CHEBIBioLinkGINAS.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
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   },
   "source": [
    "# Simple Example of multiple biological data source acquisition\n",
    "\n",
    "This notebook is intended as a starting point for other researchers and domain experts to explore and experiment with various data sources and how they can be utilized to build pipelines to support a Blackboard architecture that can address important science. Our initial modest goals are to focus on the Translator *competency questions* and begin to incorporate and integrate those data sources we anticipate being useful.\n",
    "\n",
    "## Typical Structure\n",
    "\n",
    "This Notebook, and those that are cloned from it, will follow a typical structure like this:\n",
    "\n",
    "- Background\n",
    "    - Relevant Competency Question(s) or Research Problem\n",
    "    - Current Status and remaining work (just to give the reader context about how finished the notebook is)\n",
    "- Data Sources\n",
    "    - Descriptions and reference, including the API documentation links and a brief description of their scope and content\n",
    "- Transformation and Integration\n",
    "    - Simple Data Access examples to illustrate the API usage and the type/shape of the data\n",
    "    - More sophisticated examples to examine sources and experiment/demonstrate integration possibilities\n",
    "    - Visualization and Summarization\n",
    "- Develop Prototype Pipelines (optional)\n",
    "    - Where possible, prototype a reusable set of code illustrating a desired solution or capability, with an eye towards extracting and modularizing it for presentation via BioLink or integration into other workflows."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Background\n",
    "\n",
    "### Current Status\n",
    "\n",
    "- Accesses CHEBI data via the BioLink API\n",
    "- Accesses GINAS data via their API\n",
    "- Trying to *join* information about 'acetylsalicylic acid' from both data sources, as a toy problem to get started.\n",
    "- We're going to look up 'acetylsalicylic acid' rather than 'aspirin', because it is a common term in all of the sources right now and I'm not sure that the Monarch BioLink API I'm using has the term 'aspirin' yet.\n",
    "\n",
    "\n",
    "### Next Steps\n",
    "\n",
    "- Explore [Pharos](https://pharos.nih.gov/idg/index) API and data sources\n",
    "- Use [mybinder](http://mybinder.org) badge (or a similar hosted Jupyter mechanism) to simplify invocation and editing from GitHub\n",
    "- Try to extract Drug-to-conditions and Condition-to-Drugs relations from sources. Use competency questions to guide this integration.\n",
    "- Consider WikiData as a source\n",
    "- Accommodate anticipated BROAD probability models, possibly by developing a mock API.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Data Sources"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### CHEBI Data\n",
    "\n",
    "Monarch ingests [Chemical Entities of Biological Interest (ChEBI)](https://www.ebi.ac.uk/chebi/) data and makes it available via SciGraph, the Monarch API, and the new BioLink API.\n",
    "\n",
    "For reference, here is the link to CHEBI's entry for 'acetylsalicylic acid' (aka 'Aspirin'):\n",
    "\n",
    "[CHEBI:15365 acetylsalicylic acid](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15365)\n",
    "\n",
    "\n",
    "### BioLink substance data from CHEBI via Monarch\n",
    "\n",
    "Monarch has ingested CHEBI data, and we have a `/biolink/substance/{id}/participant_in/` endpoint that seems to return some data:\n",
    "\n",
    "https://api.monarchinitiative.org/api/bioentity/substance/CHEBI:40036/participant_in/\n",
    "\n",
    "However, the basic `/biolink/substance/{id}` endpoint returns no useful data, so we'll have to use the above link until BioLink has a fleshed out `/substance` endpoint.\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### ginas API Substance data from ginas\n",
    "\n",
    "The [Global Ingredient Archival System (ginas)](https://tripod.nih.gov/ginas/#/) provides a common identifier for all of the substances used in medicinal products, utilizing a consistent definition of substances globally, including active substances under clinical investigation. More info at [NCATS ginas](https://ncats.nih.gov/expertise/preclinical/ginas).\n",
    "\n",
    "#### Examples\n",
    "\n",
    "- [ginas Aspirin](https://tripod.nih.gov/ginas/app/api/v1/substances/search?q=root_names_name:\"^ASPIRIN$\")\n",
    "\n",
    "- [ginas acetylsalicylic acid](https://tripod.nih.gov/ginas/app/api/v1/substances/search?q=root_names_name:\"^acetylsalicylic acid$\")\n",
    "\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "\n",
    "## Transformation and Integration\n",
    "\n",
    "I'm going to start out by ensuring that I can obtain useful data from each of the above sources. In this case, I am focusing on a single substance, **aspirin** or **acetylsalicylic acid** (CHEBI:15365).\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Reading BioLink's `/substance` endpoint for CHEBI data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>evidence_graph</th>\n",
       "      <th>evidence_types</th>\n",
       "      <th>id</th>\n",
       "      <th>object</th>\n",
       "      <th>object_extension</th>\n",
       "      <th>provided_by</th>\n",
       "      <th>publications</th>\n",
       "      <th>qualifiers</th>\n",
       "      <th>relation</th>\n",
       "      <th>slim</th>\n",
       "      <th>subject</th>\n",
       "      <th>subject_extension</th>\n",
       "      <th>type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>{'edges': None, 'nodes': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': 'benzoic acids', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:22723', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': None, 'description': None, 'deprecated': None, 'id': None, 'consider': None, 'synonyms': None, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': 'acetylsalicylic acid', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:15365', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>{'edges': None, 'nodes': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': 'antipyretic', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:35493', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': None, 'description': None, 'deprecated': None, 'id': None, 'consider': None, 'synonyms': None, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': 'acetylsalicylic acid', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:15365', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>{'edges': None, 'nodes': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': 'non-narcotic analgesic', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:35481', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': None, 'description': None, 'deprecated': None, 'id': None, 'consider': None, 'synonyms': None, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>{'label': 'acetylsalicylic acid', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:15365', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   evidence_graph  evidence_types  id                                                                                                                                                                                                                                              object  object_extension  provided_by  publications  qualifiers                                                                                                                                                          relation  slim                                                                                                                                                                                                                                           subject  subject_extension  type\n",
       "0  {'edges': None, 'nodes': None}             NaN NaN           {'label': 'benzoic acids', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:22723', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}               NaN          NaN           NaN         NaN  {'label': None, 'description': None, 'deprecated': None, 'id': None, 'consider': None, 'synonyms': None, 'replaced_by': None, 'categories': None, 'types': None}   NaN  {'label': 'acetylsalicylic acid', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:15365', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}                NaN   NaN\n",
       "1  {'edges': None, 'nodes': None}             NaN NaN             {'label': 'antipyretic', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:35493', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}               NaN          NaN           NaN         NaN  {'label': None, 'description': None, 'deprecated': None, 'id': None, 'consider': None, 'synonyms': None, 'replaced_by': None, 'categories': None, 'types': None}   NaN  {'label': 'acetylsalicylic acid', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:15365', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}                NaN   NaN\n",
       "2  {'edges': None, 'nodes': None}             NaN NaN  {'label': 'non-narcotic analgesic', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:35481', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}               NaN          NaN           NaN         NaN  {'label': None, 'description': None, 'deprecated': None, 'id': None, 'consider': None, 'synonyms': None, 'replaced_by': None, 'categories': None, 'types': None}   NaN  {'label': 'acetylsalicylic acid', 'xrefs': None, 'description': None, 'deprecated': None, 'id': 'CHEBI:15365', 'consider': None, 'synonyms': None, 'taxon': {'label': None, 'id': None}, 'replaced_by': None, 'categories': None, 'types': None}                NaN   NaN"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "from pandas.io.json import json_normalize\n",
    "try:\n",
    "    from urllib.parse import urlencode\n",
    "except:\n",
    "    from urllib import urlencode \n",
    "pd.set_option('max_colwidth', 3800)\n",
    "pd.set_option('display.expand_frame_repr', False)\n",
    "biolinkURL = \"https://api.monarchinitiative.org/api/bioentity/substance/CHEBI%3A15365/participant_in/?rows=20&fetch_objects=true\"\n",
    "df = pd.read_json(biolinkURL, typ=\"frame\", orient=\"records\")\n",
    "df.head(3) # Show the first 3 rows only \n",
    "# df\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now that we see the data frame from our source, we can use ordinary Python (and the pandas library) to access different parts. For example, let's grab the first row's `object` value."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'categories': None,\n",
       " 'consider': None,\n",
       " 'deprecated': None,\n",
       " 'description': None,\n",
       " 'id': 'CHEBI:22723',\n",
       " 'label': 'benzoic acids',\n",
       " 'replaced_by': None,\n",
       " 'synonyms': None,\n",
       " 'taxon': {'id': None, 'label': None},\n",
       " 'types': None,\n",
       " 'xrefs': None}"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.object[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'benzoic acids'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.object[0]['label']"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Reading ginas data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'https://tripod.nih.gov/ginas/app/api/v1/substances/search?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22'"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ginasBase = \"https://tripod.nih.gov/ginas/app/api/v1/substances/search?\"\n",
    "ginasParams = {'q': \"root_names_name:\\\"^acetylsalicylic acid$\\\"\"}\n",
    "\n",
    "ginasPath = urlencode(ginasParams)\n",
    "ginasURL = ginasBase + ginasPath\n",
    "\n",
    "ginasURL"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "One problem that I encountered is that the ginas API response is not in a format that is compatible with the `pandas` `read_json` method. So we'll need to preprocess the response to make it pandas-compatible, or alternatively, we can just use the JSON directly without using pandas, although that may inhibit some experimentation and visualization that is afforded by data frames."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"query\": \"q=root_names_name:\\\"^acetylsalicylic acid$\\\"\",\n",
      "  \"facets\": [\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=Code+System\",\n",
      "      \"name\": \"Code System\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"EMA ASSESSMENT REPORTS\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"EPA PESTICIDE CODE\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"IUPHAR\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"LIVERTOX\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"NDF-RT\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"RXCUI\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"WHO INTERNATIONAL PHARMACPOEIA\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"WHO-ATC\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"WHO-ESSENTIAL MEDICINES LIST\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"WHO-VATC\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=GInAS+Tag\",\n",
      "      \"name\": \"GInAS Tag\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"EMA EPAR\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"EP\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"GREEN BOOK\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"HPUS\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"INCI\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ORANGE BOOK\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"USP\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"USP-RS\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"VANDF\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"WHO-DD\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=WHO-ATC\",\n",
      "      \"name\": \"WHO-ATC\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"A01AD05\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"B01AC06\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"B01AC56\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"C10BX01\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"C10BX02\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"C10BX05\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"M01BA03\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"N02BA01\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"N02BA51\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"N02BA71\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=WHO-VATC\",\n",
      "      \"name\": \"WHO-VATC\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"QA01AD05\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QB01AC06\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QB01AC56\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QC10BX01\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QC10BX02\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QC10BX05\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QM01BA03\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QN02BA01\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QN02BA51\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"QN02BA71\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=EMA+ASSESSMENT+REPORTS\",\n",
      "      \"name\": \"EMA ASSESSMENT REPORTS\",\n",
      "      \"values\": [\n",
      "        {\n",
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      "        {\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=Last+Edited+By\",\n",
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      "      \"name\": \"MESH\",\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=Modifications\",\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=Molecular+Formula\",\n",
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      "      \"name\": \"Name Count\",\n",
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      "      \"name\": \"Reference Type\",\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=StereoChemistry\",\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=Stereocenters\",\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=Substance+Class\",\n",
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      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=SubstanceDeprecated\",\n",
      "      \"name\": \"SubstanceDeprecated\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"false\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=SubstanceStereochemistry\",\n",
      "      \"name\": \"SubstanceStereochemistry\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"ACHIRAL\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=WHO+INTERNATIONAL+PHARMACPOEIA\",\n",
      "      \"name\": \"WHO INTERNATIONAL PHARMACPOEIA\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"ASPIRIN\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=WIKIPEDIA\",\n",
      "      \"name\": \"WIKIPEDIA\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"ASPIRIN\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search/@facets?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22&field=ix.Class\",\n",
      "      \"name\": \"ix.Class\",\n",
      "      \"values\": [\n",
      "        {\n",
      "          \"label\": \"ix.core.models.Text\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.Amount\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.Code\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.GinasChemicalStructure\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.Name\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.NameOrg\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.Note\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.Reference\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.Relationship\",\n",
      "          \"count\": 1\n",
      "        },\n",
      "        {\n",
      "          \"label\": \"ix.ginas.models.v1.SubstanceReference\",\n",
      "          \"count\": 1\n",
      "        }\n",
      "      ]\n",
      "    }\n",
      "  ],\n",
      "  \"sha1\": \"bc199c1ddf61bf103f27b656958ec247a3bc7a70\",\n",
      "  \"version\": 1,\n",
      "  \"skip\": 0,\n",
      "  \"sideway\": [],\n",
      "  \"id\": 35878720,\n",
      "  \"etag\": \"9dcacb1b98b27f23\",\n",
      "  \"top\": 10,\n",
      "  \"uri\": \"http://tripod.nih.gov/ginas/app/api/v1/substances/search?q=root_names_name%3A%22%5Eacetylsalicylic+acid%24%22\",\n",
      "  \"total\": 1,\n",
      "  \"method\": \"GET\",\n",
      "  \"count\": 1,\n",
      "  \"path\": \"/ginas/app/api/v1/substances/search\",\n",
      "  \"content\": [\n",
      "    {\n",
      "      \"lastEdited\": 1471037433000,\n",
      "      \"_name\": \"ASPIRIN\",\n",
      "      \"structure\": {\n",
      "        \"molfile\": \"\\n  Symyx   06151614272D 1   1.00000     0.00000     0\\n\\n 13 13  0     0  0            999 V2000\\n    4.6125   -1.9917    0.0000 C   0  0  0  0  0  0           0  0  0\\n    4.6125   -0.6792    0.0000 C   0  0  0  0  0  0           0  0  0\\n    3.4542   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\\n    2.3167   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\\n    1.1542   -2.6375    0.0000 C   0  0  0  0  0  0           0  0  0\\n    5.7417   -0.0250    0.0000 O   0  0  0  0  0  0           0  0  0\\n    0.0000   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\\n    3.4792    0.0000    0.0000 O   0  0  0  0  0  0           0  0  0\\n    5.7750   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\\n    3.4542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\\n    1.1542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\\n    5.7750   -4.0042    0.0000 C   0  0  0  0  0  0           0  0  0\\n    4.5792   -4.6917    0.0000 C   0  0  0  0  0  0           0  0  0\\n  2  1  1  0     0  0\\n  3  1  2  0     0  0\\n  4  3  1  0     0  0\\n  5  4  1  0     0  0\\n  6  2  2  0     0  0\\n  7  5  2  0     0  0\\n  8  2  1  0     0  0\\n  9  1  1  0     0  0\\n 10  3  1  0     0  0\\n 11  5  1  0     0  0\\n 12  9  2  0     0  0\\n 13 12  1  0     0  0\\n 13 10  2  0     0  0\\nM  END\\n\",\n",
      "        \"smiles\": \"CC(=O)OC1=CC=CC=C1C(O)=O\",\n",
      "        \"lastEdited\": 1471037433000,\n",
      "        \"atropisomerism\": \"No\",\n",
      "        \"stereoCenters\": 0,\n",
      "        \"stereoComments\": \"\",\n",
      "        \"charge\": 0,\n",
      "        \"self\": \"http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)?view=full\",\n",
      "        \"definedStereo\": 0,\n",
      "        \"digest\": \"8f13a762c2818d1407a79edf0fe0218dc88f7a9f\",\n",
      "        \"stereochemistry\": \"ACHIRAL\",\n",
      "        \"createdBy\": \"admin\",\n",
      "        \"hash\": \"NNQ793F142LD\",\n",
      "        \"deprecated\": false,\n",
      "        \"mwt\": 180.1574,\n",
      "        \"id\": \"3d311a51-d4f2-4878-ab53-45e6d9640ae3\",\n",
      "        \"formula\": \"C9H8O4\",\n",
      "        \"_properties\": {\n",
      "          \"href\": \"http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)/properties\",\n",
      "          \"count\": 5\n",
      "        },\n",
      "        \"lastEditedBy\": \"admin\",\n",
      "        \"ezCenters\": 0,\n",
      "        \"count\": 1,\n",
      "        \"references\": [\n",
      "          \"e794afad-a478-4c69-b6bd-1c7a8fe46baf\",\n",
      "          \"25e72485-091c-47f8-9a00-7dd47689bf58\"\n",
      "        ],\n",
      "        \"opticalActivity\": \"UNSPECIFIED\",\n",
      "        \"access\": [],\n",
      "        \"created\": 1471037433000\n",
      "      },\n",
      "      \"version\": \"1\",\n",
      "      \"_references\": {\n",
      "        \"href\": \"http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/references\",\n",
      "        \"count\": 73\n",
      "      },\n",
      "      \"status\": \"approved\",\n",
      "      \"_approvalIDDisplay\": \"R16CO5Y76E\",\n",
      "      \"approved\": 1470433417000,\n",
      "      \"uuid\": \"8911c794-5da3-4934-a683-16d98d93db97\",\n",
      "      \"substanceClass\": \"chemical\",\n",
      "      \"approvalID\": \"R16CO5Y76E\",\n",
      "      \"_names\": {\n",
      "        \"href\": \"http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/names\",\n",
      "        \"count\": 76\n",
      "      },\n",
      "      \"_self\": \"http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)?view=full\",\n",
      "      \"deprecated\": false,\n",
      "      \"lastEditedBy\": \"admin\",\n",
      "      \"access\": [],\n",
      "      \"approvedBy\": \"FDA_SRS\",\n",
      "      \"definitionLevel\": \"COMPLETE\",\n",
      "      \"createdBy\": \"admin\",\n",
      "      \"_moieties\": {\n",
      "        \"href\": \"http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/moieties\",\n",
      "        \"count\": 1\n",
      "      },\n",
      "      \"definitionType\": \"PRIMARY\",\n",
      "      \"_relationships\": {\n",
      "        \"href\": \"http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/relationships\",\n",
      "        \"count\": 27\n",
      "      },\n",
      "      \"_codes\": {\n",
      "        \"href\": \"http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/codes\",\n",
      "        \"count\": 51\n",
      "      },\n",
      "      \"created\": 1471037433000\n",
      "    }\n",
      "  ],\n",
      "  \"created\": 1493909200168\n",
      "}\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[{'_approvalIDDisplay': 'R16CO5Y76E',\n",
       "  '_codes': {'count': 51,\n",
       "   'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/codes'},\n",
       "  '_moieties': {'count': 1,\n",
       "   'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/moieties'},\n",
       "  '_name': 'ASPIRIN',\n",
       "  '_names': {'count': 76,\n",
       "   'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/names'},\n",
       "  '_references': {'count': 73,\n",
       "   'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/references'},\n",
       "  '_relationships': {'count': 27,\n",
       "   'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/relationships'},\n",
       "  '_self': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)?view=full',\n",
       "  'access': [],\n",
       "  'approvalID': 'R16CO5Y76E',\n",
       "  'approved': 1470433417000,\n",
       "  'approvedBy': 'FDA_SRS',\n",
       "  'created': 1471037433000,\n",
       "  'createdBy': 'admin',\n",
       "  'definitionLevel': 'COMPLETE',\n",
       "  'definitionType': 'PRIMARY',\n",
       "  'deprecated': False,\n",
       "  'lastEdited': 1471037433000,\n",
       "  'lastEditedBy': 'admin',\n",
       "  'status': 'approved',\n",
       "  'structure': {'_properties': {'count': 5,\n",
       "    'href': 'http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)/properties'},\n",
       "   'access': [],\n",
       "   'atropisomerism': 'No',\n",
       "   'charge': 0,\n",
       "   'count': 1,\n",
       "   'created': 1471037433000,\n",
       "   'createdBy': 'admin',\n",
       "   'definedStereo': 0,\n",
       "   'deprecated': False,\n",
       "   'digest': '8f13a762c2818d1407a79edf0fe0218dc88f7a9f',\n",
       "   'ezCenters': 0,\n",
       "   'formula': 'C9H8O4',\n",
       "   'hash': 'NNQ793F142LD',\n",
       "   'id': '3d311a51-d4f2-4878-ab53-45e6d9640ae3',\n",
       "   'lastEdited': 1471037433000,\n",
       "   'lastEditedBy': 'admin',\n",
       "   'molfile': '\\n  Symyx   06151614272D 1   1.00000     0.00000     0\\n\\n 13 13  0     0  0            999 V2000\\n    4.6125   -1.9917    0.0000 C   0  0  0  0  0  0           0  0  0\\n    4.6125   -0.6792    0.0000 C   0  0  0  0  0  0           0  0  0\\n    3.4542   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\\n    2.3167   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\\n    1.1542   -2.6375    0.0000 C   0  0  0  0  0  0           0  0  0\\n    5.7417   -0.0250    0.0000 O   0  0  0  0  0  0           0  0  0\\n    0.0000   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\\n    3.4792    0.0000    0.0000 O   0  0  0  0  0  0           0  0  0\\n    5.7750   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\\n    3.4542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\\n    1.1542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\\n    5.7750   -4.0042    0.0000 C   0  0  0  0  0  0           0  0  0\\n    4.5792   -4.6917    0.0000 C   0  0  0  0  0  0           0  0  0\\n  2  1  1  0     0  0\\n  3  1  2  0     0  0\\n  4  3  1  0     0  0\\n  5  4  1  0     0  0\\n  6  2  2  0     0  0\\n  7  5  2  0     0  0\\n  8  2  1  0     0  0\\n  9  1  1  0     0  0\\n 10  3  1  0     0  0\\n 11  5  1  0     0  0\\n 12  9  2  0     0  0\\n 13 12  1  0     0  0\\n 13 10  2  0     0  0\\nM  END\\n',\n",
       "   'mwt': 180.1574,\n",
       "   'opticalActivity': 'UNSPECIFIED',\n",
       "   'references': ['e794afad-a478-4c69-b6bd-1c7a8fe46baf',\n",
       "    '25e72485-091c-47f8-9a00-7dd47689bf58'],\n",
       "   'self': 'http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)?view=full',\n",
       "   'smiles': 'CC(=O)OC1=CC=CC=C1C(O)=O',\n",
       "   'stereoCenters': 0,\n",
       "   'stereoComments': '',\n",
       "   'stereochemistry': 'ACHIRAL'},\n",
       "  'substanceClass': 'chemical',\n",
       "  'uuid': '8911c794-5da3-4934-a683-16d98d93db97',\n",
       "  'version': '1'}]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import json\n",
    "import requests\n",
    "\n",
    "r = requests.get(ginasURL)\n",
    "c = r.json()\n",
    "print(json.dumps(c, indent=2))\n",
    "c['content']\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### GINAS JSON to Data Frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>_approvalIDDisplay</th>\n",
       "      <th>_codes</th>\n",
       "      <th>_moieties</th>\n",
       "      <th>_name</th>\n",
       "      <th>_names</th>\n",
       "      <th>_references</th>\n",
       "      <th>_relationships</th>\n",
       "      <th>_self</th>\n",
       "      <th>access</th>\n",
       "      <th>approvalID</th>\n",
       "      <th>approved</th>\n",
       "      <th>approvedBy</th>\n",
       "      <th>created</th>\n",
       "      <th>createdBy</th>\n",
       "      <th>definitionLevel</th>\n",
       "      <th>definitionType</th>\n",
       "      <th>deprecated</th>\n",
       "      <th>lastEdited</th>\n",
       "      <th>lastEditedBy</th>\n",
       "      <th>status</th>\n",
       "      <th>structure</th>\n",
       "      <th>substanceClass</th>\n",
       "      <th>uuid</th>\n",
       "      <th>version</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>R16CO5Y76E</td>\n",
       "      <td>{'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/codes', 'count': 51}</td>\n",
       "      <td>{'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/moieties', 'count': 1}</td>\n",
       "      <td>ASPIRIN</td>\n",
       "      <td>{'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/names', 'count': 76}</td>\n",
       "      <td>{'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/references', 'count': 73}</td>\n",
       "      <td>{'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/relationships', 'count': 27}</td>\n",
       "      <td>http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)?view=full</td>\n",
       "      <td>[]</td>\n",
       "      <td>R16CO5Y76E</td>\n",
       "      <td>1470433417000</td>\n",
       "      <td>FDA_SRS</td>\n",
       "      <td>1471037433000</td>\n",
       "      <td>admin</td>\n",
       "      <td>COMPLETE</td>\n",
       "      <td>PRIMARY</td>\n",
       "      <td>False</td>\n",
       "      <td>1471037433000</td>\n",
       "      <td>admin</td>\n",
       "      <td>approved</td>\n",
       "      <td>{'molfile': '\n",
       "  Symyx   06151614272D 1   1.00000     0.00000     0\n",
       "\n",
       " 13 13  0     0  0            999 V2000\n",
       "    4.6125   -1.9917    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    4.6125   -0.6792    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    3.4542   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    2.3167   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    1.1542   -2.6375    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    5.7417   -0.0250    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    0.0000   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    3.4792    0.0000    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    5.7750   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    3.4542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    1.1542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    5.7750   -4.0042    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    4.5792   -4.6917    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "  2  1  1  0     0  0\n",
       "  3  1  2  0     0  0\n",
       "  4  3  1  0     0  0\n",
       "  5  4  1  0     0  0\n",
       "  6  2  2  0     0  0\n",
       "  7  5  2  0     0  0\n",
       "  8  2  1  0     0  0\n",
       "  9  1  1  0     0  0\n",
       " 10  3  1  0     0  0\n",
       " 11  5  1  0     0  0\n",
       " 12  9  2  0     0  0\n",
       " 13 12  1  0     0  0\n",
       " 13 10  2  0     0  0\n",
       "M  END\n",
       "', 'smiles': 'CC(=O)OC1=CC=CC=C1C(O)=O', 'lastEdited': 1471037433000, 'atropisomerism': 'No', 'stereoCenters': 0, 'stereoComments': '', 'charge': 0, 'self': 'http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)?view=full', 'definedStereo': 0, 'digest': '8f13a762c2818d1407a79edf0fe0218dc88f7a9f', 'stereochemistry': 'ACHIRAL', 'createdBy': 'admin', 'hash': 'NNQ793F142LD', 'deprecated': False, 'mwt': 180.1574, 'id': '3d311a51-d4f2-4878-ab53-45e6d9640ae3', 'formula': 'C9H8O4', '_properties': {'href': 'http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)/properties', 'count': 5}, 'lastEditedBy': 'admin', 'ezCenters': 0, 'count': 1, 'references': ['e794afad-a478-4c69-b6bd-1c7a8fe46baf', '25e72485-091c-47f8-9a00-7dd47689bf58'], 'opticalActivity': 'UNSPECIFIED', 'access': [], 'created': 1471037433000}</td>\n",
       "      <td>chemical</td>\n",
       "      <td>8911c794-5da3-4934-a683-16d98d93db97</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  _approvalIDDisplay                                                                                                                  _codes                                                                                                                 _moieties    _name                                                                                                                  _names                                                                                                                  _references                                                                                                                  _relationships                                                                                              _self access  approvalID       approved approvedBy        created createdBy definitionLevel definitionType deprecated     lastEdited lastEditedBy    status                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  structure substanceClass                                  uuid version\n",
       "0         R16CO5Y76E  {'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/codes', 'count': 51}  {'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/moieties', 'count': 1}  ASPIRIN  {'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/names', 'count': 76}  {'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/references', 'count': 73}  {'href': 'http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)/relationships', 'count': 27}  http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)?view=full     []  R16CO5Y76E  1470433417000    FDA_SRS  1471037433000     admin        COMPLETE        PRIMARY      False  1471037433000        admin  approved  {'molfile': '\n",
       "  Symyx   06151614272D 1   1.00000     0.00000     0\n",
       "\n",
       " 13 13  0     0  0            999 V2000\n",
       "    4.6125   -1.9917    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    4.6125   -0.6792    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    3.4542   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    2.3167   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    1.1542   -2.6375    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    5.7417   -0.0250    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    0.0000   -1.9917    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    3.4792    0.0000    0.0000 O   0  0  0  0  0  0           0  0  0\n",
       "    5.7750   -2.6792    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    3.4542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    1.1542   -3.9667    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    5.7750   -4.0042    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "    4.5792   -4.6917    0.0000 C   0  0  0  0  0  0           0  0  0\n",
       "  2  1  1  0     0  0\n",
       "  3  1  2  0     0  0\n",
       "  4  3  1  0     0  0\n",
       "  5  4  1  0     0  0\n",
       "  6  2  2  0     0  0\n",
       "  7  5  2  0     0  0\n",
       "  8  2  1  0     0  0\n",
       "  9  1  1  0     0  0\n",
       " 10  3  1  0     0  0\n",
       " 11  5  1  0     0  0\n",
       " 12  9  2  0     0  0\n",
       " 13 12  1  0     0  0\n",
       " 13 10  2  0     0  0\n",
       "M  END\n",
       "', 'smiles': 'CC(=O)OC1=CC=CC=C1C(O)=O', 'lastEdited': 1471037433000, 'atropisomerism': 'No', 'stereoCenters': 0, 'stereoComments': '', 'charge': 0, 'self': 'http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)?view=full', 'definedStereo': 0, 'digest': '8f13a762c2818d1407a79edf0fe0218dc88f7a9f', 'stereochemistry': 'ACHIRAL', 'createdBy': 'admin', 'hash': 'NNQ793F142LD', 'deprecated': False, 'mwt': 180.1574, 'id': '3d311a51-d4f2-4878-ab53-45e6d9640ae3', 'formula': 'C9H8O4', '_properties': {'href': 'http://tripod.nih.gov/ginas/app/api/v1/structures(3d311a51-d4f2-4878-ab53-45e6d9640ae3)/properties', 'count': 5}, 'lastEditedBy': 'admin', 'ezCenters': 0, 'count': 1, 'references': ['e794afad-a478-4c69-b6bd-1c7a8fe46baf', '25e72485-091c-47f8-9a00-7dd47689bf58'], 'opticalActivity': 'UNSPECIFIED', 'access': [], 'created': 1471037433000}       chemical  8911c794-5da3-4934-a683-16d98d93db97       1"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.set_option('display.max_rows', 500)\n",
    "pd.set_option('display.max_columns', 500)\n",
    "pd.set_option('display.width', 3000)\n",
    "# pd.set_option('display.max_colwidth', 50)\n",
    "\n",
    "r = requests.get(ginasURL)\n",
    "c = r.json()\n",
    "# print(json.dumps(c, indent=2))\n",
    "df = pd.DataFrame(c['content'])\n",
    "\n",
    "#df = pd.DataFrame(json_normalize(c['content']))\n",
    "\n",
    "\n",
    "\n",
    "# # df = pd.read_json(ginasURL, typ='frame', orient=\"index\")\n",
    "# # df.head(5)\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>_name</th>\n",
       "      <th>substanceClass</th>\n",
       "      <th>_self</th>\n",
       "      <th>created</th>\n",
       "      <th>approved</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ASPIRIN</td>\n",
       "      <td>chemical</td>\n",
       "      <td>http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)?view=full</td>\n",
       "      <td>2016-08-12 21:30:33</td>\n",
       "      <td>2016-08-05 21:43:37</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     _name substanceClass                                                                                              _self             created            approved\n",
       "0  ASPIRIN       chemical  http://tripod.nih.gov/ginas/app/api/v1/substances(8911c794-5da3-4934-a683-16d98d93db97)?view=full 2016-08-12 21:30:33 2016-08-05 21:43:37"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from datetime import datetime\n",
    "from datetime import date\n",
    "\n",
    "df = pd.DataFrame(c['content'])\n",
    "\n",
    "newdf = pd.DataFrame(df)\n",
    "newdf.created = newdf.created.apply(lambda d: pd.to_datetime(d / 1000, unit='s'))\n",
    "newdf.approved = newdf.approved.apply(lambda d: pd.to_datetime(d / 1000, unit='s'))\n",
    "\n",
    "newdf = newdf[['_name', 'substanceClass', '_self', 'created', 'approved']]\n",
    "\n",
    "newdf"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "---\n",
    "\n",
    "## Prototype Pipelines\n",
    "\n",
    "None available yet\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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   "codemirror_mode": {
    "name": "ipython",
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