feat(metadata): added recommended predicate for bibliographic-type ci…

…tations
biosimulators · Jan 7, 2022 · 4841da0 · 4841da0
1 parent b4581a4
commit 4841da0
Show file tree

Hide file tree

Showing 25 changed files with 284 additions and 244 deletions.
diff --git a/biosimulators_utils/_version.py b/biosimulators_utils/_version.py
@@ -1 +1 @@
-__version__ = '0.1.155'
+__version__ = '0.1.156'
diff --git a/biosimulators_utils/omex_meta/data_model.py b/biosimulators_utils/omex_meta/data_model.py
@@ -194,6 +194,19 @@ class OmexMetadataSchema(str, enum.Enum):
         'has_label': True,
         'required': False,
     },
+    'http://purl.org/dc/terms/references': {
+        'namespace': {
+            'prefix': 'dcterms',
+            'uri': 'http://purl.org/dc/terms/',
+        },
+        'uri': 'http://purl.org/dc/terms/references',
+        'attribute': 'references',
+        'label': 'References',
+        'multiple_allowed': True,
+        'has_uri': True,
+        'has_label': True,
+        'required': False,
+    },
     'http://purl.org/spar/scoro/successor': {
         'namespace': {
             'prefix': 'scoro',

diff --git a/biosimulators_utils/omex_meta/io.py b/biosimulators_utils/omex_meta/io.py
@@ -828,8 +828,11 @@ def run(self, el_metadatas, filename, config=None):
                                     object,
                                     namespaces['foaf'].accountName,
                                     rdflib.term.URIRef(value['uri']
+                                                       .replace('http://identifiers.org/orcid:',
+                                                                'https://orcid.org/')
                                                        .replace('https://identifiers.org/orcid:',
-                                                                'https://orcid.org/'))
+                                                                'https://orcid.org/')
+                                                       )
                                 ))
 
                             if value.get('label', None) is not None:

diff --git a/tests/fixtures/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.omex b/tests/fixtures/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.omex
diff --git a/tests/fixtures/omex-metadata/abbrev.rdf b/tests/fixtures/omex-metadata/abbrev.rdf
@@ -91,13 +91,13 @@
 
   <!-- taxon -->
   <rdf:Description rdf:about="local:_00001">
-    <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606"/>
+    <dc:identifier rdf:resource="http://identifiers.org/taxonomy/9606"/>
     <rdfs:label>Homo sapiens</rdfs:label>
   </rdf:Description>
 
   <!-- gene, RNA, protein, cell type, tissue, organ -->
   <rdf:Description rdf:about="local:_00002">
-    <dc:identifier rdf:resource="https://identifiers.org/CL:0001057"/>
+    <dc:identifier rdf:resource="http://identifiers.org/CL:0001057"/>
     <rdfs:label>myeloid dendritic cell, human</rdfs:label>
   </rdf:Description>
 
@@ -110,42 +110,42 @@
 
   <!-- source -->
   <rdf:Description rdf:about="local:_00004">
-    <dc:identifier rdf:resource="https://github.org/lab/project"/>
+    <dc:identifier rdf:resource="http://identifiers.org/github:lab/project"/>
     <rdfs:label>Tsur 2019 model source code</rdfs:label>
   </rdf:Description>
 
   <!-- ancestor(s) of this work -->
   <rdf:Description rdf:about="local:_00005">
-    <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000837"/>
+    <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000837"/>
     <rdfs:label>Hanson2016 - Toxicity Management in CAR T cell therapy for B-ALL</rdfs:label>
   </rdf:Description>
 
   <!-- successor(s) of this work -->
   <rdf:Description rdf:about="local:_00006">
-    <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000839"/>
+    <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000839"/>
     <rdfs:label>Almeida2019 - Transcription-based circadian ...</rdfs:label>
   </rdf:Description>
 
   <!-- related things (e.g., models of similar systems from other groups) -->
   <rdf:Description rdf:about="local:_00007">
-    <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000836"/>
+    <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000836"/>
     <rdfs:label>Radosavljevic2009_BioterroristAttack_PanicProtection_1</rdfs:label>
   </rdf:Description>
 
   <!-- other identifiers -->
   <rdf:Description rdf:about="local:_00008">
-    <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000838"/>
+    <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000838"/>
     <rdfs:label>biomodels.db:BIOMD0000000838</rdfs:label>
   </rdf:Description>
 
   <!-- citations(s) -->
   <rdf:Description rdf:about="local:_00011">
-    <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.copbio.2017.12.013"/>
+    <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.copbio.2017.12.013"/>
     <rdfs:label>Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD &amp; Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2018, 51:97-102.</rdfs:label>
   </rdf:Description>
 
   <rdf:Description rdf:about="local:_00012">
-    <dc:identifier rdf:resource="https://identifiers.org/pubmed:29275251"/>
+    <dc:identifier rdf:resource="http://identifiers.org/pubmed:29275251"/>
     <rdfs:label>Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD &amp; Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2018, 51:97-102.</rdfs:label>
   </rdf:Description>
 
@@ -154,7 +154,7 @@
     <foaf:accountName rdf:resource="https://orcid.org/0000-0001-8254-4958"/>
     <foaf:name>Jonathan Karr</foaf:name>
 
-    <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0001-8254-4958"/>
+    <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0001-8254-4958"/>
     <rdfs:label>Jonathan Karr</rdfs:label>
   </rdf:Description>
 
@@ -167,13 +167,13 @@
 
   <!-- license -->
   <rdf:Description rdf:about="local:_00013">
-    <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT"/>
+    <dc:identifier rdf:resource="http://identifiers.org/spdx:MIT"/>
     <rdfs:label>MIT</rdfs:label>
   </rdf:Description>
 
   <!-- funder -->
   <rdf:Description rdf:about="local:_00014">
-    <dc:identifier rdf:resource="https://identifiers.org/doi:10.13039/100000001"/>
+    <dc:identifier rdf:resource="http://identifiers.org/doi:10.13039/100000001"/>
     <rdfs:label>National Science Foundation</rdfs:label>
   </rdf:Description>
 </rdf:RDF>
diff --git a/tests/fixtures/omex-metadata/biosimulations-abbrev-third-b.rdf b/tests/fixtures/omex-metadata/biosimulations-abbrev-third-b.rdf
@@ -29,15 +29,15 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606"/>
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/9606"/>
         <rdfs:label>Homo sapiens</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
 
     <!-- gene, RNA, protein, cell type, tissue, organ, disease -->
     <bqbiol:encodes>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/CL:0001057"/>
+        <dc:identifier rdf:resource="http://identifiers.org/CL:0001057"/>
         <rdfs:label>myeloid dendritic cell, human</rdfs:label>
       </rdf:Description>
     </bqbiol:encodes>
@@ -54,39 +54,39 @@
     <!-- source from which model package was derived (e.g., GitHub repository) -->
     <dc:source>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://github.org/lab/project"/>
+        <dc:identifier rdf:resource="http://identifiers.org/github:lab/project"/>
         <rdfs:label>Tsur 2019 model source code</rdfs:label>
       </rdf:Description>
     </dc:source>
 
     <!-- ancestor(s) of this work -->
     <bqmodel:isDerivedFrom>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000837"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000837"/>
         <rdfs:label>Hanson2016 - Toxicity Management in CAR T cell therapy for B-ALL</rdfs:label>
       </rdf:Description>
     </bqmodel:isDerivedFrom>
 
     <!-- successor(s) of this work -->
     <scoro:successor>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000839"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000839"/>
         <rdfs:label>Almeida2019 - Transcription-based circadian ...</rdfs:label>
       </rdf:Description>
     </scoro:successor>
 
     <!-- related things to provide hyperlinks to -->
     <rdfs:seeAlso>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000836"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000836"/>
         <rdfs:label>Radosavljevic2009_BioterroristAttack_PanicProtection_1</rdfs:label>
       </rdf:Description>
     </rdfs:seeAlso>
 
     <!-- other identifiers -->
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000838"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000838"/>
         <rdfs:label>biomodels.db:BIOMD0000000838</rdfs:label>
       </rdf:Description>
     </bqmodel:is>
@@ -97,7 +97,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0001-8254-4958"/>
         <foaf:name>Jonathan Karr</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0001-8254-4958"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0001-8254-4958"/>
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:creator>
@@ -114,30 +114,30 @@
     <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.copbio.2017.12.013"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.copbio.2017.12.013"/>
         <rdfs:label>Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD &amp; Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2018, 51:97-102.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/pubmed:29275251"/>
+        <dc:identifier rdf:resource="http://identifiers.org/pubmed:29275251"/>
         <rdfs:label>Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD &amp; Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2018, 51:97-102.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT"/>
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:MIT"/>
         <rdfs:label>MIT</rdfs:label>
       </rdf:Description>
     </dc:license>
 
     <!-- funder -->
     <scoro:funder>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.13039/100000001"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.13039/100000001"/>
         <rdfs:label>National Science Foundation</rdfs:label>
       </rdf:Description>
     </scoro:funder>

diff --git a/tests/fixtures/omex-metadata/biosimulations-abbrev-third-c.rdf b/tests/fixtures/omex-metadata/biosimulations-abbrev-third-c.rdf
@@ -9,7 +9,7 @@
   <rdf:Description rdf:about="http://omex-library.org/BioSim0001.omex/sim.sedml/figure1">
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://doi.org/10.1371/journal.pcbi.1008379.g001"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1371/journal.pcbi.1008379.g001"/>
         <rdfs:label>Figure 1a</rdfs:label>
       </rdf:Description>
     </bqmodel:is>

diff --git a/tests/fixtures/omex-metadata/biosimulations-abbrev.rdf b/tests/fixtures/omex-metadata/biosimulations-abbrev.rdf
@@ -32,15 +32,15 @@
     <!-- taxon -->
     <bqbiol:hasTaxon>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/taxonomy/9606"/>
+        <dc:identifier rdf:resource="http://identifiers.org/taxonomy/9606"/>
         <rdfs:label>Homo sapiens</rdfs:label>
       </rdf:Description>
     </bqbiol:hasTaxon>
 
     <!-- gene, RNA, protein, cell type, tissue, organ, disease -->
     <bqbiol:encodes>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/CL:0001057"/>
+        <dc:identifier rdf:resource="http://identifiers.org/CL:0001057"/>
         <rdfs:label>myeloid dendritic cell, human</rdfs:label>
       </rdf:Description>
     </bqbiol:encodes>
@@ -57,39 +57,47 @@
     <!-- source from which model package was derived (e.g., GitHub repository) -->
     <dc:source>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://github.org/lab/project"/>
+        <dc:identifier rdf:resource="http://identifiers.org/github:lab/project"/>
         <rdfs:label>Tsur 2019 model source code</rdfs:label>
       </rdf:Description>
     </dc:source>
 
     <!-- ancestor(s) of this work -->
     <bqmodel:isDerivedFrom>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000837"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000837"/>
         <rdfs:label>Hanson2016 - Toxicity Management in CAR T cell therapy for B-ALL</rdfs:label>
       </rdf:Description>
     </bqmodel:isDerivedFrom>
 
+    <!-- reference(s) for this work -->
+    <dcterms:references>
+      <rdf:Description>
+        <dc:identifier rdf:resource="http://identifiers.org/pubmed:1234"/>
+        <rdfs:label>D Nadeau, C Marchand. Change in the kinetics of sulphacetamide tissue distribution in Walker tumor-bearing rats. Drug Metab Dispos 3(6): 565-76 (1975).</rdfs:label>
+      </rdf:Description>
+    </dcterms:references>
+
     <!-- successor(s) of this work -->
     <scoro:successor>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000839"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000839"/>
         <rdfs:label>Almeida2019 - Transcription-based circadian ...</rdfs:label>
       </rdf:Description>
     </scoro:successor>
 
     <!-- related things to provide hyperlinks to -->
     <rdfs:seeAlso>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000836"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000836"/>
         <rdfs:label>Radosavljevic2009_BioterroristAttack_PanicProtection_1</rdfs:label>
       </rdf:Description>
     </rdfs:seeAlso>
 
     <!-- other identifiers -->
     <bqmodel:is>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/biomodels.db:BIOMD0000000838"/>
+        <dc:identifier rdf:resource="http://identifiers.org/biomodels.db:BIOMD0000000838"/>
         <rdfs:label>biomodels.db:BIOMD0000000838</rdfs:label>
       </rdf:Description>
     </bqmodel:is>
@@ -100,7 +108,7 @@
         <foaf:accountName rdf:resource="https://orcid.org/0000-0001-8254-4958"/>
         <foaf:name>Jonathan Karr</foaf:name>
 
-        <dc:identifier rdf:resource="https://identifiers.org/orcid:0000-0001-8254-4958"/>
+        <dc:identifier rdf:resource="http://identifiers.org/orcid:0000-0001-8254-4958"/>
         <rdfs:label>Jonathan Karr</rdfs:label>
       </rdf:Description>
     </dc:creator>
@@ -117,30 +125,30 @@
     <!-- citations -->
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.1016/j.copbio.2017.12.013"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.1016/j.copbio.2017.12.013"/>
         <rdfs:label>Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD &amp; Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2018, 51:97-102.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <bqmodel:isDescribedBy>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/pubmed:29275251"/>
+        <dc:identifier rdf:resource="http://identifiers.org/pubmed:29275251"/>
         <rdfs:label>Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD &amp; Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2018, 51:97-102.</rdfs:label>
       </rdf:Description>
     </bqmodel:isDescribedBy>
 
     <!-- license -->
     <dc:license>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/spdx:MIT"/>
+        <dc:identifier rdf:resource="http://identifiers.org/spdx:MIT"/>
         <rdfs:label>MIT</rdfs:label>
       </rdf:Description>
     </dc:license>
 
     <!-- funder -->
     <scoro:funder>
       <rdf:Description>
-        <dc:identifier rdf:resource="https://identifiers.org/doi:10.13039/100000001"/>
+        <dc:identifier rdf:resource="http://identifiers.org/doi:10.13039/100000001"/>
         <rdfs:label>National Science Foundation</rdfs:label>
       </rdf:Description>
     </scoro:funder>