Merge branch 'dev' into deploy

biosimulators · Mar 1, 2022 · e2802ce · e2802ce
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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
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex">
     <!-- name -->
     <dc:title>DNA damage repair by non-homologous end joining (Dolan et al., PLoS Comput Biol, 2015)</dc:title>

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
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/test-bngl.omex">
     <!-- name -->
     <dc:title>Toy gene regulatory network (Saglam, 2020)</dc:title>

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
@@ -3,7 +3,7 @@
     xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
     xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
     xmlns:collex="http://www.collex.org/schema#"
-    xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+    xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:dcterms='http://purl.org/dc/terms/'
     xmlns:foaf="http://xmlns.com/foaf/0.1/"
     xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

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
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Lorenz-system.omex">
     <!-- name -->
     <dc:title>Lorenz system (Garny, 2019)</dc:title>

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
@@ -3,7 +3,7 @@
   xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
   xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
   xmlns:collex="http://www.collex.org/schema#"
-  xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns:dcterms='http://purl.org/dc/terms/'
   xmlns:foaf="http://xmlns.com/foaf/0.1/"
   xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

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
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Hodgkin-Huxley-cell-CVODE.omex">
     <!-- name -->
     <dc:title>Hodgkin-Huxley model (Gleeson, 2015)</dc:title>

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
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Hodgkin-Huxley-cell-Euler.omex">
     <!-- name -->
     <dc:title>Hodgkin-Huxley model (Gleeson, 2015)</dc:title>

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
@@ -3,7 +3,7 @@
   xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
   xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
   xmlns:collex="http://www.collex.org/schema#"
-  xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns:dcterms='http://purl.org/dc/terms/'
   xmlns:foaf="http://xmlns.com/foaf/0.1/"
   xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

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
@@ -3,7 +3,7 @@
     xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
     xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
     xmlns:collex="http://www.collex.org/schema#"
-    xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+    xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:dcterms='http://purl.org/dc/terms/'
     xmlns:foaf="http://xmlns.com/foaf/0.1/"
     xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

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
diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf
@@ -3,7 +3,7 @@
   xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
   xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
   xmlns:collex="http://www.collex.org/schema#"
-  xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns:dcterms='http://purl.org/dc/terms/'
   xmlns:foaf="http://xmlns.com/foaf/0.1/"
   xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
diff --git a/...les/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf b/...les/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf
@@ -3,7 +3,7 @@
   xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
   xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
   xmlns:collex="http://www.collex.org/schema#"
-  xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+  xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns:dcterms='http://purl.org/dc/terms/'
   xmlns:foaf="http://xmlns.com/foaf/0.1/"
   xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

diff --git a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex
diff --git a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf
@@ -3,7 +3,7 @@
     xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
     xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
     xmlns:collex="http://www.collex.org/schema#"
-    xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+    xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:dcterms="http://purl.org/dc/terms/"
     xmlns:foaf="http://xmlns.com/foaf/0.1/"
 

diff --git a/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex b/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex
diff --git a/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf b/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf
@@ -3,7 +3,7 @@
     xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
     xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
     xmlns:collex="http://www.collex.org/schema#"
-    xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/"
+    xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:dcterms='http://purl.org/dc/terms/'
     xmlns:foaf="http://xmlns.com/foaf/0.1/"
     xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"

diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex
diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex">
     <!-- name -->
     <dc:title>Mouse iron distribution (Parmar et al., BMC Syst Biol, 2017)</dc:title>

diff --git a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex
diff --git a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex">
     <!-- name -->
     <dc:title>Heat shock protein synthesis in response to temperature change (Szymanska &amp; Zylicz, J Theor Biol, 2009)</dc:title>

diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex
diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Tomida-EMBO-J-2003-NFAT-translocation.omex">
     <!-- name -->
     <dc:title>Calcium-induced NFAT translocation (Tomida et al., EMBO J, 2003)</dc:title>

diff --git a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex
diff --git a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex">
     <!-- name -->
     <dc:title>mTOR signalling network (Varusai &amp; Nguyen, Sci Reports, 2018)</dc:title>

diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex">
     <!-- name -->
     <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>

diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex">
     <!-- name -->
     <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>

diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex">
     <!-- name -->
     <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>

diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Vilar-PNAS-2002-minimal-circardian-clock.omex">
     <!-- name -->
     <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>

diff --git a/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex b/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex
diff --git a/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf b/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex">
     <!-- name -->
     <dc:title>Textbook model of Escherichia coli core metabolism (COBRApy Team, 2020)</dc:title>

diff --git a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex
diff --git a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://dublincore.org/specifications/dublin-core/dcmi-terms/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:collex="http://www.collex.org/schema#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
   <rdf:Description rdf:about="http://omex-library.org/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex">
     <!-- name -->
     <dc:title>EGF and TNFα signaling (Chaouiya et al., BMC Syst Biol, 2013)</dc:title>

diff --git a/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex b/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex