Check SBML metadata, refactor and move scripts (#152)

dilpath · web-flow · commit d7c52f90b15c · 2022-02-21T16:44:47.000+01:00
* add CI check for required sbml metadata * refactor scripts * moved scripts to separate dir `scripts/` * small changes to model info script * add python pip requirements file * Fix model IDs, names, and missing references (#153) * fix model ids, model names, and references (closes #147 , closes #150 ) * update overview table
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -23,12 +23,16 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install --upgrade setuptools wheel
-        pip install petab
+        pip install -r scripts/requirements.txt
 
-    - name: Check benchmark problems
-      run: ./checkBenchmarkModels.py
-      working-directory: Benchmark-Models/
+    - name: Check with petablint
+      run: ./check_petablint.py
+      working-directory: scripts/
 
     - name: Show overview
-      run: ./model_info.py
-      working-directory: Benchmark-Models/
+      run: ./overview.py
+      working-directory: scripts/
+
+    - name: Check SBML metadata
+      run: ./check_sbml_metadata.py
+      working-directory: scripts/
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
 .~lock.*
 *.DS_store
 ~$*
+__pycache__
diff --git a/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml b/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="arFramework3" id="combined_model" name="NoName">
+  <model metaid="arFramework3" id="Alkan_SciSignal2018" name="Alkan_SciSignal2018">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Alkan et al. (2018), Science Signaling  24 Jul 2018: Vol. 11, Issue 540, eaat0229</pre>
diff --git a/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml b/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="arFramework3" id="Bachmann_MSB2011" name="jak2_stat5_feedbacks">
+  <model metaid="arFramework3" id="Bachmann_MSB2011" name="Bachmann_MSB2011">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Bachmann et al. (2011), Mol Syst Biol. ; 7: 516. </pre>
diff --git a/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml b/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Beer_MolBioSystems2014" name="TwoStepSynthesisWithGlu">
+  <model id="Beer_MolBioSystems2014" name="Beer_MolBioSystems2014">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Beer et al. (2014), Mol Biosyst.;10(7):1709-18</pre>
diff --git a/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml b/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!-- Created by COPASI version 4.28 (Build 226) on 2020-11-30 20:43 with libSBML version 5.18.0. -->
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="COPASI0" id="Bertozzi2020___SIR_model_of_scenarios_of_COVID_19_spread_in_CA" name="Bertozzi2020 - SIR model of scenarios of COVID-19 spread in CA">
+  <model metaid="COPASI0" id="Bertozzi_PNAS2020" name="Bertozzi_PNAS2020">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>Bertozzi2020 - SIR model of scenarios of COVID-19 spread in CA and NY
diff --git a/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml b/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Borghans_BiophysChem1997" name="model_Borghans_BiophysChem_1997">
+  <model id="Borghans_BiophysChem1997" name="Borghans_BiophysChem1997">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Borghans et al. (1997), Biophysical Chemistry 66(1) 25-41</pre>
diff --git a/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml b/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="arFramework3" id="Brannmark_JBC2010" name="model_Mif">
+  <model metaid="arFramework3" id="Brannmark_JBC2010" name="Brannmark_JBC2010">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Brannmark et al. (2010), THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 285, NO. 26, pp. 20171–20179, </pre>
diff --git a/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml b/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Chen_MSB2009" name="model_ChenMSB2009_sin">
+  <model id="Chen_MSB2009" name="Chen_MSB2009">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Chen et al. (2009), Mol Syst Biol. ;5:239</pre>
diff --git a/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml b/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Crauste_CellSystems2017" name="ModelImmuneCells">
+  <model id="Crauste_CellSystems2017" name="Crauste_CellSystems2017">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Crauste et al. (2017), Cell Syst. 2017 Mar 22;4(3):306-317.e4</pre>
diff --git a/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml b/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Elowitz_Nature2000" name="model_Elowitz_Nature2000">
+  <model id="Elowitz_Nature2000" name="Elowitz_Nature2000">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Elowitz et al. (2000), Nature. 2000 Jan 20;403(6767):335-8</pre>
diff --git a/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml b/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Fiedler_BMC2016" name="model_RafMekErk">
+  <model id="Fiedler_BMC2016" name="Fiedler_BMC2016">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Fiedler et al. (2016), BMC Systems Biology volume 10, Article number: 80</pre>
diff --git a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
@@ -1,6 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Fujita_SciSignal2010" name="model_AktPathwayFujita">
+  <model id="Fujita_SciSignal2010" name="Fujita_SciSignal2010">
+    <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="#benchmark_models_petab">
+          <bqbiol:isDescribedBy>
+            <rdf:Bag>
+              <rdf:li rdf:resource="http://identifiers.org/doi/10.1126/scisignal.2000810"/>
+            </rdf:Bag>
+          </bqbiol:isDescribedBy>
+        </rdf:Description>
+      </rdf:RDF>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="time" name="time">
         <listOfUnits>
diff --git a/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml b/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!-- Created by COPASI version 4.29 (Build 228) on 2020-09-17 20:49 with libSBML version 5.18.0. -->
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="COPASI0" id="Giordano2020___SIDARTHE_model_of_COVID_19_spread_in_Italy" name="Giordano2020 - SIDARTHE model of COVID-19 spread in Italy">
+  <model metaid="COPASI0" id="Giordano_Nature2020" name="Giordano_Nature2020">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>This is a model created on COPASI 4.27 (Build 217) which reproduces the Figures 2b, 2d, 3b, 3d, 4b, 4d in the article - https://www.nature.com/articles/s41591-020-0883-7
diff --git a/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml b/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="Isensee_JCB2018" id="Isensee_JCB2018" name="PKA_cycle">
+  <model metaid="Isensee_JCB2018" id="Isensee_JCB2018" name="Isensee_JCB2018">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Isensee et al. (2018), The Journal of Cell Biology Jun 2018, 217 (6) 2167-2184</pre>
diff --git a/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml b/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Lucarelli_CellSystems2018" name="Complex_ModelSelectionProfile">
+  <model id="Lucarelli_CellSystems2018" name="Lucarelli_CellSystems2018">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Lucarelli et al. (2018), Cell Syst. 2018 Jan 24;6(1):75-89.e11</pre>
diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!-- Created by COPASI version 4.29 (Build 228) on 2020-12-11 16:38 with libSBML version 5.18.0. -->
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="COPASI0" id="Okuonghae2020" name="Okuonghae2020">
+  <model metaid="COPASI0" id="Okuonghae_ChaosSolitonsFractals2020" name="Okuonghae_ChaosSolitonsFractals2020">
     <annotation>
       <COPASI xmlns="http://www.copasi.org/static/sbml">
         <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
@@ -14,6 +14,15 @@
           </rdf:Description>
         </rdf:RDF>
       </COPASI>
+      <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="#COPASI0">
+          <bqbiol:isDescribedBy>
+            <rdf:Bag>
+              <rdf:li rdf:resource="http://identifiers.org/doi/10.1016/j.chaos.2020.110032"/>
+            </rdf:Bag>
+          </bqbiol:isDescribedBy>
+        </rdf:Description>
+      </rdf:RDF>
     </annotation>
     <listOfFunctionDefinitions>
       <functionDefinition metaid="COPASI41" id="Rate_Law_for_exposed_to_asymptopmatic" name="Rate Law for exposed_to_asymptopmatic">
diff --git a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!-- Created by COPASI version 4.30 (Build 240) on 2021-05-08 11:25 with libSBML version 5.19.0. -->
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="COPASI0" id="Oliveira_Nat2021__Mathematical_modeling_of_Covid_19_in_14_8_million_individuals_in_Bahia_Brazil" name="Oliveira_Nat2021 - Mathematical modeling of Covid-19 in 14.8 million individuals in Bahia, Brazil">
+  <model metaid="COPASI0" id="Oliveira_NatCommun2021" name="Oliveira_NatCommun2021">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>Oliveira, Nature 2021.
@@ -15,6 +15,15 @@ To model with a two-step transmission rate, set 'beta_2_multiplier' = 0. To mode
       </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="#COPASI0">
+          <bqbiol:isDescribedBy>
+            <rdf:Bag>
+              <rdf:li rdf:resource="http://identifiers.org/doi/10.1038/s41467-020-19798-3"/>
+            </rdf:Bag>
+          </bqbiol:isDescribedBy>
+        </rdf:Description>
+      </rdf:RDF>
       <COPASI xmlns="http://www.copasi.org/static/sbml">
         <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
           <rdf:Description rdf:about="#COPASI0">
diff --git a/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml b/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="perelson1" name="perelson1">
+  <model id="Perelson_Science1996" name="Perelson_Science1996">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Perelson et al. (1996), Science  15 Mar 1996: Vol. 271, Issue 5255, pp. 1582-1586</pre>
diff --git a/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml b/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
@@ -1,6 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
   <model substanceUnits="item" timeUnits="year" extentUnits="item" id="Rahman_MBS2016" name="Rahman_MBS2016">
+    <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="#benchmark_models_petab">
+          <bqbiol:isDescribedBy>
+            <rdf:Bag>
+              <rdf:li rdf:resource="http://identifiers.org/doi/10.1016/j.mbs.2016.07.009"/>
+            </rdf:Bag>
+          </bqbiol:isDescribedBy>
+        </rdf:Description>
+      </rdf:RDF>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="year">
         <listOfUnits>
diff --git a/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml b/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
@@ -1,6 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
   <model id="Raimundez_PCB2020" name="Raimundez_PCB2020">
+    <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="#benchmark_models_petab">
+          <bqbiol:isDescribedBy>
+            <rdf:Bag>
+              <rdf:li rdf:resource="http://identifiers.org/doi/10.1371/journal.pcbi.1007147"/>
+            </rdf:Bag>
+          </bqbiol:isDescribedBy>
+        </rdf:Description>
+      </rdf:RDF>
+    </annotation>
     <listOfUnitDefinitions>
       <unitDefinition id="time" name="time">
         <listOfUnits>
diff --git a/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml b/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
@@ -1,6 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model id="SalazarCavazos_MBoC2020" name="SalazarCavazos_MBoC2020">
+    <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="#benchmark_models_petab">
+          <bqbiol:isDescribedBy>
+            <rdf:Bag>
+              <rdf:li rdf:resource="http://identifiers.org/doi/10.1091/mbc.E19-09-0548"/>
+            </rdf:Bag>
+          </bqbiol:isDescribedBy>
+        </rdf:Description>
+      </rdf:RDF>
+    </annotation>
     <listOfCompartments>
       <compartment id="c1" size="1" units="dimensionless" constant="true"/>
     </listOfCompartments>
diff --git a/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml b/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Schwen_PONE2014" name="Kreutz_IR_binding">
+  <model id="Schwen_PONE2014" name="Schwen_PONE2014">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Schwen et al. (2015), PLoS One, 10, e0133653</pre>
diff --git a/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml b/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Sneyd_PNAS2002" name="model_Sneyd_PNAS2002">
+  <model id="Sneyd_PNAS2002" name="Sneyd_PNAS2002">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Sneyd et al. (2002), PNAS February 19, 2002 99 (4) 2398-2403</pre>
diff --git a/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml b/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Weber_BMC2015" name="model_A">
+  <model id="Weber_BMC2015" name="Weber_BMC2015">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Weber et al. (2015), BMC Syst. Biol., 9, 9</pre>
diff --git a/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml b/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!-- Created by COPASI version 4.29 (Build 228) on 2020-09-16 12:03 with libSBML version 5.18.0. -->
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model metaid="COPASI0" id="Zhao2020___SUQC_model_of_COVID_19_transmission_dynamics_in_Wuhan__Hubei__and_China" name="Zhao2020 - SUQC model of COVID-19 transmission dynamics in Wuhan, Hubei, and China">
+  <model metaid="COPASI0" id="Zhao_QuantBiol2020" name="Zhao_QuantBiol2020">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>Background - The coronavirus disease 2019 (COVID-19) is rapidly spreading in China and more than 30 countries over last two months. COVID-19 has multiple characteristics distinct from other infectious diseases, including high infectivity during incubation, time delay between real dynamics and daily observed number of confirmed cases, and the intervention effects of implemented quarantine and control measures. Methods - We develop a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model to characterize the dynamics of COVID-19 and explicitly parameterize the intervention effects of control measures, which is more suitable for analysis than other existing epidemic models. Results - The SUQC model is applied to the daily released data of the confirmed infections to analyze the outbreak of COVID-19 in Wuhan, Hubei (excluding Wuhan), China (excluding Hubei) and four first-tier cities of China. We found that, before January 30, 2020, all these regions except Beijing had a reproductive number R &gt; 1, and after January 30, all regions had a reproductive number R lesser than 1, indicating that the quarantine and control measures are effective in preventing the spread of COVID-19. The confirmation rate of Wuhan estimated by our model is 0.0643, substantially lower than that of Hubei excluding Wuhan (0.1914), and that of China excluding Hubei (0.2189), but it jumps to 0.3229 after February 12 when clinical evidence was adopted in new diagnosis guidelines. The number of unquarantined infected cases in Wuhan on February 12, 2020 is estimated to be 3,509 and declines to 334 on February 21, 2020. After fitting the model with data as of February 21, 2020, we predict that the end time of COVID-19 in Wuhan and Hubei is around late March, around mid March for China excluding Hubei, and before early March 2020 for the four tier-one cities. A total of 80,511 individuals are estimated to be infected in China, among which 49,510 are from Wuhan, 17,679 from Hubei (excluding Wuhan), and the rest 13,322 from other regions of China (excluding Hubei). Note that the estimates are from a deterministic ODE model and should be interpreted with some uncertainty. Conclusions - We suggest that rigorous quarantine and control measures should be kept before early March in Beijing, Shanghai, Guangzhou and Shenzhen, and before late March in Hubei. The model can also be useful to predict the trend of epidemic and provide quantitative guide for other countries at high risk of outbreak, such as South Korea, Japan, Italy and Iran.</pre>
diff --git a/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml b/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
-  <model id="Zheng_PNAS2012" name="HistoneMethylation">
+  <model id="Zheng_PNAS2012" name="Zheng_PNAS2012">
     <notes>
       <body xmlns="http://www.w3.org/1999/xhtml">
         <pre>PEtab implementation of the model from Zheng et al. (2012), Proc. Natl. Acad. Sci. USA, 109, 13549–13554</pre>
diff --git a/Benchmark-Models/checkBenchmarkModels.py b/Benchmark-Models/checkBenchmarkModels.py
diff --git a/README.md b/README.md
diff --git a/scripts/_helpers.py b/scripts/_helpers.py
diff --git a/scripts/check_petablint.py b/scripts/check_petablint.py
diff --git a/scripts/check_sbml_metadata.py b/scripts/check_sbml_metadata.py
diff --git a/scripts/overview.py b/scripts/overview.py
diff --git a/scripts/requirements.txt b/scripts/requirements.txt
