          <layout:compartmentGlyph layout:compartment="comp_5" layout:id="SbmlCompartmentExporter_1">
+            <layout:boundingBox>
+              <layout:position layout:x="270.75" layout:y="-32.22321319580078" layout:z="1"/>
+              <layout:dimensions layout:height="431.47320556640625" layout:width="678.240966796875"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+          <layout:compartmentGlyph layout:compartment="comp_6" layout:id="SbmlCompartmentExporter_2">
+            <layout:boundingBox>
+              <layout:position layout:x="296.63836669921875" layout:y="-15.598212242126465" layout:z="3"/>
+              <layout:dimensions layout:height="69.22321319580078" layout:width="627.9866333007812"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+          <layout:compartmentGlyph layout:compartment="comp_7" layout:id="SbmlCompartmentExporter_3">
+            <layout:boundingBox>
+              <layout:position layout:x="342.6555480957031" layout:y="-135.92633056640625" layout:z="4"/>
+              <layout:dimensions layout:height="68" layout:width="241.095703125"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+          <layout:compartmentGlyph layout:compartment="default" layout:id="default_compartment">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0" layout:z="0"/>
+              <layout:dimensions layout:height="374.27801513671875" layout:width="1074.7820358276367"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="SbmlSpeciesExporter_1" layout:species="species_0">
+            <layout:boundingBox>
+              <layout:position layout:x="397.09588623046875" layout:y="480.204345703125" layout:z="5"/>
+              <layout:dimensions layout:height="30" layout:width="60"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:id="text_SbmlCompartmentExporter_0" layout:originOfText="SbmlCompartmentExporter_0" layout:text="Cytosol">
+            <layout:boundingBox>
+              <layout:position layout:x="293.375" layout:y="102.75" layout:z="3"/>
+              <layout:dimensions layout:height="279.875" layout:width="638.990966796875"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:id="text_SbmlCompartmentExporter_1" layout:originOfText="SbmlCompartmentExporter_1" layout:text="CELL ">
+            <layout:boundingBox>
+              <layout:position layout:x="276.75" layout:y="-26.22321319580078" layout:z="2"/>
+              <layout:dimensions layout:height="425.47320556640625" layout:width="672.240966796875"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:id="text_SbmlCompartmentExporter_2" layout:originOfText="SbmlCompartmentExporter_2" layout:text="Cell Membrane">
+            <layout:boundingBox>
+              <layout:position layout:x="302.63836669921875" layout:y="-9.598212242126465" layout:z="4"/>
+              <layout:dimensions layout:height="63.22321319580078" layout:width="621.9866333007812"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:id="text_SbmlCompartmentExporter_3" layout:originOfText="SbmlCompartmentExporter_3" layout:text="Bloodstream/Extracellular Space">
+            <layout:boundingBox>
+              <layout:position layout:x="348.6555480957031" layout:y="-129.92633056640625" layout:z="5"/>
+              <layout:dimensions layout:height="62" layout:width="235.095703125"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:id="text_SbmlSpeciesExporter_1" layout:originOfText="SbmlSpeciesExporter_1" layout:text="CRS">
+            <layout:boundingBox>
+              <layout:position layout:x="397.09588623046875" layout:y="480.204345703125" layout:z="6"/>
+              <layout:dimensions layout:height="30" layout:width="60"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <multi:listOfSpeciesTypes xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1">
+      <multi:speciesType multi:id="minerva_species_type_Phenotype" multi:name="Phenotype" sboTerm="SBO:0000358">
+        <multi:listOfSpeciesFeatureTypes>
+          <multi:speciesFeatureType multi:id="minerva_position_to_compartment_Phenotype" multi:name="Position to compartment" multi:occur="1">
+            <multi:listOfPossibleSpeciesFeatureValues>
+              <multi:possibleSpeciesFeatureValue multi:id="minerva_position_to_compartment_Phenotype_37" multi:name="NULL"/>
+            </multi:listOfPossibleSpeciesFeatureValues>
+          </multi:speciesFeatureType>
+          <multi:speciesFeatureType multi:id="minerva_activity_Phenotype" multi:name="Activity" multi:occur="1">
+            <multi:listOfPossibleSpeciesFeatureValues>
+              <multi:possibleSpeciesFeatureValue multi:id="minerva_activity_Phenotype_38" multi:name="false"/>
+            </multi:listOfPossibleSpeciesFeatureValues>
+          </multi:speciesFeatureType>
+        </multi:listOfSpeciesFeatureTypes>
+      </multi:speciesType>
+    </multi:listOfSpeciesTypes>
+    <listOfUnitDefinitions>
+      <unitDefinition id="area_unit" name="area">
+        <listOfUnits>
+          <unit exponent="2" kind="metre" multiplier="1" scale="0"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment constant="false" id="comp_4" multi:isType="false" name="Cytosol" size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#comp_4">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+      <compartment constant="false" id="comp_5" multi:isType="false" name="CELL " size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#comp_5">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+      <compartment constant="false" id="comp_6" multi:isType="false" name="Cell Membrane" size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#comp_6">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+      <compartment constant="false" id="comp_7" multi:isType="false" name="Bloodstream/Extracellular Space" size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#comp_7">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+      <compartment constant="false" id="default" multi:isType="false" size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#default">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="species_0" initialConcentration="0" multi:speciesType="minerva_species_type_Phenotype" name="CRS" sboTerm="SBO:0000358">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+     <p/>
+  </body>
+        </notes>
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#species_0">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+              <multi:listOfSpeciesFeatures>
+          <multi:speciesFeature xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" multi:occur="1" multi:speciesFeatureType="minerva_position_to_compartment_Phenotype">
+            <multi:listOfSpeciesFeatureValues>
+              <multi:speciesFeatureValue multi:value="minerva_position_to_compartment_Phenotype_37"/>
+            </multi:listOfSpeciesFeatureValues>
+          </multi:speciesFeature>
+          <multi:speciesFeature xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1" multi:occur="1" multi:speciesFeatureType="minerva_activity_Phenotype">
+            <multi:listOfSpeciesFeatureValues>
+              <multi:speciesFeatureValue multi:value="minerva_activity_Phenotype_38"/>
+            </multi:listOfSpeciesFeatureValues>
+          </multi:speciesFeature>
+        </multi:listOfSpeciesFeatures>
+      </species>
+    </listOfSpecies>
+  </model>
+</sbml>
\ No newline at end of file
-- 
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