chores: remove example_usage.py script and update Notebook

Author: ecarrenolozano

example_usage.py

@@ -129,7 +129,7 @@
     "# 1. Standard library imports\n",
     "import sys\n",
     "\n",
-    "sys.path.append('/home/ecarreno/SSC-Projects/b_REPOSITORIES/ontograph')\n",
+    "sys.path.append(\"/home/ecarreno/SSC-Projects/b_REPOSITORIES/ontograph\")\n",
     "\n",
     "from pathlib import Path\n",
     "\n",
@@ -156,7 +156,18 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cache_dir = Path('../data/out')"
+    "import os\n",
+    "\n",
+    "os.getcwd()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cache_dir = Path(\"../data/out\")"
    ]
   },
   {
@@ -168,6 +179,11 @@
     "We are going to create a registry based on all the metadata that OBO Foundy has."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -177,6 +193,15 @@
     "onto_registry = OBORegistryAdapter(cache_dir=cache_dir)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "onto_registry.cache_dir"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -241,7 +266,7 @@
    "source": [
     "# This function looks if the given ontology has a link with a given extension\n",
     "\n",
-    "print('Link: {}'.format(onto_registry.get_download_url('chebi', 'obo')))"
+    "print(\"Link: {}\".format(onto_registry.get_download_url(\"chebi\", \"obo\")))"
    ]
   },
   {
@@ -257,7 +282,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(onto_registry.get_available_formats(ontology_id='chebi'))"
+    "print(onto_registry.get_available_formats(ontology_id=\"chebi\"))"
    ]
   },
   {
@@ -301,18 +326,18 @@
    "source": [
     "# Put the ontologies and their formats as a dictionary\n",
     "resources = [\n",
-    "    {'name_id': 'chebi', 'format': 'owl'},\n",
-    "    {'name_id': 'go', 'format': 'obo'},\n",
-    "    {'name_id': 'ado', 'format': 'owl'},\n",
+    "    {\"name_id\": \"chebi\", \"format\": \"owl\"},\n",
+    "    {\"name_id\": \"go\", \"format\": \"obo\"},\n",
+    "    {\"name_id\": \"ado\", \"format\": \"owl\"},\n",
     "]\n",
     "\n",
     "# Use the downloader, it has a cache in case you have already downloaded the ontologies.\n",
     "batch_results = downloader.fetch_batch(resources)\n",
     "\n",
     "# Print all the paths where your ontologies are located\n",
-    "print('Ontologies in cache:')\n",
+    "print(\"Ontologies in cache:\")\n",
     "for ontology_name, ontology_path in batch_results.items():\n",
-    "    print(f'\\t{ontology_name}: {ontology_path}')"
+    "    print(f\"\\t{ontology_name}: {ontology_path}\")"
    ]
   },
   {
@@ -351,13 +376,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "name_id_go = 'go'\n",
-    "format_go = 'obo'\n",
+    "name_id_go = \"go\"\n",
+    "format_go = \"obo\"\n",
     "\n",
     "gene_ontology = ontology_loader.load(name_id=name_id_go, format=format_go)\n",
     "\n",
-    "print(f'Loaded ontology: {name_id_go}.{format_go}')\n",
-    "print(f'Number of terms: {len(gene_ontology.terms())}')"
+    "print(f\"Loaded ontology: {name_id_go}.{format_go}\")\n",
+    "print(f\"Number of terms: {len(gene_ontology.terms())}\")"
    ]
   },
   {
@@ -375,7 +400,7 @@
    "source": [
     "# term_id = \"GO:0008150\" # biological_process\n",
     "# term_id = \"GO:0160266\"  # anestrus phase\n",
-    "term_id = 'GO:0070360'  # symbiont-mediated actin polymerization-dependent cell-to-cell migration in host"
+    "term_id = \"GO:0070360\"  # symbiont-mediated actin polymerization-dependent cell-to-cell migration in host"
    ]
   },
   {
@@ -387,9 +412,9 @@
     "queries = OntologyQueries(gene_ontology)\n",
     "\n",
     "# Print term relations\n",
-    "print(f'Term: {term_id}')\n",
-    "print(f'  Parents     : {queries.parents(term_id)}')\n",
-    "print(f'  Children    : {queries.children(term_id)}')\n",
+    "print(f\"Term: {term_id}\")\n",
+    "print(f\"  Parents     : {queries.parents(term_id)}\")\n",
+    "print(f\"  Children    : {queries.children(term_id)}\")\n",
     "\n",
     "\n",
     "# print(f\"  Ancestors   : {queries.ancestors(term_id)}\")\n",