Merge branch 'dev' into deploy

biosimulators · Jan 5, 2022 · a56c52d · a56c52d
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diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
@@ -1 +1 @@
-__version__ = '0.1.81'
+__version__ = '0.1.82'
diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex
diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf
@@ -18,7 +18,7 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606" />
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/9606" />
         <rdfs:label>Homo sapiens</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
@@ -83,21 +83,21 @@
       <rdf:Description>
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080" />
         <foaf:name>Jonathan Karr</foaf:name>
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080" />
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080" />
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
     <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1371/journal.pcbi.1004246" />
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1371/journal.pcbi.1004246" />
         <rdfs:label>David W. P. Dolan, Anze Zupanic, Glyn Nelson, Philip Hall, Satomi Miwa, Thomas B. L. Kirkwood &amp; Daryl P. Shanley. Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling. PLoS Comput Biol 11, 5 (2015): e1004246.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT" />
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:MIT" />
         <rdfs:label>MIT</rdfs:label>
       </rdf:Description>
     </dc:license>

diff --git a/examples/bngl/test-bngl.omex b/examples/bngl/test-bngl.omex
diff --git a/examples/bngl/test-bngl/metadata.rdf b/examples/bngl/test-bngl/metadata.rdf
@@ -24,14 +24,14 @@
       <rdf:Description>
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080" />
         <foaf:name>Jonathan Karr</foaf:name>
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080" />
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080" />
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT" />
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:MIT" />
         <rdfs:label>MIT</rdfs:label>
       </rdf:Description>
     </dc:license>

diff --git a/examples/cellml/Elowitz-Nature-2000-Repressilator.omex b/examples/cellml/Elowitz-Nature-2000-Repressilator.omex
diff --git a/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf b/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf
@@ -26,7 +26,7 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/562"/>
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/562"/>
         <rdfs:label>Escherichia coli</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
@@ -42,7 +42,7 @@
     <!-- other identifiers -->
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000012"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000012"/>
         <rdfs:label>biomodels.db:BIOMD0000000012</rdfs:label>
       </rdf:Description>
     </bqmodel:is>
@@ -60,7 +60,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-1221-0967"/>
         <foaf:name>Michael Elowitz</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-1221-0967"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-1221-0967"/>
         <rdfs:label>Michael Elowitz</rdfs:label>
       </rdf:Description>
     </dc:creator>
@@ -111,23 +111,23 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080"/>
         <foaf:name>Jonathan Karr</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080"/>
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
 
      <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/35002125"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1038/35002125"/>
         <rdfs:label>Michael B Elowitz &amp; Stanislas Leibler. A synthetic oscillatory network of transcriptional regulators. Nature 403, 6767 (2000) 335-338.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0"/>
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:CC0-1.0"/>
         <rdfs:label>CC0-1.0</rdfs:label>
       </rdf:Description>
     </dc:license>
@@ -151,7 +151,7 @@
   <rdf:Description rdf:about="http://omex-library.org/Elowitz-Nature-2000-Repressilator.omex/simulation.sedml/Figure_1c">
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/35002125"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1038/35002125"/>
         <rdfs:label>Figure 1c</rdfs:label>
       </rdf:Description>
     </bqmodel:is>

diff --git a/examples/cellml/Lorenz-system.omex b/examples/cellml/Lorenz-system.omex
diff --git a/examples/cellml/Lorenz-system/metadata.rdf b/examples/cellml/Lorenz-system/metadata.rdf
@@ -24,21 +24,21 @@
       <rdf:Description>
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080" />
         <foaf:name>Jonathan Karr</foaf:name>
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080" />
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080" />
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
     <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.3389/fphys.2015.00026" />
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.3389/fphys.2015.00026" />
         <rdfs:label>Alan Garny &amp; Peter J. Hunter. OpenCOR: a modular and interoperable approach to computational biology. Front Physiol 6 (2015): 26.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:GPL-3.0-only" />
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:GPL-3.0-only" />
         <rdfs:label>GPL-3.0-only</rdfs:label>
       </rdf:Description>
     </dc:license>

diff --git a/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex b/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex
diff --git a/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf b/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf
@@ -23,7 +23,7 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606"/>
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/9606"/>
         <rdfs:label>Homo sapiens</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
@@ -93,23 +93,23 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080"/>
         <foaf:name>Jonathan Karr</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080"/>
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
 
      <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.cels.2015.10.003"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.cels.2015.10.003"/>
         <rdfs:label>Aarash Bordbar, Douglas McCloskey, Daniel C Zielinski, Nikolaus Sonnenschein, Neema Jamshidi &amp; Bernhard O Palsson. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst 1, 4 (2015): 283-292.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT"/>
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:MIT"/>
         <rdfs:label>MIT</rdfs:label>
       </rdf:Description>
     </dc:license>

diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex
diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf
@@ -24,21 +24,21 @@
       <rdf:Description>
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080" />
         <foaf:name>Jonathan Karr</foaf:name>
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080" />
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080" />
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
     <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.3389/fninf.2014.00079" />
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.3389/fninf.2014.00079" />
         <rdfs:label>Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini &amp; R. Angus Silver. LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front Neuroinform 8 (2014): 79.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:LGPL-3.0-only" />
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:LGPL-3.0-only" />
         <rdfs:label>LGPL-3.0-only</rdfs:label>
       </rdf:Description>
     </dc:license>

diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex
diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf
@@ -24,21 +24,21 @@
       <rdf:Description>
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080" />
         <foaf:name>Jonathan Karr</foaf:name>
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080" />
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080" />
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
     <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.3389/fninf.2014.00079" />
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.3389/fninf.2014.00079" />
         <rdfs:label>Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini &amp; R. Angus Silver. LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front Neuroinform 8 (2014): 79.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:LGPL-3.0-only" />
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:LGPL-3.0-only" />
         <rdfs:label>LGPL-3.0-only</rdfs:label>
       </rdf:Description>
     </dc:license>

diff --git a/examples/rba/Escherichia-coli-K12-WT.omex b/examples/rba/Escherichia-coli-K12-WT.omex
diff --git a/examples/rba/Escherichia-coli-K12-WT/metadata.rdf b/examples/rba/Escherichia-coli-K12-WT/metadata.rdf
@@ -25,15 +25,15 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/83333"/>
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/83333"/>
         <rdfs:label>Escherichia coli K-12</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
 
     <!-- ancestor(s) of this work -->
     <bqmodel:isDerivedFrom>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/msb.2011.65"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1038/msb.2011.65"/>
         <rdfs:label>Jeffrey D Orth, Tom M Conrad, Jessica Na, Joshua A Lerman, Hojung Nam, Adam M Feist &amp; Bernhard Ø Palsson. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011. Molecular Systems Biology 7 (2011): 535.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDerivedFrom>
@@ -123,23 +123,23 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080"/>
         <foaf:name>Jonathan Karr</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080"/>
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
 
      <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.ymben.2019.06.001"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.ymben.2019.06.001"/>
         <rdfs:label>Ana Bulović, Stephan Fischer, Marc Dinh, Felipe Golib, Wolfram Liebermeister, Christian Poirier, Laurent Tournier, Edda Klipp, Vincent Fromion &amp; Anne Goelzer. Automated generation of bacterial resource allocation models. Metabolic Engineering 55 (2019): 12-22.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:GPL-3.0-or-later"/>
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:GPL-3.0-or-later"/>
         <rdfs:label>GPL-3.0-or-later</rdfs:label>
       </rdf:Description>
     </dc:license>
@@ -163,7 +163,7 @@
   <rdf:Description rdf:about="http://omex-library.org/Escherichia-coli-K12-WT.omex/flux-map.vg.json">
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.ymben.2019.06.001"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.ymben.2019.06.001"/>
         <rdfs:label>Figure S13</rdfs:label>
       </rdf:Description>
     </bqmodel:is>

diff --git a/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex b/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
diff --git a/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf b/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf
@@ -27,23 +27,23 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606"/>
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/9606"/>
         <rdfs:label>Homo sapiens</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
 
     <!-- ancestor(s) of this work -->
     <bqmodel:isDerivedFrom>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1007/s002850050127"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1007/s002850050127"/>
         <rdfs:label>Denise Kirschner &amp; John Carl Panetta. Modeling immunotherapy of the tumor-immune interaction. Journal of Mathematical Biology 37, 3 (1998): 235-252.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDerivedFrom>
 
     <!-- other identifiers -->
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000912"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000912"/>
         <rdfs:label>biomodels.db:BIOMD0000000912</rdfs:label>
       </rdf:Description>
     </bqmodel:is>
@@ -54,7 +54,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0003-4240-3265"/>
         <foaf:name>Giulio Caravagna</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0003-4240-3265"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0003-4240-3265"/>
         <rdfs:label>Giulio Caravagna</rdfs:label>
       </rdf:Description>
     </dc:creator>
@@ -64,7 +64,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2190-272"/>
         <foaf:name>Alberto d'Onofrio</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2190-272X"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2190-272X"/>
         <rdfs:label>Alberto d'Onofrio</rdfs:label>
       </rdf:Description>
     </dc:creator>
@@ -74,7 +74,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-7309-6424"/>
         <foaf:name>Paolo Milazzo</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-7309-6424"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-7309-6424"/>
         <rdfs:label>Paolo Milazzo</rdfs:label>
       </rdf:Description>
     </dc:creator>
@@ -92,7 +92,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0001-9521-6012"/>        
         <foaf:name>Mohammad Umer Sharif Shohan</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0001-9521-6012"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0001-9521-6012"/>
         <rdfs:label>Mohammad Umer Sharif Shohan</rdfs:label>
       </rdf:Description>
     </dc:contributor>
@@ -102,23 +102,23 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0002-2605-5080"/>        
         <foaf:name>Jonathan Karr</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0002-2605-5080"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0002-2605-5080"/>
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:contributor>
 
      <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.jtbi.2010.05.013"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.jtbi.2010.05.013"/>
         <rdfs:label>Giulio Caravagna, Alberto d'Onofrio, Paolo Milazzo &amp; Roberto Barbuti. Journal of Theoretical Biology 265, 3 (2010) 336-345.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0"/>
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:CC0-1.0"/>
         <rdfs:label>CC0-1.0</rdfs:label>
       </rdf:Description>
     </dc:license>
@@ -142,7 +142,7 @@
   <rdf:Description rdf:about="http://omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left">
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.jtbi.2010.05.013"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.jtbi.2010.05.013"/>
         <rdfs:label>Figure 1 (bottom left)</rdfs:label>
       </rdf:Description>
     </bqmodel:is>

diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex