Repository: biosimulators/Biosimulators_test_suite (language: python)

Issue:
Add metadata about examples following OMEX Metadata guidelines
- OMEX Meta guidelines: https://biosimulators.dev/conventions/metadata
- Complete example: https://github.com/biosimulators/Biosimulators_utils/blob/dev/tests/fixtures/omex-meta/biosimulations-with-file-annotations.rdf

- `sbml-core/`
  - [x] `Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations`
  - [x] `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous`
  - [x] `Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Felhberg`
  - [x] `Edelstein-Biol-Cybern-1996-Nicotinic-excitation`
  - [x] `Parmar-BMC-Syst-Biol-2017-iron-distribution`
  - [x] `Szymanska-J-Theor-Biol-2009-HSP-synthesis`
  - [x] `Tomida-EMBO-J-2003-NFAT-translocation`
  - [x] `Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML`
  - [x] `Vilar-PNAS-2002-minimal-circardian-clock`
  - [x] `Vilar-PNAS-2002-minimal-circardian-clock-continuous` (metadata is the same as `Vilar-PNAS-2002-minimal-circardian-clock`)
  - [x] `Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM` (metadata is the same as `Vilar-PNAS-2002-minimal-circardian-clock`)
  - [x] `Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA` (metadata is the same as `Vilar-PNAS-2002-minimal-circardian-clock`)
- `sbml-fbc/`
  - [x] `Escherichia-coli-core-metabolism`
- `sbml-qual/`
  - [x] `Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling`
- `cellml/`
  - [x] `Lorenz-system`
- `neuroml-lems/`
  - [x] `Hodgkin-Huxley-cell-CVODE`
  - [x] `Hodgkin-Huxley-cell-Euler` (annotation will be the same as for `Hodgkin-Huxley-cell-CVODE`)
- `bngl/`
  - [x] `Dolan-PLoS-Comput-Biol-2015-NHEJ`
  - [x] `test-bngl`
- `smoldyn/`
  - [x] `Lotka-Volterra`
Added metadata information.



Discussion / hints:
Instructions
- Clone this repository
- Navigate to the directory `examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation`. This directory contains files which describe a simulation of a model and metadata about the biology that the model represents.
- Open `metadata.rdf` in this directory
- We want to expand the information captured by this file and represent it in a slightly different format.
- Use https://github.com/biosimulators/Biosimulators_utils/blob/dev/tests/fixtures/omex-meta/biosimulations-with-file-annotations.rdf as a template. 
- Copy information from `metadata.rdf` into the template.
- Gather additional information from the [BioModels entry](http://identifiers.org/biomodels.db/BIOMD0000000002) and [publication](https://doi.org/10.1007/s004220050302) for this model and copy it into the template. This information includes
  - Organism (Tetronarce californica)
  - Biology represented by the model
    -  Neuromuscular synaptic transmission
    - transmission of nerve impulse
    - cell surface receptor signaling pathway
  - Thumbnail image: Figure 2 of publication
  - Citation for the publication (Edelstein SJ, Schaad O, Henry E, Bertrand D, Changeux JP. A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biol. Cybern. 1996 Nov; 75(5):361-79)
- Save the modified template to `metadata.rdf` in the directory
- Add the thumbnail image(s) to `manifest.xml` in the directory, e.g.
   ```xml
   <content location="Figure2.png" format="http://purl.org/NET/mediatypes/image/png" master="false"/>
   ```
- Commit and push your change to the repository
   ```
   git add \
      examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf \
      examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/manifest.xml \
      examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/Figure2.png
   ```

Three additional examples include the `metadata.rdf` files in `examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` and `examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous`.
@bilalshaikh42 above is an outline for Ryann. I've worked through a couple of OMEX files as examples.


Fix patch:
diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Figure1.png b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Figure1.png
new file mode 100644
index 0000000..049acd6
Binary files /dev/null and b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Figure1.png differ
diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/manifest.xml b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/manifest.xml
index 1b9c514..43bb48b 100644
--- a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/manifest.xml
+++ b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/manifest.xml
@@ -6,4 +6,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.png" format="http://purl.org/NET/mediatypes/image/png" master="false"/>
 </omexManifest>
diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf
index 961165c..9e1533e 100644
--- a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf
+++ b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf
@@ -1,64 +1,117 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF
-  xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
-  xmlns:dcterms='http://purl.org/dc/terms/'
-  xmlns:vCard='http://www.w3.org/2006/vcard/ns#'
-  xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
->
-  <rdf:Description rdf:about='./Dolan2015.bngl'>
-    <dcterms:description>Dolan et al. PLoS Computational Biology 2015: DNA damage repair by non-homologous end joining</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Dolan</vCard:family-name>
-        <vCard:given-name>David</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Zupanic</vCard:family-name>
-        <vCard:given-name>Anze</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Nelson</vCard:family-name>
-        <vCard:given-name>Glyn</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Hall</vCard:family-name>
-        <vCard:given-name>Philip</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Miwa</vCard:family-name>
-        <vCard:given-name>Satomi</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Kirkwood</vCard:family-name>
-        <vCard:given-name>Thomas</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Shanley</vCard:family-name>
-        <vCard:given-name>Daryl</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1371/journal.pcbi.1004246"/>
-      </rdf:Bag>
-    </bqmodel:isDescribedBy>
+<?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="https://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:Description rdf:about="http://omex-libary.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>
+    <!-- short summary -->
+    <dc:abstract>An integrated stochastic model of DNA damage repair by non-homologous end joining and of gamma irradiation-induced cellular senescence in human cells that are not apoptosis-prone, which successfully explains the changes that occur in the dynamics of DNA damage repair after irradiation.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Cellular Senescence</prism:keyword>
+    <prism:keyword>Cyclin-Dependent Kinase Inhibitor p21</prism:keyword>
+    <prism:keyword>DNA damage</prism:keyword>
+    <prism:keyword>DNA End-Joining Repair</prism:keyword>
+    <prism:keyword>Tumor Suppressor Protein p53</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex/Figure1.png" />
+    <!-- long description -->
+    <dc:description>An integrated stochastic model of DNA damage repair by non-homologous end joining and of gamma irradiation-induced cellular senescence in human cells that are not apoptosis-prone. The integrated model successfully explains the changes that occur in the dynamics of DNA damage repair after irradiation. Simulations of p53/p21 dynamics after irradiation agree well with previously published experimental studies. Additionally, the model captures that low-dose fractionated irradiation of cells leads to temporal patterns in p53/p21 that lead to significant cellular senescence. The integrated model is valuable for studying the processes of DNA damage induced cell fate and predicting the effectiveness of DNA damage related medical interventions at the cellular level.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606" />
+        <rdfs:label>Homo sapiens</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- other identifiers -->
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://github.com/RuleWorld/RuleHub/tree/master/Published/Dolan2015"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://github.com/RuleWorld/RuleHub/tree/master/Published/Dolan2015" />
+        <rdfs:label>RuleHub:Dolan2015</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>https://opensource.org/licenses/MIT</dcterms:license>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>David W. P. Dolan</foaf:name>
+        <rdfs:label>David W. P. Dolan</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Anze Zupanic</foaf:name>
+        <rdfs:label>Anze Zupanic</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Glyn Nelson</foaf:name>
+        <rdfs:label>Glyn Nelson</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Philip Hall</foaf:name>
+        <rdfs:label>Philip Hall</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Satomi Miwa</foaf:name>
+        <rdfs:label>Satomi Miwa</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Thomas B. L. Kirkwood</foaf:name>
+        <rdfs:label>Thomas B. L. Kirkwood</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Daryl P. Shanley</foaf:name>
+        <rdfs:label>Daryl P. Shanley</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>James Faeder</foaf:name>
+        <rdfs:label>James Faeder</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <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" />
+        <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" />
+        <rdfs:label>MIT</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2015-05-28</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/cellml/Lorenz-system/metadata.rdf b/examples/cellml/Lorenz-system/metadata.rdf
index 12029b6..18fe71e 100644
--- a/examples/cellml/Lorenz-system/metadata.rdf
+++ b/examples/cellml/Lorenz-system/metadata.rdf
@@ -1,18 +1,58 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./lorenz.cellml'>
-    <dcterms:description>Lorenz model</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Alan</vCard:family-name>
-        <vCard:given-name>Garny</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Lorenz-system.omex">
+    <!-- name -->
+    <dc:title>Lorenz system (Garny, 2019)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>An example CellML model of a Lorenz system.</dc:abstract>
+    <!-- other identifiers -->
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://github.com/opencor/opencor/blob/master/models/tests/cellml/lorenz.cellml"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://raw.githubusercontent.com/opencor/opencor/master/models/tests/cellml/lorenz.cellml" />
+        <rdfs:label>github:opencor/opencor/models/tests/cellml/lorenz.cellml</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>https://raw.githubusercontent.com/opencor/opencor/master/LICENSE.txt</dcterms:license>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Alan Garny</foaf:name>
+        <rdfs:label>Alan Garny</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <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" />
+        <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" />
+        <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" />
+        <rdfs:label>GPL-3.0-only</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2019-11-18</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf
index c5f9c49..611d3b8 100644
--- a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf
+++ b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf
@@ -1,18 +1,58 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='.'>
-    <dcterms:description>Hodgkin-Huxley cell with simple morphology</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Padraig</vCard:family-name>
-        <vCard:given-name>Gleeson</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Hodgkin-Huxley-cell-CVODE.omex">
+    <!-- name -->
+    <dc:title>Hodgkin-Huxley model (Gleeson, 2015)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>A LEMS/NeuroML example of the Hodgkin-Huxley model.</dc:abstract>
+    <!-- other identifiers -->
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://github.com/NeuroML/pyNeuroML/blob/master/examples/LEMS_NML2_Ex5_DetCell.xml"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://raw.githubusercontent.com/NeuroML/pyNeuroML/master/examples/LEMS_NML2_Ex5_DetCell.xml" />
+        <rdfs:label>github:NeuroML/pyNeuroML/examples/LEMS_NML2_Ex5_DetCell.xml</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser</dcterms:license>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Padraig Gleeson</foaf:name>
+        <rdfs:label>Padraig Gleeson</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <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" />
+        <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" />
+        <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" />
+        <rdfs:label>LGPL-3.0-only</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2015-02-09</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf
index c5f9c49..29bdfb2 100644
--- a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf
+++ b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf
@@ -1,18 +1,58 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='.'>
-    <dcterms:description>Hodgkin-Huxley cell with simple morphology</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Padraig</vCard:family-name>
-        <vCard:given-name>Gleeson</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Hodgkin-Huxley-cell-Euler.omex">
+    <!-- name -->
+    <dc:title>Hodgkin-Huxley model (Gleeson, 2015)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>A LEMS/NeuroML example of the Hodgkin-Huxley model.</dc:abstract>
+    <!-- other identifiers -->
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://github.com/NeuroML/pyNeuroML/blob/master/examples/LEMS_NML2_Ex5_DetCell.xml"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://raw.githubusercontent.com/NeuroML/pyNeuroML/master/examples/LEMS_NML2_Ex5_DetCell.xml" />
+        <rdfs:label>github:NeuroML/pyNeuroML/examples/LEMS_NML2_Ex5_DetCell.xml</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser</dcterms:license>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Padraig Gleeson</foaf:name>
+        <rdfs:label>Padraig Gleeson</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <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" />
+        <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" />
+        <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" />
+        <rdfs:label>LGPL-3.0-only</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2015-02-09</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
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
index 989e8b4..c09b461 100644
--- 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
@@ -11,7 +11,7 @@
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
 >
   <rdf:Description rdf:about='http://omex-libary.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex'>
-    <dc:title>Tumor-suppressive oscillations (Caravagna et al., Journal of Theoretical Biology, 2010)</dc:title>
+    <dc:title>Tumor-suppressive oscillations (Caravagna et al., J Theor Biol, 2010)</dc:title>
 
     <dc:abstract>Hybrid-stochastic model of tumour suppression by the immune system through stochastic oscillations</dc:abstract>
 
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
index bf9a019..b7288df 100644
--- 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
@@ -11,7 +11,7 @@
   xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
   >
   <rdf:Description rdf:about='http://omex-libary.org/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex'>
-    <dc:title>Morphogenesis checkpoint in budding yeast (continuous) (Ciliberto et al., Journal Cell Biology, 2003)</dc:title>
+    <dc:title>Morphogenesis checkpoint in budding yeast (continuous) (Ciliberto et al., J Cell Biol, 2003)</dc:title>
 
     <dc:abstract>Continuous kinetic model of the molecular network that controls Swe1 and the regulation of cyclin-dependent kinase.</dc:abstract>
 
@@ -34,6 +34,28 @@
       </rdf:Description>
     </bqbiol:hasTaxon>
 
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/kegg.pathway:ko04111" />
+        <rdfs:label>cell cycle</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0009653" />
+        <rdfs:label>anatomical structure morphogenesis</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0044879" />
+        <rdfs:label>mitotic morphogenesis checkpoint signaling</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
     <!-- ancestor(s) of this work -->
     <bqmodel:isDerivedFrom>
       <rdf:Description>
diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf
index 9537f6d..7aa8605 100644
--- a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf
+++ b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf
@@ -11,7 +11,7 @@
   xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
   >
   <rdf:Description rdf:about='http://omex-libary.org/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'>
-    <dc:title>Morphogenesis checkpoint in budding yeast (continuous) (Ciliberto et al., Journal Cell Biology, 2003)</dc:title>
+    <dc:title>Morphogenesis checkpoint in budding yeast (continuous) (Ciliberto et al., J Cell Biol, 2003)</dc:title>
 
     <dc:abstract>Continuous kinetic model of the molecular network that controls Swe1 and the regulation of cyclin-dependent kinase.</dc:abstract>
 
@@ -34,6 +34,28 @@
       </rdf:Description>
     </bqbiol:hasTaxon>
 
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/kegg.pathway:ko04111" />
+        <rdfs:label>cell cycle</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0009653" />
+        <rdfs:label>anatomical structure morphogenesis</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0044879" />
+        <rdfs:label>mitotic morphogenesis checkpoint signaling</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
     <!-- ancestor(s) of this work -->
     <bqmodel:isDerivedFrom>
       <rdf:Description>
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
index ffc0423..6e745b7 100644
--- a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf
+++ b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf
@@ -6,15 +6,14 @@
     xmlns:dc="https://dublincore.org/specifications/dublin-core/dcmi-terms/"
     xmlns:dcterms="http://purl.org/dc/terms/"
     xmlns:foaf="http://xmlns.com/foaf/0.1/"
-    xmlns:om="http://ontology.eil.utoronto.ca/icity/OM/"
+   
     xmlns:prism="http://prismstandard.org/namespaces/basic/2.0/"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
-    xmlns:scoro="http://purl.org/spar/scoro/"
 >
   <rdf:Description rdf:about="http://omex-libary.org/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex">
     <!-- name -->
-    <dc:title>Nicotinic excitatory post-synaptic potential (Edelstein et al., Biological Cybernetics, 1996)</dc:title>
+    <dc:title>Nicotinic excitatory post-synaptic potential (Edelstein et al., Biol Cybern, 1996)</dc:title>
 
     <!-- short summary -->
     <dc:abstract>Model of a nicotinic Excitatory Post-Synaptic Potential in a Torpedo electric organ. Acetylcholine is represented explicitely as a molecular species.</dc:abstract>
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
index 03ffb7d..bfff873 100644
Binary files a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex and b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex differ
diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/Figure1.jpg b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/Figure1.jpg
new file mode 100644
index 0000000..4886ac6
Binary files /dev/null and b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/Figure1.jpg differ
diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/manifest.xml b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/manifest.xml
index bdbb179..e2510f9 100644
--- a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/manifest.xml
+++ b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/manifest.xml
@@ -7,4 +7,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/image/jpeg" master="false"/>
 </omexManifest>
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
index 84c44e7..837ef87 100644
--- 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
@@ -1,41 +1,194 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2006/vcard/ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about="./BIOMD0000000734.xml">
-    <dcterms:description>Parmar et al. BMC Systems Biology 2017: Mouse iron distribution</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Parmar</vCard:family-name>
-        <vCard:given-name>Jignesh</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Davis</vCard:family-name>
-        <vCard:given-name>Grey</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Shevchuk</vCard:family-name>
-        <vCard:given-name>Hope</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Mendes</vCard:family-name>
-        <vCard:given-name>Pedro</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<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="https://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:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex">
+    <!-- name -->
+    <dc:title>Mouse iron distribution (Parmar et al., BMC Syst Biol, 2017)</dc:title>
+
+    <!-- short summary -->
+    <dc:abstract>Dynamic model of iron distribution in mice. This model includes normal iron and radioactive labelled tracer iron species and was used for parameter estimation given the data from Lopes et al. 2010 for mice fed an adequate iron diet.</dc:abstract>
+
+    <!-- keywords -->
+    <prism:keyword>anemia</prism:keyword>
+    <prism:keyword>Hemochromatosis</prism:keyword>
+    <prism:keyword>Hepcidins</prism:keyword>
+    <prism:keyword>iron</prism:keyword>
+    <prism:keyword>metabolism</prism:keyword>
+
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Figure1.png"/>
+
+    <!-- long description -->
+    <dc:description>Iron is an essential element of most living organisms but is a dangerous substance when poorly liganded in solution. The hormone hepcidin regulates the export of iron from tissues to the plasma contributing to iron homeostasis and also restricting its availability to infectious agents. Disruption of iron regulation in mammals leads to disorders such as anemia and hemochromatosis, and contributes to the etiology of several other diseases such as cancer and neurodegenerative diseases. Here we test the hypothesis that hepcidin alone is able to regulate iron distribution in different dietary regimes in the mouse using a computational model of iron distribution calibrated with radioiron tracer data.</dc:description>
+
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/10090" />
+        <rdfs:label>Mus musculus</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0055072" />
+        <rdfs:label>iron ion homeostasis</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000734" />
+        <rdfs:label>biomodels.db:BIOMD0000000734</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Jignesh H Parmar</foaf:name>
+        <rdfs:label>Jignesh H Parmar</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Grey Davis</foaf:name>
+        <rdfs:label>Grey Davis</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Hope Shevchuk</foaf:name>
+        <rdfs:label>Hope Shevchuk</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Pedro Mendes</foaf:name>
+        <rdfs:label>Pedro Mendes</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Krishna Kumar Tiwari</foaf:name>
+        <rdfs:label>Krishna Kumar Tiwari</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Ryann Jordan</foaf:name>
+        <rdfs:label>Ryann Jordan</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1186/s12918-017-0431-3"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Jignesh H Parmar, Grey Davis, Hope Shevchuk &amp; Pedro Mendes. Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. BMC Syst Biol 11, 1 (2017): 57.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2017-05-18</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3b">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3b</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3c">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3c</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3d">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3d</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3e">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3e</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3f">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3f</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3g">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3g</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+
+  <rdf:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex/Parmar2017_Deficient_Rich_tracer.sedml/Figure_3h">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000734"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/s12918-017-0431-3" />
+        <rdfs:label>Figure 3h</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
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
index aa11895..b7b89c6 100644
Binary files a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex and b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex differ
diff --git a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/Figure1.jpg b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/Figure1.jpg
new file mode 100644
index 0000000..7dcb923
Binary files /dev/null and b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/Figure1.jpg differ
diff --git a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/manifest.xml b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/manifest.xml
index 3eb35df..d03ba26 100644
--- a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/manifest.xml
+++ b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/manifest.xml
@@ -6,4 +6,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/image/jpeg" master="false"/>
 </omexManifest>
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
index e2b4c9c..ac25be5 100644
--- 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
@@ -1,29 +1,106 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./Szymanska2009.xml'>
-    <dcterms:description>Szymańska &amp; Zylicz. Journal of Theoretical Biology 2009: heat shock protein synthesis in response to temperature change</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Szymańska</vCard:family-name>
-        <vCard:given-name>Zuzanna</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Zylicz</vCard:family-name>
-        <vCard:given-name>Maciej</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.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>
+    <!-- short summary -->
+    <dc:abstract>This is a mathematical model of heat shock protein synthesis induced by an external temperature stimulus. The model consists of a system of nine nonlinear ordinary differential equations describing the temporal evolution of key variables involved in the regulation of HSP synthesis.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Heat shock proteins</prism:keyword>
+    <prism:keyword>Heat shock response</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex/Figure1.jpg" />
+    <!-- long description -->
+    <dc:description>Mathematical model of heat shock protein synthesis induced by an external temperature stimulus. Our model consists of a system of nine nonlinear ordinary differential equations describing the temporal evolution of the key variables involved in the regulation of HSP synthesis.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606" />
+        <rdfs:label>Homo sapiens</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/ncit:C17132" />
+        <rdfs:label>signaling pathway</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000896" />
+        <rdfs:label>biomodels.db:BIOMD0000000896</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Zuzanna Szymańska</foaf:name>
+        <rdfs:label>Zuzanna Szymańska</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Maciej Zylicz</foaf:name>
+        <rdfs:label>Maciej Zylicz</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Johannes Meyer</foaf:name>
+        <rdfs:label>Johannes Meyer</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Ryann Jordan</foaf:name>
+        <rdfs:label>Ryann Jordan</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1016/j.jtbi.2009.03.021"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.jtbi.2009.03.021" />
+        <rdfs:label>Zuzanna Szymańska Z &amp; Maciej Zylicz. Mathematical modeling of heat shock protein synthesis in response to temperature change. Journal of Theoretical Biology 259, 3 (2009): 562-569.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2009-08-07</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex/BIOMD0000000896_sim.sedml/Figure_3">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000896"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.jtbi.2009.03.021" />
+        <rdfs:label>Figure 3</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex
index 4d20979..c48cf2a 100644
Binary files a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex and b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex differ
diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/Figure3a.jpg b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/Figure3a.jpg
new file mode 100644
index 0000000..fa7e1a2
Binary files /dev/null and b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/Figure3a.jpg differ
diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/manifest.xml b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/manifest.xml
index 60ca4a1..3367301 100644
--- a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/manifest.xml
+++ b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/manifest.xml
@@ -7,4 +7,5 @@
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
   <content location="Figure_3c.vega.json" format="http://purl.org/NET/mediatypes/application/vega+json" master="false"/>
+  <content location="Figure3a.jpg" format="http://purl.org/NET/mediatypes/image/jpeg" master="false"/>
 </omexManifest>
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
index 62b196d..c5f7ea8 100644
--- a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf
+++ b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf
@@ -1,47 +1,131 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./BIOMD0000000678_url.xml'>
-    <dcterms:description>Tomida et al. EMBO Journal 2003: Calcium-induced NFAT translocation</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Tomida</vCard:family-name>
-        <vCard:given-name>Taichiro</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Hirose</vCard:family-name>
-        <vCard:given-name>Kenzo</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Takizawa</vCard:family-name>
-        <vCard:given-name>Azusa</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Shibasaki</vCard:family-name>
-        <vCard:given-name>Futoshi</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Iino</vCard:family-name>
-        <vCard:given-name>Masamitsu</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Tomida-EMBO-J-2003-NFAT-translocation.omex">
+    <!-- name -->
+    <dc:title>Calcium-induced NFAT translocation (Tomida et al., EMBO J, 2003)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>Model of the kinetics of dephosphorylation and translocation of NFAT. The model captures the rapid Ca(2+)-dependent dephosphorylation of NFAT and its slow rephosphorylation and nuclear transport which govern the lifetime of NFAT in the cytoplasm.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Calcium Signaling</prism:keyword>
+    <prism:keyword>Cricetinae</prism:keyword>
+    <prism:keyword>NFATC Transcription Factors</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Tomida-EMBO-J-2003-NFAT-translocation.omex/Figure3a.jpg" />
+    <!-- long description -->
+    <dc:description>Transcription by the nuclear factor of activated T cells (NFAT) is regulated by the frequency of Ca(2+) oscillation. However, why and how Ca(2+) oscillation regulates NFAT activity remain elusive. NFAT is dephosphorylated by Ca(2+)-dependent phosphatase calcineurin and translocates from the cytoplasm to the nucleus to initiate transcription. We analyzed the kinetics of dephosphorylation and translocation of NFAT. We show that Ca(2+)-dependent dephosphorylation proceeds rapidly, while the rephosphorylation and nuclear transport of NFAT proceed slowly. Therefore, after brief Ca(2+) stimulation, dephosphorylated NFAT has a lifetime of several minutes in the cytoplasm. Thus, Ca(2+) oscillation induces a build-up of dephosphorylated NFAT in the cytoplasm, allowing effective nuclear translocation, provided that the oscillation interval is shorter than the lifetime of dephosphorylated NFAT. We also show that Ca(2+) oscillation is more cost-effective in inducing the translocation of NFAT than continuous Ca(2+) signaling. Thus, the lifetime of dephosphorylated NFAT functions as a working memory of Ca(2+) signals and enables the control of NFAT nuclear translocation by the frequency of Ca(2+) oscillation at a reduced cost of Ca(2+) signaling.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606" />
+        <rdfs:label>Homo sapiens</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0033173" />
+        <rdfs:label>calcineurin-NFAT signaling cascade</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/BTO:0000661" />
+        <rdfs:label>JURKAT cell</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000678" />
+        <rdfs:label>biomodels.db:BIOMD0000000678</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Taichiro Tomida</foaf:name>
+        <rdfs:label>Taichiro Tomida</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Kenzo Hirose</foaf:name>
+        <rdfs:label>Kenzo Hirose</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Azusa Takizawa</foaf:name>
+        <rdfs:label>Azusa Takizawa</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Futoshi Shibasaki</foaf:name>
+        <rdfs:label>Futoshi Shibasaki</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Masamitsu Iino</foaf:name>
+        <rdfs:label>Masamitsu Iino</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributors -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Vijayalakshmi Chelliah</foaf:name>
+        <rdfs:label>Vijayalakshmi Chelliah</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Ryann Jordan</foaf:name>
+        <rdfs:label>Ryann Jordan</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1093/emboj/cdg381"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1093/emboj/cdg381" />
+        <rdfs:label>Taichiro Tomida, Kenzo Hirose, Azusa Takizawa, Futoshi Shibasaki &amp; Masamitsu Iino. NFAT functions as a working memory of Ca2+ signals in decoding Ca2+ oscillation. EMBO J 22, 15 (2003): 3825-3832.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2003-08-01</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Tomida-EMBO-J-2003-NFAT-translocation.omex/BIOMD0000000678_sim.sedml/Figure_3c">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000678"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1093/emboj/cdg381" />
+        <rdfs:label>Figure 3c</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
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
index 788f78c..f7a1e51 100644
Binary files a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex and b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex differ
diff --git a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/Figure1.jpg b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/Figure1.jpg
new file mode 100644
index 0000000..a3f91b3
Binary files /dev/null and b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/Figure1.jpg differ
diff --git a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/manifest.xml b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/manifest.xml
index be5f447..6a9e375 100644
--- a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/manifest.xml
+++ b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/manifest.xml
@@ -7,4 +7,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/image/jpeg" master="false"/>
 </omexManifest>
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
index eecfa15..602cf1d 100644
--- 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
@@ -1,29 +1,111 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2006/vcard/ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about="./Varusai2018.xml">
-    <dcterms:description>Varusai &amp; Nguyen Scientific Reports 2018: mTOR signalling network</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Varusai</vCard:family-name>
-        <vCard:given-name>Thawfeek</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Nguyen</vCard:family-name>
-        <vCard:given-name>Lan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<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="https://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:Description rdf:about="http://omex-libary.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>
+    <!-- short summary -->
+    <dc:abstract>This is a mathematical describing the effect that DEP domain-containing mTOR-interacting protein (DEPTOR) has on the mammalian target of rapamycin (mTOR) signalling network.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Signal Transduction</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex/Figure1.jpg" />
+    <!-- long description -->
+    <dc:description>Model of the mechanistic Target of Rapamycin (mTOR) signalling network, an evolutionarily conserved network that controls key cellular processes, including cell growth and metabolism. The model represents the major kinase complexes mTOR Complex 1 and 2 (mTORC1/2) and captures their interactions and feedback loops. The model captures the recently identified DEP domain-containing mTOR-interacting protein (DEPTOR), an endogenous inhibitor of both mTORC1 and 2 through direct interactions which are degraded by mTORC1/2. The model captures abrupt, bistable switches, oscillations and co-existing bistable/oscillatory responses.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606" />
+        <rdfs:label>Homo sapiens</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/PW:0000180" />
+        <rdfs:label>mTOR signaling pathway</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/ncit:C101595" />
+        <rdfs:label>DEP Domain-Containing mTOR-Interacting Protein</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000823" />
+        <rdfs:label>biomodels.db:BIOMD0000000823</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Thawfeek M Varusai</foaf:name>
+        <rdfs:label>Thawfeek M Varusai</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Lan K Nguyen</foaf:name>
+        <rdfs:label>Lan K Nguyen</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Johannes Meyer</foaf:name>
+        <rdfs:label>Johannes Meyer</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Ryann Jordan</foaf:name>
+        <rdfs:label>Ryann Jordan</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1038/s41598-017-18400-z"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/s41598-017-18400-z" />
+        <rdfs:label>Thawfeek M Varusai &amp; Lan K Nguyen. Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR. Sci Rep 8, 1 (2018): 643.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2018-01-12</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex/LSODA.sedml/Figure_2c">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000823"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/s41598-017-18400-z" />
+        <rdfs:label>Figure 2c</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/Figure1.jpg b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/Figure1.jpg
new file mode 100644
index 0000000..2e10865
Binary files /dev/null and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/Figure1.jpg differ
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/manifest.xml b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/manifest.xml
index 2db3c27..78aa236 100644
--- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/manifest.xml
+++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/manifest.xml
@@ -6,4 +6,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/images/jpeg" master="false"/>
 </omexManifest>
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
index 450f3c2..cb5babb 100644
--- 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
@@ -1,41 +1,126 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./model_ODE_deterministic.xml'>
-    <dcterms:description>Vilar et al. PNAS 2002: Minimal circadian clock (deterministic)</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Vilar</vCard:family-name>
-        <vCard:given-name>José</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Kueh</vCard:family-name>
-        <vCard:given-name>Hao Yuan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Barkai</vCard:family-name>
-        <vCard:given-name>Naama</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Leibler</vCard:family-name>
-        <vCard:given-name>Stanislas</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex">
+    <!-- name -->
+    <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>A minimal model of genomically based oscillation, based on two mutually interacting genes, an activator and a repressor. Postive feedback is provided by the activator protein, which binds to the promotors of both the activator and the repressor genes. Negative feedback is provided by the repressor protein which binds to the activator protein.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Circadian Rhythm</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex/Figure1.jpg" />
+    <!-- long description -->
+    <dc:description>Model of the circardian clock that incorporates just the essential elements found experimentally: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/131567" />
+        <rdfs:label>cellular organisms</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0042752" />
+        <rdfs:label>regulation of circadian rhythm</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- ancestor(s) of this work -->
+    <bqmodel:isDerivedFrom>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/35002258" />
+        <rdfs:label>Naama Barkai &amp; Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDerivedFrom>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000035" />
+        <rdfs:label>biomodels.db:BIOMD0000000035</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>José M G Vilar</foaf:name>
+        <rdfs:label>José M G Vilar</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Hao Yuan Kueh</foaf:name>
+        <rdfs:label>Hao Yuan Kueh</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Naama Barkai</foaf:name>
+        <rdfs:label>Naama Barkai</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Stanislas Leibler</foaf:name>
+        <rdfs:label>Stanislas Leibler</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Nicolas Le Novère</foaf:name>
+        <rdfs:label>Nicolas Le Novère</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1073/pnas.092133899"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>José M Vilar, Hao Y Kueh, Naama Barkai &amp; Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2002-04-30</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex/simulation.sedml/plot2d_Fig_1a">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>Figure 1a</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex/simulation.sedml/Figure_2ab">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000035"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>Figure 2ab</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/Figure1.jpg b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/Figure1.jpg
new file mode 100644
index 0000000..2e10865
Binary files /dev/null and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/Figure1.jpg differ
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/manifest.xml b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/manifest.xml
index f01d327..13165a5 100644
--- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/manifest.xml
+++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/manifest.xml
@@ -6,4 +6,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/images/jpeg" master="false"/>
 </omexManifest>
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
index e3c4943..103af8e 100644
--- 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
@@ -1,41 +1,118 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./model_ODE_stochastic.xml'>
-    <dcterms:description>Vilar et al. PNAS 2002: Minimal circadian clock (stochastic, Next Reaction Method)</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Vilar</vCard:family-name>
-        <vCard:given-name>José</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Kueh</vCard:family-name>
-        <vCard:given-name>Hao Yuan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Barkai</vCard:family-name>
-        <vCard:given-name>Naama</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Leibler</vCard:family-name>
-        <vCard:given-name>Stanislas</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex">
+    <!-- name -->
+    <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>A minimal model of genomically based oscillation, based on two mutually interacting genes, an activator and a repressor. Postive feedback is provided by the activator protein, which binds to the promotors of both the activator and the repressor genes. Negative feedback is provided by the repressor protein which binds to the activator protein.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Circadian Rhythm</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex/Figure1.jpg" />
+    <!-- long description -->
+    <dc:description>Model of the circardian clock that incorporates just the essential elements found experimentally: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/131567" />
+        <rdfs:label>cellular organisms</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0042752" />
+        <rdfs:label>regulation of circadian rhythm</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- ancestor(s) of this work -->
+    <bqmodel:isDerivedFrom>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/35002258" />
+        <rdfs:label>Naama Barkai &amp; Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDerivedFrom>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000035" />
+        <rdfs:label>biomodels.db:BIOMD0000000035</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>José M G Vilar</foaf:name>
+        <rdfs:label>José M G Vilar</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Hao Yuan Kueh</foaf:name>
+        <rdfs:label>Hao Yuan Kueh</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Naama Barkai</foaf:name>
+        <rdfs:label>Naama Barkai</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Stanislas Leibler</foaf:name>
+        <rdfs:label>Stanislas Leibler</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Nicolas Le Novère</foaf:name>
+        <rdfs:label>Nicolas Le Novère</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1073/pnas.092133899"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>José M Vilar, Hao Y Kueh, Naama Barkai &amp; Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2002-04-30</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex/simulation.sedml/plot2d_Fig_1_c">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000035"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>Figure 1c</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/Figure1.jpg b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/Figure1.jpg
new file mode 100644
index 0000000..2e10865
Binary files /dev/null and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/Figure1.jpg differ
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/manifest.xml b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/manifest.xml
index f01d327..13165a5 100644
--- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/manifest.xml
+++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/manifest.xml
@@ -6,4 +6,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/images/jpeg" master="false"/>
 </omexManifest>
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
index f591707..0332178 100644
--- 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
@@ -1,41 +1,118 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./model_ODE_stochastic.xml'>
-    <dcterms:description>Vilar et al. PNAS 2002: Minimal circadian clock (stochastic, SSA)</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Vilar</vCard:family-name>
-        <vCard:given-name>José</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Kueh</vCard:family-name>
-        <vCard:given-name>Hao Yuan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Barkai</vCard:family-name>
-        <vCard:given-name>Naama</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Leibler</vCard:family-name>
-        <vCard:given-name>Stanislas</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex">
+    <!-- name -->
+    <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>A minimal model of genomically based oscillation, based on two mutually interacting genes, an activator and a repressor. Postive feedback is provided by the activator protein, which binds to the promotors of both the activator and the repressor genes. Negative feedback is provided by the repressor protein which binds to the activator protein.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Circadian Rhythm</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex/Figure1.jpg" />
+    <!-- long description -->
+    <dc:description>Model of the circardian clock that incorporates just the essential elements found experimentally: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/131567" />
+        <rdfs:label>cellular organisms</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0042752" />
+        <rdfs:label>regulation of circadian rhythm</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- ancestor(s) of this work -->
+    <bqmodel:isDerivedFrom>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/35002258" />
+        <rdfs:label>Naama Barkai &amp; Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDerivedFrom>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000035" />
+        <rdfs:label>biomodels.db:BIOMD0000000035</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>José M G Vilar</foaf:name>
+        <rdfs:label>José M G Vilar</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Hao Yuan Kueh</foaf:name>
+        <rdfs:label>Hao Yuan Kueh</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Naama Barkai</foaf:name>
+        <rdfs:label>Naama Barkai</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Stanislas Leibler</foaf:name>
+        <rdfs:label>Stanislas Leibler</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Nicolas Le Novère</foaf:name>
+        <rdfs:label>Nicolas Le Novère</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1073/pnas.092133899"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>José M Vilar, Hao Y Kueh, Naama Barkai &amp; Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2002-04-30</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex/simulation.sedml/plot2d_Fig_1_c">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000035"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>Figure 1c</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/Figure1.jpg b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/Figure1.jpg
new file mode 100644
index 0000000..2e10865
Binary files /dev/null and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/Figure1.jpg differ
diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/manifest.xml b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/manifest.xml
index 4d9c028..72fc8f8 100644
--- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/manifest.xml
+++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/manifest.xml
@@ -7,4 +7,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure1.jpg" format="http://purl.org/NET/mediatypes/images/jpeg" master="false"/>
 </omexManifest>
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
index a8ec78c..7b7c27d 100644
--- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf
+++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf
@@ -1,80 +1,126 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./model_ODE_deterministic.xml'>
-    <dcterms:description>Vilar et al. PNAS 2002: Minimal circadian clock (deterministic)</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Vilar</vCard:family-name>
-        <vCard:given-name>José</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Kueh</vCard:family-name>
-        <vCard:given-name>Hao Yuan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Barkai</vCard:family-name>
-        <vCard:given-name>Naama</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Leibler</vCard:family-name>
-        <vCard:given-name>Stanislas</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock.omex">
+    <!-- name -->
+    <dc:title>Minimal circadian clock (Vilar et al. PNAS, 2002)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>A minimal model of genomically based oscillation, based on two mutually interacting genes, an activator and a repressor. Postive feedback is provided by the activator protein, which binds to the promotors of both the activator and the repressor genes. Negative feedback is provided by the repressor protein which binds to the activator protein.</dc:abstract>
+    <!-- keywords -->
+    <prism:keyword>Circadian Rhythm</prism:keyword>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock.omex/Figure1.jpg" />
+    <!-- long description -->
+    <dc:description>Model of the circardian clock that incorporates just the essential elements found experimentally: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/131567" />
+        <rdfs:label>cellular organisms</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0042752" />
+        <rdfs:label>regulation of circadian rhythm</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- ancestor(s) of this work -->
+    <bqmodel:isDerivedFrom>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1038/35002258" />
+        <rdfs:label>Naama Barkai &amp; Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDerivedFrom>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000035" />
+        <rdfs:label>biomodels.db:BIOMD0000000035</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>José M G Vilar</foaf:name>
+        <rdfs:label>José M G Vilar</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Hao Yuan Kueh</foaf:name>
+        <rdfs:label>Hao Yuan Kueh</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Naama Barkai</foaf:name>
+        <rdfs:label>Naama Barkai</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Stanislas Leibler</foaf:name>
+        <rdfs:label>Stanislas Leibler</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Nicolas Le Novère</foaf:name>
+        <rdfs:label>Nicolas Le Novère</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
     <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1073/pnas.092133899"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>José M Vilar, Hao Y Kueh, Naama Barkai &amp; Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992.</rdfs:label>
+      </rdf:Description>
     </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2002-04-30</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock.omex/simulation.sedml/plot2d_Fig_1a">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000035"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>Figure 1a</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-
-  <rdf:Description rdf:about='./model_ODE_stochastic.xml'>
-    <dcterms:description>Vilar et al. PNAS 2002: Minimal circadian clock (stochastic, Next Reaction Method)</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Vilar</vCard:family-name>
-        <vCard:given-name>José</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Kueh</vCard:family-name>
-        <vCard:given-name>Hao Yuan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Barkai</vCard:family-name>
-        <vCard:given-name>Naama</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Leibler</vCard:family-name>
-        <vCard:given-name>Stanislas</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <bqmodel:isDescribedBy>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://doi.org/10.1073/pnas.092133899"/>
-      </rdf:Bag>
-    </bqmodel:isDescribedBy>
+  <rdf:Description rdf:about="http://omex-libary.org/Vilar-PNAS-2002-minimal-circardian-clock.omex/simulation.sedml/plot2d_Fig_1_c">
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000035"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1073/pnas.092133899" />
+        <rdfs:label>Figure 1c</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf b/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf
index b914fe5..2ca9e2c 100644
--- a/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf
+++ b/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf
@@ -1,18 +1,71 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:dcterms='http://purl.org/dc/terms/' xmlns:vCard='http://www.w3.org/2006/vcard/ns#' xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-  <rdf:Description rdf:about='./model.xml'>
-    <dcterms:description>Textbook Escherichia coli core metabolism</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>COBRAPy</vCard:family-name>
-        <vCard:given-name>Team</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex">
+    <!-- name -->
+    <dc:title>Textbook model of Escherichia coli core metabolism (COBRApy Team, 2020)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>An example flux balance analysis model of the core metabolism of Escherichia coli.</dc:abstract>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/562" />
+        <rdfs:label>Escherichia coli</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- other identifiers -->
     <bqmodel:is>
-      <rdf:Bag>
-        <rdf:li rdf:resource="https://github.com/opencobra/cobrapy/blob/devel/src/cobra/test/data/textbook.xml.gz"/>
-      </rdf:Bag>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://github.com/opencobra/cobrapy/blob/devel/src/cobra/test/data/textbook.xml.gz" />
+        <rdfs:label>github:opencobra/cobrapy/src/cobra/test/data/textbook.xml.gz</rdfs:label>
+      </rdf:Description>
     </bqmodel:is>
-    <dcterms:license>https://spdx.org/licenses/GPL-2.0.html</dcterms:license>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>COBRApy Team</foaf:name>
+        <rdfs:label>COBRApy Team</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Moritz E. Beber</foaf:name>
+        <rdfs:label>Moritz E. Beber</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
+    <bqmodel:isDescribedBy>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/1752-0509-7-74" />
+        <rdfs:label>Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson &amp; Daniel R Hyduke. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol 7 (2013): 74.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:GPL-2.0" />
+        <rdfs:label>GPL-2.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2020-07-17</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file
diff --git a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/Figure3.jpg b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/Figure3.jpg
new file mode 100644
index 0000000..bbf7a6d
Binary files /dev/null and b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/Figure3.jpg differ
diff --git a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/manifest.xml b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/manifest.xml
index 6669c7b..bdb0914 100644
--- a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/manifest.xml
+++ b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/manifest.xml
@@ -6,4 +6,5 @@
   <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
   <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
   <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
+  <content location="Figure3.jpg" format="http://purl.org/NET/mediatypes/image/jpeg" master="false"/>
 </omexManifest>
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
index ba73478..f34d3cc 100644
--- 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
@@ -1,165 +1,242 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF
-    xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
-    xmlns:dcterms='http://purl.org/dc/terms/'
-    xmlns:vCard='http://www.w3.org/2006/vcard/ns#'
-    xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-    <rdf:Description rdf:about='./BIOMD0000000562_url.xml'>
-        <dcterms:description>Chaouiya et al. BMC Systems Biology 2013: EGF and TNFα signaling</dcterms:description>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Chaouiya</vCard:family-name>
-                <vCard:given-name>Claudine</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Bérenguier</vCard:family-name>
-                <vCard:given-name>Duncan</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Keating</vCard:family-name>
-                <vCard:given-name>Sarah</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Naldi</vCard:family-name>
-                <vCard:given-name>Aurélien</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>van Iersel</vCard:family-name>
-                <vCard:given-name>Martijn</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Rodriguez</vCard:family-name>
-                <vCard:given-name>Nicolas</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Dräger</vCard:family-name>
-                <vCard:given-name>Andreas</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Büchel</vCard:family-name>
-                <vCard:given-name>Finja</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Cokelaer</vCard:family-name>
-                <vCard:given-name>Thomas</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Kowal</vCard:family-name>
-                <vCard:given-name>Bryan</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Wicks</vCard:family-name>
-                <vCard:given-name>Benjamin</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Gonçalves</vCard:family-name>
-                <vCard:given-name>Emanuel</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Dorier</vCard:family-name>
-                <vCard:given-name>Julien</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Page</vCard:family-name>
-                <vCard:given-name>Michel</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Monteiro</vCard:family-name>
-                <vCard:given-name>Pedro</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>von Kamp</vCard:family-name>
-                <vCard:given-name>Axel</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Xenarios</vCard:family-name>
-                <vCard:given-name>Ioannis</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>de Jong</vCard:family-name>
-                <vCard:given-name>Hidde</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Hucka</vCard:family-name>
-                <vCard:given-name>Michael</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Klamt</vCard:family-name>
-                <vCard:given-name>Steffen</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Thieffry</vCard:family-name>
-                <vCard:given-name>Denis</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Le Novère</vCard:family-name>
-                <vCard:given-name>Nicolas</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Saez-Rodriguez</vCard:family-name>
-                <vCard:given-name>Julio</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Helikar</vCard:family-name>
-                <vCard:given-name>Tomáš</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <bqmodel:isDescribedBy>
-            <rdf:Bag>
-                <rdf:li rdf:resource="https://doi.org/10.1186/1752-0509-7-135"/>
-            </rdf:Bag>
-        </bqmodel:isDescribedBy>
-        <bqmodel:is>
-            <rdf:Bag>
-                <rdf:li rdf:resource="https://identifiers.org/biomodels.db/BIOMD0000000562"/>
-            </rdf:Bag>
-        </bqmodel:is>
-        <dcterms:license>http://creativecommons.org/publicdomain/zero/1.0/</dcterms:license>
-    </rdf:Description>
+<?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="https://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:Description rdf:about="http://omex-libary.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>
+    <!-- short summary -->
+    <dc:abstract>Qualitative model of the EGF and TNFα signaling pathways.</dc:abstract>
+    <!-- thumbnail image -->
+    <collex:thumbnail rdf:resource="http://omex-libary.org/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex/Figure3.jpg" />
+    <!-- long description -->
+    <dc:description>Qualitative model of the EGF and TNFα signaling pathways which captures how EGF and TNFα ligands stimulate ERK, JNK and p38 MAPK cascades, the PI3K/AKT pathways, and the NFκB cascade. In addition, the model encompasses cross-talks between these pathways, as well as two negative feedback loops: one in the NFκB cascade and one in the MAPK cascade.</dc:description>
+    <!-- taxon -->
+    <bqbiol:hasTaxon>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606" />
+        <rdfs:label>Homo sapiens</rdfs:label>
+      </rdf:Description>
+    </bqbiol:hasTaxon>
+    <!-- encoded biology -->
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0033209" />
+        <rdfs:label>tumor necrosis factor-mediated signaling pathway</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <bqbiol:encodes>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/GO:0007173" />
+        <rdfs:label>epidermal growth factor receptor signaling pathway</rdfs:label>
+      </rdf:Description>
+    </bqbiol:encodes>
+    <!-- ancestor(s) of this work -->
+    <bqmodel:isDerivedFrom>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1088/1478-3975/9/4/045003" />
+        <rdfs:label>Aidan MacNamara, Camille Terfve, David Henriques, Beatriz Peñalver Bernabé &amp; Julio Saez-Rodriguez. State-time spectrum of signal transduction logic models. Phys Biol 7 (2012): 045003.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDerivedFrom>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000562" />
+        <rdfs:label>biomodels.db:BIOMD0000000562</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Claudine Chaouiya</foaf:name>
+        <rdfs:label>Claudine Chaouiya</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Duncan Bérenguier</foaf:name>
+        <rdfs:label>Duncan Bérenguier</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Sarah M Keating</foaf:name>
+        <rdfs:label>Sarah M Keating</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Aurélien Naldi</foaf:name>
+        <rdfs:label>Aurélien Naldi</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Martijn P van Iersel</foaf:name>
+        <rdfs:label>Martijn P van Iersel</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Nicolas Rodriguez</foaf:name>
+        <rdfs:label>Nicolas Rodriguez</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Andreas Dräger</foaf:name>
+        <rdfs:label>Andreas Dräger</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Finja Büchel</foaf:name>
+        <rdfs:label>Finja Büchel</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Thomas Cokelaer</foaf:name>
+        <rdfs:label>Thomas Cokelaer</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Bryan Kowal</foaf:name>
+        <rdfs:label>Bryan Kowal</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Benjamin Wicks</foaf:name>
+        <rdfs:label>Benjamin Wicks</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Emanuel Gonçalves</foaf:name>
+        <rdfs:label>Emanuel Gonçalves</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Julien Dorier</foaf:name>
+        <rdfs:label>Julien Dorier</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Michel Page</foaf:name>
+        <rdfs:label>Michel Page</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Pedro T Monteiro</foaf:name>
+        <rdfs:label>Pedro T Monteiro</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Axel von Kamp</foaf:name>
+        <rdfs:label>Axel von Kamp</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Ioannis Xenarios</foaf:name>
+        <rdfs:label>Ioannis Xenarios</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Hidde de Jong</foaf:name>
+        <rdfs:label>Hidde de Jong</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Michael Hucka</foaf:name>
+        <rdfs:label>Michael Hucka</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Steffen Klamt</foaf:name>
+        <rdfs:label>Steffen Klamt</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Denis Thieffry</foaf:name>
+        <rdfs:label>Denis Thieffry</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Nicolas Le Novère</foaf:name>
+        <rdfs:label>Nicolas Le Novère</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Julio Saez-Rodriguez</foaf:name>
+        <rdfs:label>Julio Saez-Rodriguez</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Tomáš Helikar</foaf:name>
+        <rdfs:label>Tomáš Helikar</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <rdf:Description>
+        <foaf:name>Thomas Cokelaer</foaf:name>
+        <rdfs:label>Thomas Cokelaer</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
+    <bqmodel:isDescribedBy>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/1752-0509-7-135" />
+        <rdfs:label>Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez &amp; Tomáš Helikar. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol 7 (2013): 135.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:CC0-1.0" />
+        <rdfs:label>CC0-1.0</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2013-12-10</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
+  <!-- links from SED-ML plots to figures of articles -->
+  <rdf:Description rdf:about="http://omex-libary.org/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex/simulation.sedml/Figure_4a">
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1186/1752-0509-7-135" />
+        <rdfs:label>Figure 4a</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file
diff --git a/examples/smoldyn/Lotka-Volterra/metadata.rdf b/examples/smoldyn/Lotka-Volterra/metadata.rdf
index 6a83c82..8aec462 100644
--- a/examples/smoldyn/Lotka-Volterra/metadata.rdf
+++ b/examples/smoldyn/Lotka-Volterra/metadata.rdf
@@ -1,22 +1,58 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF
-    xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
-    xmlns:dcterms='http://purl.org/dc/terms/'
-    xmlns:vCard='http://www.w3.org/2006/vcard/ns#'
-    xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-    <rdf:Description rdf:about='./model.txt'>
-        <dcterms:description>Lotka-Volterra model</dcterms:description>
-        <dcterms:creator rdf:parseType='Resource'>
-            <vCard:hasName rdf:parseType='Resource'>
-                <vCard:family-name>Steven</vCard:family-name>
-                <vCard:given-name>Andrews</vCard:given-name>
-            </vCard:hasName>
-        </dcterms:creator>
-        <bqmodel:is>
-            <rdf:Bag>
-                <rdf:li rdf:resource="http://www.smoldyn.org/archive/examples/S8_reactions/lotvolt/lotvolt.txt"/>
-            </rdf:Bag>
-        </bqmodel:is>
-        <dcterms:license>https://github.com/ssandrews/Smoldyn/blob/master/LICENSE</dcterms:license>
-    </rdf:Description>
+<?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="https://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:Description rdf:about="http://omex-libary.org/Lotka-Volterra.omex">
+    <!-- name -->
+    <dc:title>Lotka-Volterra predator-prey model (Andrews, 2019)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>An example Smoldyn Lotka-Volterra model of predator-prey system.</dc:abstract>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="http://www.smoldyn.org/archive/examples/S8_reactions/lotvolt/lotvolt.txt" />
+        <rdfs:label>smoldyn:S8_reactions/lotvolt/lotvolt.txt</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Steven Andrews</foaf:name>
+        <rdfs:label>Steven Andrews</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- citations -->
+    <bqmodel:isDescribedBy>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1093/bioinformatics/btw700" />
+        <rdfs:label>Steven S. Andrews. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 33, 5 (2017): 710-717.</rdfs:label>
+      </rdf:Description>
+    </bqmodel:isDescribedBy>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:GPL-3.0-only" />
+        <rdfs:label>GPL-3.0-only</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2019-02-22</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
+  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file


Test patch:
diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
index 3c9e21f..c387faf 100644
--- a/biosimulators_test_suite/_version.py
+++ b/biosimulators_test_suite/_version.py
@@ -1,1 +1,1 @@
-__version__ = '0.1.46'
+__version__ = '0.1.47'
diff --git a/examples/bngl/test-bngl/metadata.rdf b/examples/bngl/test-bngl/metadata.rdf
index 2920e92..b95d822 100644
--- a/examples/bngl/test-bngl/metadata.rdf
+++ b/examples/bngl/test-bngl/metadata.rdf
@@ -1,18 +1,51 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<rdf:RDF
-  xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
-  xmlns:dcterms='http://purl.org/dc/terms/'
-  xmlns:vCard='http://www.w3.org/2006/vcard/ns#'
-  xmlns:bqmodel="http://biomodels.net/model-qualifiers/"
->
-  <rdf:Description rdf:about='.'>
-    <dcterms:description>Toy gene regulatory network</dcterms:description>
-    <dcterms:creator rdf:parseType='Resource'>
-      <vCard:hasName rdf:parseType='Resource'>
-        <vCard:family-name>Karr</vCard:family-name>
-        <vCard:given-name>Jonathan</vCard:given-name>
-      </vCard:hasName>
-    </dcterms:creator>
-    <dcterms:license>https://opensource.org/licenses/MIT</dcterms:license>
+<?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="https://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:Description rdf:about="http://omex-libary.org/test-bngl.omex">
+    <!-- name -->
+    <dc:title>Toy gene regulatory network (Saglam, 2020)</dc:title>
+    <!-- short summary -->
+    <dc:abstract>Toy model of a gene regulatory network.</dc:abstract>
+    <!-- other identifiers -->
+    <bqmodel:is>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://github.com/biosimulators/Biosimulators_BioNetGen/blob/dev/tests/fixtures/test.bngl" />
+        <rdfs:label>github:biosimulators/Biosimulators_BioNetGen/tests/fixtures/test.bngl</rdfs:label>
+      </rdf:Description>
+    </bqmodel:is>
+    <!-- authors(s) -->
+    <dc:creator>
+      <rdf:Description>
+        <foaf:name>Ali Sinan Saglam</foaf:name>
+        <rdfs:label>Ali Sinan Saglam</rdfs:label>
+      </rdf:Description>
+    </dc:creator>
+    <!-- contributor(s) -->
+    <dc:contributor>
+      <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" />
+        <rdfs:label>Jonathan Karr</rdfs:label>
+      </rdf:Description>
+    </dc:contributor>
+    <!-- license -->
+    <dc:license>
+      <rdf:Description>
+        <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT" />
+        <rdfs:label>MIT</rdfs:label>
+      </rdf:Description>
+    </dc:license>
+    <!-- created -->
+    <dc:created>
+      <rdf:Description>
+        <dc:W3CDTF>2020-04-13</dc:W3CDTF>
+      </rdf:Description>
+    </dc:created>
+    <!-- modified -->
+    <dc:modified>
+      <rdf:Description>
+        <dc:W3CDTF>2021-07-21</dc:W3CDTF>
+      </rdf:Description>
+    </dc:modified>
   </rdf:Description>
-</rdf:RDF>
+</rdf:RDF>
\ No newline at end of file