fixes #615, more tests on rdf conversion

Author: oerc0042

isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb

@@ -7,7 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install git+https://github.com/isa-tools/isa-api.git@develop"
+    "#!pip install git+https://github.com/isa-tools/isa-api.git@develop"
    ]
   },
   {
@@ -125,6 +125,14 @@
    "metadata": {},
    "outputs": [],
    "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e7699e28-dac1-44f0-be46-5b8c732de381",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb

@@ -13,7 +13,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install -e ."
+    "#!pip install -e ."
    ]
   },
   {

isa-cookbook/content/notebooks/isa-json-conversion-to-rdf-linked-data.ipynb

@@ -44,7 +44,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install -e .\n"
+    "#!pip install -e .\n"
    ]
   },
   {
@@ -152,8 +152,8 @@
     "isa_json_ld_path = os.path.join(os.getcwd(),\"output/BII-S-3-synth/\", \"BII-S-3-isa-rdf-\" + ontology + \"-v3.json\")\n",
     "print(isa_json_ld_path)\n",
     "\n",
-    "with open(isa_json_ld_path, 'w') as outfile:\n",
-    "    json.dump(jsonldcontent,  outfile, ensure_ascii=False, indent=4)"
+    "# with open(isa_json_ld_path, 'w') as outfile:\n",
+    "#     json.dump(jsonldcontent,  outfile, ensure_ascii=False, indent=4)"
    ]
   },
   {

isa-cookbook/content/notebooks/output/BII-S-3-synth/BII-S-3-isa-rdf-obo-v3.json

@@ -35,12 +35,12 @@
       "@type": "obo:OBI_0000968"
     },
     "materials": {
-      "@id": "obo:OBI_0000047",
+      "@id": "obo:COB_0000026",
       "@type": "obo:BFO_0000040"
     },
     "othermaterials": {
-      "@id": "obo:OBI_0000047",
-      "@type": "OBI_0000047"
+      "@id": "obo:COB_0000026",
+      "@type": "obo:COB_0000026"
     },
     "characteristicCategories": {
       "@id": "obo:IAO_0000235",

isa-cookbook/content/notebooks/output/BII-S-3-synth/BII-S-3-isa-rdf-obo-v3.ttl

@@ -4,7 +4,7 @@
     "obo": "http://purl.obolibrary.org/obo/",
     "xsd": "http://www.w3.org/2001/XMLSchema#",
     "Material": {
-      "@id": "obo:OBI_0000047"
+      "@id": "obo:COB_0000026"
     },
     "type": {
       "@id": "obo:RO_0000086",

isa-cookbook/content/notebooks/output/BII-S-3-synth/BII-S-3-isa.json

@@ -39,7 +39,7 @@
       "@id": "obo:OBI_0001933"
     },
     "Material": {
-      "@id": "obo:OBI_0000047"
+      "@id": "obo:COB_0000026"
     },
     "OntologyAnnotation": {
       "@id": "obo:OBI_0001933"
@@ -118,7 +118,7 @@
       "@type": "obo:OBI_0100051"
     },
     "otherMaterials": {
-      "@id": "obo:OBI_0000047",
+      "@id": "obo:COB_0000026",
       "@type": "obo:OBI_0000423"
     },
     "characteristics": {
@@ -171,7 +171,7 @@
     },
     "dataFiles": {
       "@id": "obo:EFO_0004095",
-      "@type": "obo:OBI_0000047"
+      "@type": "obo:MS_1000577"
     },
     "filename": {
       "@id": "obo:IAO_0000590",