docs/src/main/paradox/docs/getting-started/notebooks/dataset_from_different_sources.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "jcyB6NFmQReL"
   },
   "source": [
    "# Tutorial: Integrate Neuroscience Datasets from Multiple Sources using MINDS"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Initialize and configure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install nexusforge==0.7.0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install allensdk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install neurom[plotly]==3.0.1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!pip install --upgrade nest-asyncio==1.5.1"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get an authentication token"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The [Nexus sandbox application](https://sandbox.bluebrainnexus.io) can be used to get a token:\n",
    "\n",
    "- Step 1: From the [web page](https://sandbox.bluebrainnexus.io), click on the login button in the top right corner and follow the instructions on screen.\n",
    "\n",
    "- Step 2: Once logged in, click on the button on the top right that displays your GitHub username. From the dropdown select `Copy token` option. This will copy the token to your clipboard.\n"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Once a token is obtained, proceed to paste it as the value of the `TOKEN` variable below.\n",
    "\n",
    "__Important__: A Nexus token is valid for 8 hours, if your working session is open for more than 8 hours, you may need to refresh the value of the token and reintialize the forge client in the _'Configure a forge client to store, manage and access datasets'_ section below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import getpass"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "TOKEN = getpass.getpass()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Configure a forge client to store, manage and access datasets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import uuid\n",
    "import base64\n",
    "import requests\n",
    "import json\n",
    "from pathlib import Path\n",
    "\n",
    "from kgforge.core import KnowledgeGraphForge\n",
    "from kgforge.specializations.mappings import DictionaryMapping\n",
    "\n",
    "from allensdk.api.queries.cell_types_api import CellTypesApi\n",
    "from allensdk.core.cell_types_cache import CellTypesCache"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
    "dirpath = './rdfmodel'\n",
    "Path(dirpath).mkdir(parents=True, exist_ok=True)\n",
    "with open(f'{dirpath}/jsonldcontext.json', 'w') as outfile:\n",
    "    json.dump(r.json(), outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ORG = \"github-users\"\n",
    "PROJECT = \"\"  # Provide here the automatically created project name created when you logged into the Nexus sandbox instance."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
    "                            bucket=f\"{ORG}/{PROJECT}\",\n",
    "                            endpoint=\"https://sandbox.bluebrainnexus.io/v1\",\n",
    "                            token=TOKEN)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "9W5M5Ck9Tq7q"
   },
   "source": [
    "## Download datasets from Allen Cell Types Database and MouseLight"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download mouse neuron morphologies from the Allen Cell Types Database"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will be downloading mouse neuron morphology data from the [Allen Cell Types Database](https://celltypes.brain-map.org/). The [AllenSDK](https://allensdk.readthedocs.io/en/latest/) can be used for data download."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ALLEN_DIR = \"allen_cell_types_database\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ctc = CellTypesCache(manifest_file=f\"{ALLEN_DIR}/manifest.json\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "MAX_CELLS = 10 # Increase to include more cells\n",
    "SPECIES = CellTypesApi.MOUSE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "nm_allen_identifiers = [cell[\"id\"] for cell in ctc.get_cells(species=[SPECIES], require_reconstruction = True)][:MAX_CELLS]\n",
    "print(f\"Selected a mouse neuron with identifier: {nm_allen_identifiers}\")"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Select metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(f\"{ALLEN_DIR}/cells.json\") as f:\n",
    "    allen_cell_types_metadata = json.load(f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "nm_allen_metadata = [neuron for neuron in allen_cell_types_metadata if neuron[\"specimen__id\"] in nm_allen_identifiers]"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Download reconstruction files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for identifier in nm_allen_identifiers:\n",
    "    ctc.get_reconstruction(identifier)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download mouse neuron electrophysiology recordings from the Allen Cell Types Database"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Download Electrophysiology recordings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for identifier in nm_allen_identifiers:\n",
    "    ctc.get_ephys_data(identifier)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download mouse neuron morphologies from MouseLight project"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will be downloading mouse neuron morphology data from the [MouseLight project](https://www.janelia.org/project-team/mouselight)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "URL_GRAPHQL = \"http://ml-neuronbrowser.janelia.org/graphql/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "URL_JSON = \"http://ml-neuronbrowser.janelia.org/export\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "URL_SWC = \"http://ml-neuronbrowser.janelia.org/export\""
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Select metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "nm_request = requests.post(URL_GRAPHQL, json={\"operationName\":\"SearchNeurons\",\n",
    "                                \"variables\":{\n",
    "                                    \"context\":{\n",
    "                                        \"scope\":6,\n",
    "                                        \"nonce\":\"ckzmxfe9600033e68qnwoa59t\",\n",
    "                                        \"ccfVersion\": \"CCFV25\",\n",
    "                                        \"predicates\":[{\n",
    "                                            \"predicateType\":\"ANATOMICAL\",\n",
    "                                            \"tracingIdsOrDOIs\":[\"1\"],\n",
    "                                            \"tracingIdsOrDOIsExactMatch\":False,\n",
    "                                            \"tracingStructureIds\":[\"68e76074-1777-42b6-bbf9-93a6a5f02fa4\"],\n",
    "                                            \"nodeStructureIds\":[\"c37953e1-a1e9-4b9a-847e-08d9566ced65\"],\n",
    "                                            \"operatorId\":None,\n",
    "                                            \"amount\":0,\n",
    "                                            \"brainAreaIds\":[],\n",
    "                                            \"arbCenter\":{\n",
    "                                                \"x\":None,\n",
    "                                                \"y\":None,\n",
    "                                                \"z\":None},\n",
    "                                            \"arbSize\":None,\n",
    "                                            \"invert\":False,\n",
    "                                            \"composition\":3\n",
    "                                        }]\n",
    "                                    }\n",
    "                                },\n",
    "                                \"query\":\"\"\"query SearchNeurons($context: SearchContext) {\\n  searchNeurons(context: $context) \n",
    "                                            {\\n    totalCount\\n    queryTime\\n    nonce\\n    \\n    neurons {\\n      id\\n      \n",
    "                                            idString\\n      tracings {\\n        id\\n        tracingStructure {\\n          id\\n          \n",
    "                                            name\\n          value\\n          __typename\\n        }\\n        soma {\\n          id\\n          \n",
    "                                            x\\n          y\\n          z\\n          radius\\n          parentNumber\\n          \n",
    "                                            sampleNumber\\n          brainAreaIdCcfV30\\n          structureIdentifierId\\n          \n",
    "                                            __typename\\n        }\\n        __typename\\n      }\\n      __typename\\n    }\\n    \n",
    "                                            __typename\\n  }\\n}\\n\"\"\"\n",
    "                               })\n",
    "nm_mouselight_graphql = json.loads(nm_request.text)[\"data\"][\"searchNeurons\"][\"neurons\"]\n",
    "nm_mouselight_names = [x[\"idString\"] for x in nm_mouselight_graphql]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "nm_mouselight_metadata = list()\n",
    "for name in nm_mouselight_names[0:MAX_CELLS]:\n",
    "    a = requests.post(URL_JSON, \n",
    "                          json={\"ids\": [name],\"format\":1},\n",
    "                          headers={\"Accept\": \"*/*\", \"Content-Type\": \"application/json\"})\n",
    "    #print(a.content.decode('utf-8'))\n",
    "    c = a.json()\n",
    "    if c[\"contents\"][\"neurons\"]:\n",
    "        nm_mouselight_metadata.append(c[\"contents\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i, nm in enumerate(nm_mouselight_metadata):\n",
    "    allneurons = nm[\"neurons\"]\n",
    "    allenId = nm[\"neurons\"][0][\"soma\"][\"allenId\"]\n",
    "    allenInfo = nm[\"neurons\"][0][\"allenInformation\"]\n",
    "    for info in allenInfo:\n",
    "        if info[\"allenId\"] == allenId:\n",
    "            allenLabel = info[\"name\"]\n",
    "    nm_mouselight_metadata[i][\"neurons\"][0][\"allenLabel\"] = allenLabel"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Download reconstruction files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for name in nm_mouselight_names[0:MAX_CELLS]:\n",
    "    a = requests.post(URL_SWC, \n",
    "                      json={\"ids\": [name],\"format\":0},\n",
    "                      headers={\"Accept\": \"*/*\", \"Content-Type\": \"application/json\"})\n",
    "    c = a.json()\n",
    "    if not c[\"contents\"]:\n",
    "        print(f\"Skipping empty dataset: {c}\")\n",
    "        continue\n",
    "    \n",
    "    base64_message = c[\"contents\"]\n",
    "    base64_bytes = base64_message.encode('ascii')\n",
    "    message_bytes = base64.b64decode(base64_bytes)\n",
    "    dirpath = './mouselight'\n",
    "    Path(dirpath).mkdir(parents=True, exist_ok=True)\n",
    "    with open(f\"{dirpath}/{name}.swc\", \"wb\") as f:\n",
    "        f.write(message_bytes)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Mapping"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Map the Allen Cell Types Database neuron morphologies to Neuroshapes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "allen_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_morphology_dataset.hjson\") # TODO\n",
    "nm_allen_resources = forge.map(nm_allen_metadata, allen_nm_mapping)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Map the Allen Cell Types Database neuron electrophysiology recordings to Neuroshapes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "allen_ephys_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_ephys_dataset.hjson\") # TODO\n",
    "nephys_allen_resources = forge.map(nm_allen_metadata, allen_ephys_mapping)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Map the MouseLight neuron morphologies to Neuroshapes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "mouselight_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/mouselight_dataset.hjson\") # TODO\n",
    "nm_mouselight_resources = forge.map(nm_mouselight_metadata, mouselight_nm_mapping)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Register\n",
    "\n",
    "If the registration fails, try refreshing the access token and reinitializing the forge client in the _'Configure a forge client to store, manage and access datasets'_ section."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Register the Allen Cell Types Database neuron morphologies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for resource in nm_allen_resources:\n",
    "    resource.id = forge.format(\"identifier\", \"neuronmorphologies\", str(uuid.uuid4()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.register(nm_allen_resources)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Register the Allen Cell Types Database neuron electrophysiology recordings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for resource in nephys_allen_resources:\n",
    "    resource.id = forge.format(\"identifier\", \"traces\", str(uuid.uuid4()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.register(nephys_allen_resources)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Register the MouseLight neuron morphologies"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for resource in nm_mouselight_resources:\n",
    "    resource.id = forge.format(\"identifier\", \"neuronmorphologies\", str(uuid.uuid4()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.register(nm_mouselight_resources)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Save the created resources in JSON files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dirpath = './database'\n",
    "Path(dirpath).mkdir(parents=True, exist_ok=True)\n",
    "with open(f\"{dirpath}/mouselight-protocols.json\",\"w\") as f:\n",
    "    json.dump(forge.as_jsonld(nm_mouselight_resources, form=\"expanded\"),f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(f\"{dirpath}/allen-morphologies-protocols.json\",\"w\") as f:\n",
    "    json.dump(forge.as_jsonld(nm_allen_resources, form=\"expanded\"),f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(f\"{dirpath}/allen-ephys-protocols.json\",\"w\") as f:\n",
    "    json.dump(forge.as_jsonld(nephys_allen_resources, form=\"expanded\"),f)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Access"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set filters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "_type = \"NeuronMorphology\"\n",
    "\n",
    "filters = {\"type\": _type}"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run Query"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "number_of_results = 10  # You can limit the number of results, pass `None` to fetch all the results\n",
    "\n",
    "data = forge.search(filters, limit=number_of_results)\n",
    "\n",
    "print(f\"{str(len(data))} dataset(s) of type {_type} found\")"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Display the results as pandas dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "property_to_display = [\"id\",\"name\",\"subject\",\"brainLocation.brainRegion.id\",\"brainLocation.brainRegion.label\",\"brainLocation.layer.id\",\"brainLocation.layer.label\", \"contribution\",\"brainLocation.layer.id\",\"brainLocation.layer.label\",\"distribution.name\",\"distribution.contentUrl\",\"distribution.encodingFormat\"]\n",
    "reshaped_data = forge.reshape(data, keep=property_to_display)\n",
    "\n",
    "forge.as_dataframe(reshaped_data)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dirpath = \"./downloaded/\"\n",
    "forge.download(data, \"distribution.contentUrl\", dirpath)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ls ./downloaded/"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Display a result as 3D Neuron Morphology"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from neurom import load_morphology\n",
    "from neurom.view.plotly_impl import plot_morph3d\n",
    "import IPython"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "neuron = load_morphology(f\"{dirpath}/{data[0].distribution.name}\")\n",
    "plot_morph3d(neuron, inline=False)\n",
    "IPython.display.HTML(filename='./morphology-3D.html')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Version the dataset\n",
    "Tagging a dataset is equivalent to `git tag`. It allows to version a dataset."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.tag(data, value=\"releaseV112\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# The version argument can be specified to retrieve the dataset at a given tag.\n",
    "\n",
    "tagged_data = forge.retrieve(id=data[0].id, version=\"releaseV112\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.as_dataframe(tagged_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "data[0].description=\"Neuron Morphology from Allen\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.update(data[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "non_tagged_data = forge.retrieve(id=data[0].id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "forge.as_dataframe(non_tagged_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
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