chores: update notebook to include demo showing how to interact with the client

Author: ecarrenolozano

notebooks/quickstart_demo.ipynb

@@ -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",
@@ -167,7 +167,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cache_dir = Path('../data/out')"
+    "cache_dir = Path(\"../data/out\")"
    ]
   },
   {
@@ -266,7 +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\")))"
    ]
   },
   {
@@ -282,7 +282,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(onto_registry.get_available_formats(ontology_id='chebi'))"
+    "print(onto_registry.get_available_formats(ontology_id=\"chebi\"))"
    ]
   },
   {
@@ -326,18 +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}\")"
    ]
   },
   {
@@ -376,13 +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())}\")"
    ]
   },
   {
@@ -400,7 +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"
    ]
   },
   {
@@ -412,34 +412,135 @@
     "queries = OntologyQueries(gene_ontology)\n",
     "\n",
     "# Print term relations\n",
-    "print(f'Term: {term_id}')\n",
-    "print(f'  Parents     : {queries.ancestors(term_id)}')\n",
-    "print(f'  Children    : {queries.descendants(term_id)}')\n",
+    "print(f\"Term: {term_id}\")\n",
+    "print(f\"  Parents     : {queries.ancestors(term_id)}\")\n",
+    "print(f\"  Children    : {queries.descendants(term_id)}\")\n",
     "\n",
     "\n",
     "# print(f\"  Ancestors   : {queries.ancestors(term_id)}\")\n",
     "# print(f\"  Descendants : {queries.descendants(term_id)}\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Step 5. Client"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Import the library"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "import ontograph as op"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Interact with the registry"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "# Load the ontogragh catalog of ontologies\n",
+    "onto_registry = op.registry(\"../data/out\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# In case you want to force downloading the registry you can use\n",
+    "onto_registry.load_registry(force_download=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# You can save ALL the catalog as a Python dictionary. The original OBO Foundry registry comes from a YAML file.\n",
+    "onto_registry_dict = onto_registry.registry_as_dict()"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
+   "source": [
+    "# You can verify the id and description of all the ontologies in the catalog\n",
+    "onto_registry.list_available_ontologies()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# You can print the current schema or possible fields the catalog store for each ontology.\n",
+    "onto_registry.print_registry_schema_tree()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# You can get the metadata of each ontology and store it in a variable. At the same time, you can print it using `show_metadata=True`\n",
+    "go_metadata = onto_registry.get_ontology_metadata(\"go\", show_metadata=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# The catalog contains different formats for the same ontology. You can verify all the formats available for a specific ontology.\n",
+    "onto_registry.get_available_formats(\"chebi\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Interact with a specific ontology."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
    "source": []
   },
   {
@@ -470,7 +571,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,