{ "cells": [ { "cell_type": "markdown", "id": "a0e66342-662c-4ecc-ac84-c0194a07e5a7", "metadata": { "id": "a0e66342-662c-4ecc-ac84-c0194a07e5a7" }, "source": [ "# ImmPort Data - CDE Data Discovery and Interoperability" ] }, { "cell_type": "markdown", "id": "ufoXwSMhjROK", "metadata": { "id": "ufoXwSMhjROK" }, "source": [ "This tutorial demonstrates data discovery and extract, transform, and load (ETL) of ImmPort data using Common Data Elements (CDEs). We also show their interoperability with CDEs in the external [NIH CDE repository](https://cde.nlm.nih.gov/home). To learn more about the mapping of ImmPort data elements to CDEs, see [here](https://docs.immport.org/home/commondataelements/)." ] }, { "cell_type": "markdown", "id": "fspmvzAqsj6d", "metadata": { "id": "fspmvzAqsj6d" }, "source": [ "# Import required packages" ] }, { "cell_type": "code", "execution_count": 1, "id": "4ysQLb80sklW", "metadata": { "id": "4ysQLb80sklW" }, "outputs": [], "source": [ "import sys\n", "import os\n", "import requests\n", "import json\n", "import pandas as pd\n", "\n", "import warnings\n", "warnings.filterwarnings('ignore')" ] }, { "cell_type": "markdown", "id": "wfKSNfcjsrFt", "metadata": { "id": "wfKSNfcjsrFt" }, "source": [ "# Helper function to handle ImmPort API endpoint requests, with and without authentication" ] }, { "cell_type": "code", "execution_count": 2, "id": "e8ea280c-5643-43d8-8ae9-41765b43786a", "metadata": { "id": "e8ea280c-5643-43d8-8ae9-41765b43786a" }, "outputs": [], "source": [ "# Setup base URLs common to all API endpoints\n", "\n", "API_ENDPOINT_BASE_URL = \"https://www.immport.org\"\n", "DATA_QUERY_URL = API_ENDPOINT_BASE_URL + \"/data/query\"\n", "\n", "# Authentication: Use a scoped API key.\n", "# Create an API key at: https://www.immport.org/auth/api/keys\n", "\n", "# best practice is to set the API key as an environment variable outside the notebook and then use the environment variable directly\n", "# export IMMPORT_API_KEY=\"\"\n", "# IMMPORT_API_KEY = os.getenv('IMMPORT_API_KEY')\n", "\n", "# for simplicity, we will enter it here in the notebook\n", "IMMPORT_API_KEY = \"INSERT_API_KEY_HERE\"\n", "\n", "\n", "def api_data_query(endpoint, authorization=True, format=\"json\"):\n", " '''Use the Data Query API by first checking for authorization if needed, then call the API endpoint to retrieve the results.\n", "\n", " param endpoint: Data Query endpoint\n", " param authorization: Indicates if endpoint requires authorization\n", " param format: String (json, tsv)\n", "\n", " return: results or None\n", " '''\n", " headers = {}\n", " results = None\n", "\n", " if authorization:\n", " # Use API key\n", " api_key = IMMPORT_API_KEY\n", " if not api_key:\n", " print(\"ERROR: IMMPORT_API_KEY not set\", file=sys.stderr)\n", " return None\n", " bearer = \"Bearer \" + api_key\n", " if format == \"json\":\n", " headers = {\n", " 'Authorization': bearer,\n", " 'Content-Type': \"application/json\"\n", " }\n", " else:\n", " headers = {\n", " 'Authorization': bearer,\n", " 'Content-Type': \"text/plain\"\n", " }\n", "\n", " else:\n", " if format == \"json\":\n", " headers = {\n", " 'Content-Type': \"application/json\"\n", " }\n", " else:\n", " headers = {\n", " 'Content-Type': \"text/plain\"\n", " }\n", "\n", " results = requests.get(endpoint, headers=headers)\n", " if results.status_code == 200:\n", " if results is None:\n", " print(\"ERROR: API Endpoint failed to return results\", file = sys.stderr)\n", " return None\n", " if format == \"json\":\n", " return results.json()\n", " else:\n", " return results.text\n", " else:\n", " print(\"ERROR: API Status Code: \" + str(results.status_code), file = sys.stderr)\n", " return None\n" ] }, { "cell_type": "markdown", "id": "n05EjAnljLlJ", "metadata": { "id": "n05EjAnljLlJ" }, "source": [ "# Study Search\n", "\n", "## Endpoints to support text and faceted search of study and subject metadata" ] }, { "cell_type": "markdown", "id": "88ce1a1f-0a3f-4ab0-af91-73399fe6e007", "metadata": { "id": "88ce1a1f-0a3f-4ab0-af91-73399fe6e007" }, "source": [ "Let's say we are interested in research on vaccine response to the pneumonia vaccine. In particular, we are interested in whether the weight of a subject affects vaccine response.\n", "\n", "We know that subject weight has a corresponding CDE named \"Vital Signs Type\" (CDE ID: [GOr1OFJAKC](https://cde.nlm.nih.gov/deView?tinyId=GOr1OFJAKC)), where one of the permissible values is \"Weight\" (Concept Identifier: C81328). In the ImmPort database, these values are represented as \"cdeId\" = \"GOr1OFJAKC\" and \"cdePvId\" = \"C81328\", respectively. Since we are specifically interested in studies that contain data about subject weight, rather than data about other subject vital signs, we will use the permissible value concept identifier, or cdePvId, to search.\n", "\n", "\n", "We want to search for studies using \"researchFocus\" = \"Vaccine Response\", \"conditionOrDisease\" = \"Streptococcus pneumonia\" and \"cdePvId\" = \"C81328\". (Note that, if we wanted to expand our search to include data about other vital signs, we could use \"cdeId\" = \"GOr1OFJAKC\" instead of \"cdePvId\" = \"C81328\".)\n", "\n", "/api/search/study\n", "\n", "Notes:\n", "* search endpoints do not require authorization\n", "* Default pageSize = 10 (Maximum number of records to return per page), so we may need to enter a larger number to see full results\n", "\n" ] }, { "cell_type": "code", "execution_count": 4, "id": "skqiarQ1di3M", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "skqiarQ1di3M", "outputId": "7b826f53-d4c2-478d-c65a-f916b2dc3f10", "scrolled": true }, "outputs": [ { "data": { "text/plain": [ "{'took': 20,\n", " 'timed_out': False,\n", " '_shards': {'total': 5, 'successful': 5, 'skipped': 0, 'failed': 0},\n", " 'hits': {'total': {'value': 2, 'relation': 'eq'},\n", " 'max_score': 0.0,\n", " 'hits': [{'_index': 'study_mapping_common_dr68',\n", " '_id': 'SDY87',\n", " '_score': 0.0,\n", " '_source': {'clinical_trial': 'N',\n", " 'gender': ['Male'],\n", " 'ethnicity': ['Hispanic or Latino', 'Not Hispanic or Latino'],\n", " 'brief_title': 'In-Depth Characterization of Immune Responses to Pneumovax Vaccination in Healthy Subjects',\n", " 'initial_data_release_version_number': 18.0,\n", " 'program_name': ['Human Immunology Project Consortium (HIPC) RFA-AI-14-007, RFA-AI-09-040'],\n", " 'latest_data_release_version': 'DR68',\n", " 'arm_name': ['Pneumovax'],\n", " 'lab_test_panel_count': ['Blood Cell Count with Differential (90)',\n", " 'Chemistry Test (180)'],\n", " 'assay_method_count': ['Flow Cytometry (198)'],\n", " 'clinicaltrials_link': [],\n", " 'pubmed_id': [],\n", " 'age_range': '22.0-49.0',\n", " 'planned_visit_total_count': [8],\n", " 'arm_accession': ['ARM564'],\n", " 'minimum_age': ' 22.00',\n", " 'has_lab_test': 'Y',\n", " 'latest_data_release_date': '2026-09-24',\n", " 'study_size_number': 78973470,\n", " 'gender_included': 'Male',\n", " 'analyte_preferred_count': [],\n", " 'maximum_age': ' 49.00',\n", " 'research_focus': ['Vaccine Response'],\n", " 'contract_grant_external_id': ['AI089987'],\n", " 'study_accession_number': 87,\n", " 'latest_data_release_version_number': 68.0,\n", " 'race': ['Other', 'White'],\n", " 'actual_enrollment': 5,\n", " 'initial_data_release_date': '2016-03-18',\n", " 'brief_description': 'This study will measure the immune response to the Pneumovax vaccine The long-term goal is to develop improved vaccines to infectious diseases such as influenza. Blood will be collected from patients at several visits before and after vaccination. The blood will be used in a series of immunological tests to measure the strength and breadth of immune response. These assays may include T cell and B cell activation assays, microarray testing, Epimax, Epigen, and flow cytometry.',\n", " 'biosample_type': ['Other', 'Whole blood'],\n", " 'shared_subject_count': [],\n", " 'max_age': 49.0,\n", " 'study_accession': 'SDY87',\n", " 'contract_grant_name': ['Systems Analysis Vaccine Responses in Healthy and Hyporesponsive Humans'],\n", " 'study_size': '75.31 MB',\n", " 'study_pi': ['A. Karolina Palucka: Baylor Research Institute'],\n", " 'species': ['Homo sapiens'],\n", " 'initial_data_release_version': 'DR18',\n", " 'condition_or_disease': ['Streptococcus pneumonia'],\n", " 'has_assessment': 'Y',\n", " 'assessment_panel_count': ['Vitals (65)',\n", " 'Medical History (209)',\n", " 'Followup Questionnaire (51)',\n", " 'Vaccination History (13)',\n", " 'Eligibility (95)',\n", " 'End of Study (30)'],\n", " 'age_unit': 'Years',\n", " 'assay_method': ['Flow Cytometry'],\n", " 'min_age': 22.0,\n", " 'doi': '10.21430/M3AA0XR32D'}},\n", " {'_index': 'study_mapping_common_dr68',\n", " '_id': 'SDY180',\n", " '_score': 0.0,\n", " '_source': {'clinical_trial': 'N',\n", " 'gender': ['Female', 'Male'],\n", " 'ethnicity': ['Hispanic or Latino', 'Not Hispanic or Latino'],\n", " 'brief_title': 'Systems scale interactive exploration reveals quantitative and qualitative differences in response to 2009-2010 Fluzone influenza vaccine and pneumococcal vaccine',\n", " 'initial_data_release_version_number': 6.0,\n", " 'program_name': ['Human Immunology Project Consortium (HIPC) RFA-AI-14-007, RFA-AI-09-040'],\n", " 'latest_data_release_version': 'DR58',\n", " 'arm_name': ['Study group 1 2009-2010 Fluzone',\n", " 'Study group 2 2009-2010 Fluzone',\n", " 'Study group 3 2009-2010 Fluzone',\n", " 'Study group 1 Saline',\n", " 'Study group 1 Pneunomax23',\n", " 'Study group 3 Pneunomax23',\n", " 'Study group 2 Pneunomax23',\n", " 'Study group 2 Saline'],\n", " 'lab_test_panel_count': ['Blood Cell Count (1836)'],\n", " 'assay_method_count': ['Flow Cytometry (2208)',\n", " 'Hemagglutination Inhibition (66)',\n", " 'Luminex xMAP (229)',\n", " 'Nanostring (18)',\n", " 'Neutralizing Antibody Titer Assay (27)',\n", " 'Transcription profiling by array (703)',\n", " 'Virus Neutralization (89)'],\n", " 'clinicaltrials_link': [],\n", " 'pubmed_id': ['23601689'],\n", " 'age_range': '22.0-49.0',\n", " 'planned_visit_total_count': [17],\n", " 'arm_accession': ['ARM777',\n", " 'ARM775',\n", " 'ARM776',\n", " 'ARM780',\n", " 'ARM778',\n", " 'ARM774',\n", " 'ARM773',\n", " 'ARM779'],\n", " 'minimum_age': ' 22.00',\n", " 'has_lab_test': 'Y',\n", " 'latest_data_release_date': '2025-10-30',\n", " 'study_size_number': 34131077431,\n", " 'gender_included': 'Female, Male',\n", " 'analyte_preferred_count': ['CCL22 (182)',\n", " 'CSF3 (182)',\n", " 'Eotaxin (182)',\n", " 'GMCSF (182)',\n", " 'GRO (182)',\n", " 'IFNA2 (182)',\n", " 'IFNG (182)',\n", " 'IL10 (182)',\n", " 'IL12p40 (182)',\n", " 'IL12p70 (182)',\n", " 'IL13 (182)',\n", " 'IL15 (182)',\n", " 'IL17A (182)',\n", " 'IL1A (182)',\n", " 'IL1B (182)',\n", " 'IL1R1 (182)',\n", " 'IL2 (182)',\n", " 'IL2RA (182)',\n", " 'IL3 (182)',\n", " 'IL4 (182)',\n", " 'IL5 (182)',\n", " 'IL6 (182)',\n", " 'IL7 (182)',\n", " 'IL8 (182)',\n", " 'IL9 (182)',\n", " 'IP-10 (182)',\n", " 'MCP1 (182)',\n", " 'MCP3 (182)',\n", " 'MIP1A (182)',\n", " 'MIP1B (182)',\n", " 'PDGFA (182)',\n", " 'RANTES (182)',\n", " 'TGFA (182)',\n", " 'TNFA (182)',\n", " 'TNFB (182)',\n", " 'VEGFA (182)'],\n", " 'maximum_age': ' 49.00',\n", " 'research_focus': ['Vaccine Response'],\n", " 'contract_grant_external_id': ['AI089987'],\n", " 'study_accession_number': 180,\n", " 'latest_data_release_version_number': 58.0,\n", " 'race': ['Black or African American', 'White', 'Asian'],\n", " 'actual_enrollment': 46,\n", " 'initial_data_release_date': '2013-12-18',\n", " 'brief_description': 'Systems approach to study immune response to seasonal influenza and 23-valent pneumoccocal vaccination in healthy adults.',\n", " 'biosample_type': ['Serum', 'Whole blood', 'Protein'],\n", " 'shared_subject_count': [],\n", " 'max_age': 49.0,\n", " 'study_accession': 'SDY180',\n", " 'contract_grant_name': ['Systems Analysis Vaccine Responses in Healthy and Hyporesponsive Humans'],\n", " 'study_size': '31.79 GB',\n", " 'study_pi': ['A. Karolina Palucka: Baylor Reasearch Institute'],\n", " 'species': ['Homo sapiens'],\n", " 'initial_data_release_version': 'DR6',\n", " 'condition_or_disease': ['healthy',\n", " 'Streptococcus pneumonia',\n", " 'influenza'],\n", " 'has_assessment': 'N',\n", " 'assessment_panel_count': [],\n", " 'age_unit': 'Years',\n", " 'assay_method': ['Nanostring',\n", " 'Virus Neutralization',\n", " 'Hemagglutination Inhibition',\n", " 'Luminex xMAP',\n", " 'Flow Cytometry',\n", " 'Transcription profiling by array',\n", " 'Neutralizing Antibody Titer Assay'],\n", " 'min_age': 22.0,\n", " 'doi': '10.21430/M3I44H8R17'}}]},\n", " 'aggregations': {'research_focus': {'doc_count_error_upper_bound': 0,\n", " 'sum_other_doc_count': 0,\n", " 'buckets': [{'key': 'Vaccine Response', 'doc_count': 2},\n", " {'key': 'Atopy/Allergy', 'doc_count': 0},\n", " {'key': 'Autoimmune', 'doc_count': 0},\n", " {'key': 'Cardiovascular system disease', 'doc_count': 0},\n", " {'key': 'Cell Biology', 'doc_count': 0},\n", " {'key': 'Computational Modelling', 'doc_count': 0},\n", " {'key': 'Development', 'doc_count': 0},\n", " {'key': 'Epidemiology', 'doc_count': 0},\n", " {'key': 'Exposome', 'doc_count': 0},\n", " {'key': 'Immune Response', 'doc_count': 0},\n", " {'key': 'Infection Response', 'doc_count': 0},\n", " {'key': 'Method Development', 'doc_count': 0},\n", " {'key': 'Molecular Biology', 'doc_count': 0},\n", " {'key': 'No Research Focus Specified', 'doc_count': 0},\n", " {'key': 'Oncology', 'doc_count': 0},\n", " {'key': 'Other', 'doc_count': 0},\n", " {'key': 'Pregnancy', 'doc_count': 0},\n", " {'key': 'Preterm Birth', 'doc_count': 0},\n", " {'key': 'Psychopathology', 'doc_count': 0},\n", " {'key': 'Radiation Biology', 'doc_count': 0},\n", " {'key': 'Transplantation', 'doc_count': 0},\n", " {'key': 'Vaccine Development', 'doc_count': 0}]},\n", " 'clinical_trial': {'doc_count_error_upper_bound': 0,\n", " 'sum_other_doc_count': 0,\n", " 'buckets': [{'key': 'N', 'doc_count': 2}, {'key': 'Y', 'doc_count': 0}]},\n", " 'gender': {'doc_count_error_upper_bound': 0,\n", " 'sum_other_doc_count': 0,\n", " 'buckets': [{'key': 'Male', 'doc_count': 2},\n", " {'key': 'Female', 'doc_count': 1},\n", " {'key': 'Not Specified', 'doc_count': 0},\n", " {'key': 'Other', 'doc_count': 0},\n", " {'key': 'Unknown', 'doc_count': 0}]},\n", " 'race': {'doc_count_error_upper_bound': 0,\n", " 'sum_other_doc_count': 0,\n", " 'buckets': [{'key': 'White', 'doc_count': 2},\n", " {'key': 'Asian', 'doc_count': 1},\n", " {'key': 'Black or African American', 'doc_count': 1},\n", " {'key': 'Other', 'doc_count': 1},\n", " {'key': 'American Indian or Alaska Native', 'doc_count': 0},\n", " {'key': 'Multiracial', 'doc_count': 0},\n", " {'key': 'Native Hawaiian or Other Pacific Islander', 'doc_count': 0},\n", " {'key': 'Not Specified', 'doc_count': 0},\n", " {'key': 'Unknown', 'doc_count': 0}]},\n", " 'ethnicity': {'doc_count_error_upper_bound': 0,\n", " 'sum_other_doc_count': 0,\n", " 'buckets': [{'key': 'Hispanic or Latino', 'doc_count': 2},\n", " {'key': 'Not Hispanic or Latino', 'doc_count': 2},\n", " {'key': 'Not Specified', 'doc_count': 0},\n", " {'key': 'Other', 'doc_count': 0}]},\n", " 'program_name': {'doc_count_error_upper_bound': 0,\n", " 'sum_other_doc_count': 0,\n", " 'buckets': [{'key': 'Human Immunology Project Consortium (HIPC) RFA-AI-14-007, RFA-AI-09-040',\n", " 'doc_count': 2},\n", " {'key': 'Accelerating Medicines Partnership RA/SLE (AMP RA/SLE) RFA-AR-14-016',\n", " 'doc_count': 0},\n", " {'key': 'Asthma and Allergic Diseases Cooperative Research Centers',\n", " 'doc_count': 0},\n", " {'key': 'Asthma and Allergic Diseases Cooperative Research Centers (AADCRC) RFA-AI-12-006',\n", " 'doc_count': 0},\n", " {'key': 'Asthma and Allergic Diseases Cooperative Research Centers (AADCRC) RFA-AI-15-032',\n", " 'doc_count': 0},\n", " {'key': 'Asthma and Allergic Diseases Cooperative Research Centers (AADCRC) RFA-AI-16-065',\n", " 'doc_count': 0},\n", " {'key': 'Atopic Dermatitis & Vaccinia Network (ADVN)', 'doc_count': 0},\n", " {'key': 'Atopic Dermatitis Research Network (ADRN) RFA-AI-14-033',\n", " 'doc_count': 0},\n", " {'key': 'Autoimmunity Centers of Excellence (ACE) AI-12-060, AI-12-059',\n", " 'doc_count': 0},\n", " {'key': 'Autoimmunity Centers of Excellence (ACE), Basic Research Program RFA-AI-18-002',\n", " 'doc_count': 0},\n", " {'key': 'Bill and Melinda Gates Foundation (BMGF)', 'doc_count': 0},\n", " {'key': 'CEIRR Centers of Excellence for Influenza Research and Response',\n", " 'doc_count': 0},\n", " {'key': 'CIVICs Collaborative Influenza Vaccine Innovation Centers',\n", " 'doc_count': 0},\n", " {'key': 'Centers for Medical Countermeasures Against Radiation Consortium (CMCRC) RFA-AI-19-012',\n", " 'doc_count': 0},\n", " {'key': \"Children's Environmental Health and Disease Prevention Research Centers\",\n", " 'doc_count': 0},\n", " {'key': 'Clinical Islet Transplantation Consortium RFA-DK-09-501',\n", " 'doc_count': 0},\n", " {'key': 'Clinical Trials in Organ Transplantation (CTOT)', 'doc_count': 0},\n", " {'key': 'Clinical Trials in Organ Transplantation in Children (CTOT-C) RFA-AI-12-005',\n", " 'doc_count': 0},\n", " {'key': 'Clinical and Translational Science Award', 'doc_count': 0},\n", " {'key': 'Consortium for Food Allergy Research (CoFAR) RFA-AI-14-003,RFA-AI-09-039,RFA-AI-04-034',\n", " 'doc_count': 0},\n", " {'key': 'Cooperative Centers on Human Immunology RFA-AI-17-040',\n", " 'doc_count': 0},\n", " {'key': 'Cooperative Clinical Trials in Pediatric Transplantation (CCTPT)',\n", " 'doc_count': 0},\n", " {'key': 'DMID Sanaria Grant Program', 'doc_count': 0},\n", " {'key': 'Defining Genomic Influence on Gene Network Regulation',\n", " 'doc_count': 0},\n", " {'key': 'Development of Sample Sparing Assays for Monitoring Immune Responses (U24 Clinical Trial Not Allowed) RFA-AI-19-017',\n", " 'doc_count': 0},\n", " {'key': 'Development of Sample Sparing Assays for Monitoring Immune Responses RFA-AI-14-027',\n", " 'doc_count': 0},\n", " {'key': 'Enhance Applicability of Mouse Models for Translational Research (Oncology Model, OMF)',\n", " 'doc_count': 0},\n", " {'key': 'European Union’s Horizon 2020 Program', 'doc_count': 0},\n", " {'key': 'Genomics of Transplantation Cooperative Research Program (GEN) RFA-AI-10-019',\n", " 'doc_count': 0},\n", " {'key': 'HLA Region Genetics in Immune-mediated Diseases I',\n", " 'doc_count': 0},\n", " {'key': 'HLA Region Genetics in Immune-mediated Diseases II',\n", " 'doc_count': 0},\n", " {'key': 'HLA and KIR Region Genomics in Immune-Mediated Diseases RFA-AI-14-012, RFA-AI-14-013',\n", " 'doc_count': 0},\n", " {'key': 'Human Immunology Project Consortium (HIPC) RFA-AI-15-041',\n", " 'doc_count': 0},\n", " {'key': 'Human Immunology Project Consortium (HIPC) RFA-AI-20-079',\n", " 'doc_count': 0},\n", " {'key': 'ITN: Collaborative Network for Clinical Research on Immune Tolerance Network',\n", " 'doc_count': 0},\n", " {'key': 'Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations',\n", " 'doc_count': 0},\n", " {'key': 'Immune Mechanisms of Protection Against Mycobacterium tuberculosis Center (IMPAc-TB)',\n", " 'doc_count': 0},\n", " {'key': 'Immunity in Neonates and Infants (U01) RFA-AI-16-001',\n", " 'doc_count': 0},\n", " {'key': 'Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC)',\n", " 'doc_count': 0},\n", " {'key': 'Inner City Asthma Consortium (ICAC) RFA-AI-13-036',\n", " 'doc_count': 0},\n", " {'key': 'La Jolla Institute for Immunology CMI Flu', 'doc_count': 0},\n", " {'key': 'Lung Diseases Research', 'doc_count': 0},\n", " {'key': 'March of Dimes', 'doc_count': 0},\n", " {'key': 'Mechanisms of Immune Protection from TB among HIV-infected Individuals (R01) RFA-AI-14-072',\n", " 'doc_count': 0},\n", " {'key': 'Mentored Patient-Oriented Research Career Development Award (Parent K23)',\n", " 'doc_count': 0},\n", " {'key': 'Modeling Immunity for Biodefense I', 'doc_count': 0},\n", " {'key': 'Modeling Immunity for Biodefense II', 'doc_count': 0},\n", " {'key': 'Modeling Immunity for Biodefense RFA-AI-14-028', 'doc_count': 0},\n", " {'key': 'Molecular Transducers of Physical Activity Consortium (MoTrPAC)',\n", " 'doc_count': 0},\n", " {'key': 'NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS)',\n", " 'doc_count': 0},\n", " {'key': 'NIAID Investigator Initiated Program PAR-20-072', 'doc_count': 0},\n", " {'key': 'NIAID Investigator Initiated Program Project Applications (P01) PAR-16-413, PAR-13-254',\n", " 'doc_count': 0},\n", " {'key': 'NIAID Laboratory of Immunogenetics', 'doc_count': 0},\n", " {'key': 'NIAID Program Research Project Grant (Parent R01)',\n", " 'doc_count': 0},\n", " {'key': 'NIAID SBIR Phase II Clinical Trial Implementation Cooperative Agreement (U44)',\n", " 'doc_count': 0},\n", " {'key': 'NIAID Vaccine Research Center (VRC)', 'doc_count': 0},\n", " {'key': 'NIAMS Rheumatic Diseases Research Resource-based Centers (P30) 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\n" ], "text/plain": [ " _index _id _score clinical_trial gender \\\n", "0 study_mapping_common_dr68 SDY87 0 N [Male] \n", "1 study_mapping_common_dr68 SDY180 0 N [Female, Male] \n", "\n", " ethnicity \\\n", "0 [Hispanic or Latino, Not Hispanic or Latino] \n", "1 [Hispanic or Latino, Not Hispanic or Latino] \n", "\n", " brief_title \\\n", "0 In-Depth Characterization of Immune Responses ... \n", "1 Systems scale interactive exploration reveals ... \n", "\n", " initial_data_release_version_number \\\n", "0 18.0 \n", "1 6.0 \n", "\n", " program_name \\\n", "0 [Human Immunology Project Consortium (HIPC) RF... \n", "1 [Human Immunology Project Consortium (HIPC) RF... \n", "\n", " latest_data_release_version ... \\\n", "0 DR68 ... \n", "1 DR58 ... \n", "\n", " study_pi species \\\n", "0 [A. Karolina Palucka: Baylor Research Institute] [Homo sapiens] \n", "1 [A. Karolina Palucka: Baylor Reasearch Institute] [Homo sapiens] \n", "\n", " initial_data_release_version condition_or_disease \\\n", "0 DR18 [Streptococcus pneumonia] \n", "1 DR6 [healthy, Streptococcus pneumonia, influenza] \n", "\n", " has_assessment assessment_panel_count age_unit \\\n", "0 Y [Vitals (65), Medical History (209), Followup ... Years \n", "1 N [] Years \n", "\n", " assay_method min_age \\\n", "0 [Flow Cytometry] 22.0 \n", "1 [Nanostring, Virus Neutralization, Hemagglutin... 22.0 \n", "\n", " doi \n", "0 10.21430/M3AA0XR32D \n", "1 10.21430/M3I44H8R17 \n", "\n", "[2 rows x 49 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Normalize the nested column\n", "source_expanded = pd.json_normalize(df['_source'])\n", "\n", "# Join it back to the original DataFrame and drop the old column\n", "df_final = df.drop(columns=['_source']).join(source_expanded)\n", "df_final.head()" ] }, { "cell_type": "markdown", "id": "GqPPAv_EjViF", "metadata": { "id": "GqPPAv_EjViF" }, "source": [ "# Study Data\n", "\n", "## Endpoints to support the retrieval of study data for a single study including subject, experiment, etc" ] }, { "cell_type": "markdown", "id": "c2b06a52-aeef-4cc8-854e-0b96578c7ad9", "metadata": { "id": "c2b06a52-aeef-4cc8-854e-0b96578c7ad9", "tags": [] }, "source": [ "There are two ImmPort studies that matched our search.\n", "\n", "Let's find out more about this first study, SDY87. \n", "
\n", "\n", "Start with basic study information.\n", "\n", "/api/study/{studyAccession}" ] }, { "cell_type": "code", "execution_count": 12, "id": "fc4f068e-a0fe-4f18-bda7-01b5bf476a83", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "fc4f068e-a0fe-4f18-bda7-01b5bf476a83", "outputId": "b3019dcd-c847-44a5-daa2-f144d5e0df56", "scrolled": true }, "outputs": [ { "data": { "text/plain": [ "[{'studyAccession': 'SDY87',\n", " 'actualCompletionDate': None,\n", " 'actualEnrollment': 5,\n", " 'actualStartDate': None,\n", " 'ageUnit': 'Years',\n", " 'briefDescription': 'This study will measure the immune response to the Pneumovax vaccine The long-term goal is to develop improved vaccines to infectious diseases such as influenza. Blood will be collected from patients at several visits before and after vaccination. The blood will be used in a series of immunological tests to measure the strength and breadth of immune response. These assays may include T cell and B cell activation assays, microarray testing, Epimax, Epigen, and flow cytometry.',\n", " 'briefTitle': 'In-Depth Characterization of Immune Responses to Pneumovax Vaccination in Healthy Subjects',\n", " 'clinicalTrial': 'N',\n", " 'description': 'This study will measure the immune response to the Pneumovax vaccine The long-term goal is to develop improved vaccines to infectious diseases such as influenza. Blood will be collected from patients at several visits before and after vaccination. The blood will be used in a series of immunological tests to measure the strength and breadth of immune response. These assays may include T cell and B cell activation assays, microarray testing, Epimax, Epigen, and flow cytometry.',\n", " 'dclId': 2,\n", " 'doi': '10.21430/M3AA0XR32D',\n", " 'endpoints': 'N/A',\n", " 'genderIncluded': 'Male',\n", " 'hypothesis': 'That immune responses can be measured longitudinally after vaccination and that the information gained may be useful for developing novel vaccines.',\n", " 'initialDataReleaseDate': '2016-03-18',\n", " 'initialDataReleaseVersion': 'DR18',\n", " 'interventionAgent': '23PPV Pneumovax (Merck)',\n", " 'latestDataReleaseDate': '2026-09-24',\n", " 'latestDataReleaseVersion': 'DR68',\n", " 'maximumAge': ' 49.00',\n", " 'minimumAge': ' 22.00',\n", " 'objectives': 'To measure immune responses to vaccination with Pneumovax vaccine in healthy adult subjects.',\n", " 'officialTitle': 'In-Depth Characterization of Immune Responses to Pneumovax Vaccination in Healthy Subjects',\n", " 'sharedStudy': 'Y',\n", " 'sponsoringOrganization': 'NIAID',\n", " 'targetEnrollment': None}]" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "endpoint = DATA_QUERY_URL + \"/api/study/SDY87\"\n", "results = api_data_query(endpoint)\n", "results" ] }, { "cell_type": "markdown", "id": "qIA_gcRerJ8G", "metadata": { "id": "qIA_gcRerJ8G" }, "source": [ "Now let's see if there are other CDEs associated with the data for this study." ] }, { "cell_type": "markdown", "id": "6a8tofZZoENQ", "metadata": { "id": "6a8tofZZoENQ" }, "source": [ "Retrieve study CDEs\n", "\n", "/api/study/cde/{studyAccession}" ] }, { "cell_type": "code", "execution_count": 7, "id": "RjaH7VSrnHG6", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "RjaH7VSrnHG6", "outputId": "5dd04d29-9232-4caa-99a4-f388e393dd60", "scrolled": true }, "outputs": [ { "data": { "text/plain": [ "[{'study2CdeMappingId': 12586,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'fmMMaUGpKS',\n", " 'name': 'Age',\n", " 'cdePvId': None,\n", " 'pvLabel': None,\n", " 'immportTableName': 'arm_2_subject',\n", " 'immportColumnName': 'min_subject_age',\n", " 'immportColumnValue': None},\n", " {'study2CdeMappingId': 12587,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'FiTk9B5lx',\n", " 'name': 'Study Identifier',\n", " 'cdePvId': None,\n", " 'pvLabel': None,\n", " 'immportTableName': 'study',\n", " 'immportColumnName': 'study_accession',\n", " 'immportColumnValue': 'SDY87'},\n", " {'study2CdeMappingId': 12588,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GOr1OFJAKC',\n", " 'name': 'Vital Signs Type',\n", " 'cdePvId': 'C25298',\n", " 'pvLabel': 'Systolic Blood Pressure',\n", " 'immportTableName': 'assessment_component',\n", " 'immportColumnName': 'name_preferred',\n", " 'immportColumnValue': 'Systolic Blood Pressure'},\n", " {'study2CdeMappingId': 12589,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GOr1OFJAKC',\n", " 'name': 'Vital Signs Type',\n", " 'cdePvId': 'C25299',\n", " 'pvLabel': 'Diastolic Blood Pressure',\n", " 'immportTableName': 'assessment_component',\n", " 'immportColumnName': 'name_preferred',\n", " 'immportColumnValue': 'Diastolic Blood Pressure'},\n", " {'study2CdeMappingId': 12590,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GOr1OFJAKC',\n", " 'name': 'Vital Signs Type',\n", " 'cdePvId': 'C49677',\n", " 'pvLabel': 'Heart Rate',\n", " 'immportTableName': 'assessment_component',\n", " 'immportColumnName': 'name_preferred',\n", " 'immportColumnValue': 'Heart Rate'},\n", " {'study2CdeMappingId': 12591,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GOr1OFJAKC',\n", " 'name': 'Vital Signs Type',\n", " 'cdePvId': 'C49678',\n", " 'pvLabel': 'Respiratory Rate',\n", " 'immportTableName': 'assessment_component',\n", " 'immportColumnName': 'name_preferred',\n", " 'immportColumnValue': 'Respiration Rate'},\n", " {'study2CdeMappingId': 12592,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GOr1OFJAKC',\n", " 'name': 'Vital Signs Type',\n", " 'cdePvId': 'C81328',\n", " 'pvLabel': 'Weight',\n", " 'immportTableName': 'assessment_component',\n", " 'immportColumnName': 'name_preferred',\n", " 'immportColumnValue': 'Weight'},\n", " {'study2CdeMappingId': 12593,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GOr1OFJAKC',\n", " 'name': 'Vital Signs Type',\n", " 'cdePvId': 'C164634',\n", " 'pvLabel': 'Height',\n", " 'immportTableName': 'assessment_component',\n", " 'immportColumnName': 'name_preferred',\n", " 'immportColumnValue': 'Height'},\n", " {'study2CdeMappingId': 12594,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'Aguk0xu_dB',\n", " 'name': 'Subject ID',\n", " 'cdePvId': None,\n", " 'pvLabel': None,\n", " 'immportTableName': 'subject',\n", " 'immportColumnName': 'subject_accession',\n", " 'immportColumnValue': 'Subjects Exists'},\n", " {'study2CdeMappingId': 12595,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'PDjBiGXjO',\n", " 'name': 'Age',\n", " 'cdePvId': None,\n", " 'pvLabel': None,\n", " 'immportTableName': 'arm_2_subject',\n", " 'immportColumnName': 'min_subject_age',\n", " 'immportColumnValue': None},\n", " {'study2CdeMappingId': 12596,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 's0OB4q7Pxk',\n", " 'name': 'Age Units',\n", " 'cdePvId': 'C29848',\n", " 'pvLabel': 'Years',\n", " 'immportTableName': 'arm_2_subject',\n", " 'immportColumnName': 'age_unit',\n", " 'immportColumnValue': 'Years'},\n", " {'study2CdeMappingId': 12597,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'GNVoEdFQR0',\n", " 'name': 'Age Units',\n", " 'cdePvId': 'C29848',\n", " 'pvLabel': 'Years',\n", " 'immportTableName': 'arm_2_subject',\n", " 'immportColumnName': 'age_unit',\n", " 'immportColumnValue': 'Years'},\n", " {'study2CdeMappingId': 12598,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'sznvIp17G',\n", " 'name': 'Unique ID',\n", " 'cdePvId': None,\n", " 'pvLabel': None,\n", " 'immportTableName': 'subject',\n", " 'immportColumnName': 'subject_accession',\n", " 'immportColumnValue': 'Subjects Exists'},\n", " {'study2CdeMappingId': 12599,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'rGEh0ckdmr',\n", " 'name': 'Sex at Birth',\n", " 'cdePvId': 'C20197',\n", " 'pvLabel': 'Male',\n", " 'immportTableName': 'subject',\n", " 'immportColumnName': 'sex',\n", " 'immportColumnValue': 'Male'},\n", " {'study2CdeMappingId': 12600,\n", " 'studyAccession': 'SDY87',\n", " 'cdeId': 'Fakc6Jy2x',\n", " 'name': 'Race',\n", " 'cdePvId': 'C41261',\n", " 'pvLabel': 'White',\n", " 'immportTableName': 'subject',\n", " 'immportColumnName': 'race',\n", " 'immportColumnValue': 'White'}]" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "endpoint = DATA_QUERY_URL + \"/api/study/cde/SDY87\"\n", "results = api_data_query(endpoint)\n", "results" ] }, { "cell_type": "code", "execution_count": 8, "id": "sI37efJKlPjs", "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 520 }, "id": "sI37efJKlPjs", "outputId": "a6b3f9d8-f7bd-454e-d209-50bae0a1b8fe" }, "outputs": [ { "data": { "application/vnd.google.colaboratory.intrinsic+json": { "summary": "{\n \"name\": \"df_immport_study_cde_sdy87\",\n \"rows\": 15,\n \"fields\": [\n {\n \"column\": \"study2CdeMappingId\",\n \"properties\": {\n \"dtype\": \"number\",\n \"std\": 4,\n \"min\": 12586,\n \"max\": 12600,\n \"num_unique_values\": 15,\n \"samples\": [\n 12595,\n 12597,\n 12586\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"studyAccession\",\n \"properties\": {\n \"dtype\": \"category\",\n \"num_unique_values\": 1,\n \"samples\": [\n \"SDY87\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"cdeId\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 10,\n \"samples\": [\n \"rGEh0ckdmr\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"name\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 8,\n \"samples\": [\n \"Study Identifier\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"cdePvId\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 9,\n \"samples\": [\n \"C20197\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"pvLabel\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 9,\n \"samples\": [\n \"Male\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"immportTableName\",\n \"properties\": {\n \"dtype\": \"category\",\n \"num_unique_values\": 4,\n \"samples\": [\n \"study\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"immportColumnName\",\n \"properties\": {\n \"dtype\": \"category\",\n \"num_unique_values\": 7,\n \"samples\": [\n \"min_subject_age\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"immportColumnValue\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 11,\n \"samples\": [\n \"Weight\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n }\n ]\n}", "type": "dataframe", "variable_name": "df_immport_study_cde_sdy87" }, "text/html": [ "\n", "
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study2CdeMappingIdstudyAccessioncdeIdnamecdePvIdpvLabelimmportTableNameimmportColumnNameimmportColumnValue
012586SDY87fmMMaUGpKSAgeNoneNonearm_2_subjectmin_subject_ageNone
112587SDY87FiTk9B5lxStudy IdentifierNoneNonestudystudy_accessionSDY87
212588SDY87GOr1OFJAKCVital Signs TypeC25298Systolic Blood Pressureassessment_componentname_preferredSystolic Blood Pressure
312589SDY87GOr1OFJAKCVital Signs TypeC25299Diastolic Blood Pressureassessment_componentname_preferredDiastolic Blood Pressure
412590SDY87GOr1OFJAKCVital Signs TypeC49677Heart Rateassessment_componentname_preferredHeart Rate
512591SDY87GOr1OFJAKCVital Signs TypeC49678Respiratory Rateassessment_componentname_preferredRespiration Rate
612592SDY87GOr1OFJAKCVital Signs TypeC81328Weightassessment_componentname_preferredWeight
712593SDY87GOr1OFJAKCVital Signs TypeC164634Heightassessment_componentname_preferredHeight
812594SDY87Aguk0xu_dBSubject IDNoneNonesubjectsubject_accessionSubjects Exists
912595SDY87PDjBiGXjOAgeNoneNonearm_2_subjectmin_subject_ageNone
1012596SDY87s0OB4q7PxkAge UnitsC29848Yearsarm_2_subjectage_unitYears
1112597SDY87GNVoEdFQR0Age UnitsC29848Yearsarm_2_subjectage_unitYears
1212598SDY87sznvIp17GUnique IDNoneNonesubjectsubject_accessionSubjects Exists
1312599SDY87rGEh0ckdmrSex at BirthC20197MalesubjectsexMale
1412600SDY87Fakc6Jy2xRaceC41261WhitesubjectraceWhite
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\n" ], "text/plain": [ " study2CdeMappingId studyAccession cdeId name cdePvId \\\n", "0 12586 SDY87 fmMMaUGpKS Age None \n", "1 12587 SDY87 FiTk9B5lx Study Identifier None \n", "2 12588 SDY87 GOr1OFJAKC Vital Signs Type C25298 \n", "3 12589 SDY87 GOr1OFJAKC Vital Signs Type C25299 \n", "4 12590 SDY87 GOr1OFJAKC Vital Signs Type C49677 \n", "5 12591 SDY87 GOr1OFJAKC Vital Signs Type C49678 \n", "6 12592 SDY87 GOr1OFJAKC Vital Signs Type C81328 \n", "7 12593 SDY87 GOr1OFJAKC Vital Signs Type C164634 \n", "8 12594 SDY87 Aguk0xu_dB Subject ID None \n", "9 12595 SDY87 PDjBiGXjO Age None \n", "10 12596 SDY87 s0OB4q7Pxk Age Units C29848 \n", "11 12597 SDY87 GNVoEdFQR0 Age Units C29848 \n", "12 12598 SDY87 sznvIp17G Unique ID None \n", "13 12599 SDY87 rGEh0ckdmr Sex at Birth C20197 \n", "14 12600 SDY87 Fakc6Jy2x Race C41261 \n", "\n", " pvLabel immportTableName immportColumnName \\\n", "0 None arm_2_subject min_subject_age \n", "1 None study study_accession \n", "2 Systolic Blood Pressure assessment_component name_preferred \n", "3 Diastolic Blood Pressure assessment_component name_preferred \n", "4 Heart Rate assessment_component name_preferred \n", "5 Respiratory Rate assessment_component name_preferred \n", "6 Weight assessment_component name_preferred \n", "7 Height assessment_component name_preferred \n", "8 None subject subject_accession \n", "9 None arm_2_subject min_subject_age \n", "10 Years arm_2_subject age_unit \n", "11 Years arm_2_subject age_unit \n", "12 None subject subject_accession \n", "13 Male subject sex \n", "14 White subject race \n", "\n", " immportColumnValue \n", "0 None \n", "1 SDY87 \n", "2 Systolic Blood Pressure \n", "3 Diastolic Blood Pressure \n", "4 Heart Rate \n", "5 Respiration Rate \n", "6 Weight \n", "7 Height \n", "8 Subjects Exists \n", "9 None \n", "10 Years \n", "11 Years \n", "12 Subjects Exists \n", "13 Male \n", "14 White " ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df_immport_study_cde_sdy87 = pd.read_json(json.dumps(results))\n", "df_immport_study_cde_sdy87" ] }, { "cell_type": "markdown", "id": "np_nEuMbaYer", "metadata": { "id": "np_nEuMbaYer" }, "source": [ "We can see that this study includes multiple other CDEs beyond the one we were initially interested in, if we'd like to explore them further." ] }, { "cell_type": "markdown", "id": "yMFwSNMNjgyz", "metadata": { "id": "yMFwSNMNjgyz" }, "source": [ "# Join with data from another repository\n", "\n", "## Use the CDE ID to pull additional information about the CDE of interest (Vital Signs Type) from the NIH CDE repository." ] }, { "cell_type": "code", "execution_count": 12, "id": "14SxY8YtpSf7", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "collapsed": true, "id": "14SxY8YtpSf7", "jupyter": { "outputs_hidden": true }, "outputId": "ed4021fc-832f-4046-c76e-f7bd948ef745" }, "outputs": [ { "data": { "text/plain": [ "{'stewardOrg': {'name': 'Project 5'},\n", " 'createdBy': {'username': 'NIH CDE Repository Team'},\n", " 'property': {'concepts': []},\n", " 'dataElementConcept': {'concepts': [{'name': 'Vital Signs Measurement',\n", " 'origin': 'NCI Thesaurus',\n", " 'originId': 'C49672'},\n", " {'name': 'Type', 'origin': 'NCI Thesaurus', 'originId': 'C25284'}]},\n", " 'objectClass': {'concepts': []},\n", " 'valueDomain': {'identifiers': [],\n", " 'ids': [],\n", " 'datatype': 'Value List',\n", " 'permissibleValues': [{'permissibleValue': 'Systolic blood pressure',\n", " 'valueMeaningDefinition': 'The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart C25298',\n", " 'conceptId': 'C25298',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Diastolic blood pressure',\n", " 'valueMeaningDefinition': 'The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling C25299',\n", " 'conceptId': 'C25299',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Heart rate',\n", " 'valueMeaningDefinition': 'The number of heartbeats per unit of time, usually expressed as beats per minute. C49677',\n", " 'conceptId': 'C49677',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Respiratory rate',\n", " 'valueMeaningDefinition': 'The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute C49678',\n", " 'conceptId': 'C49678',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Body temperature',\n", " 'valueMeaningDefinition': 'A measurement of the temperature of the body C174446',\n", " 'conceptId': 'C174446',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Weight',\n", " 'valueMeaningDefinition': 'The weight of a subject C81328',\n", " 'conceptId': 'C81328',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Height',\n", " 'valueMeaningDefinition': 'The vertical measurement or distance from the base to the top of a subject or participant C164634',\n", " 'conceptId': 'C164634',\n", " 'conceptSource': 'NCI Thesaurus'},\n", " {'permissibleValue': 'Oxygen Saturation',\n", " 'valueMeaningDefinition': 'The measurement of the ratio of oxygenated hemoglobin to total hemoglobin in the blood C60832',\n", " 'conceptId': 'C60832',\n", " 'conceptSource': 'NCI Thesaurus'}]},\n", " '_id': '62432240ad66cd31638d50d4',\n", " 'elementType': 'cde',\n", " 'nihEndorsed': True,\n", " 'tinyId': 'GOr1OFJAKC',\n", " 'designations': [{'designation': 'Vital Signs Type',\n", " 'tags': [],\n", " 'sources': ['Project 5']},\n", " {'designation': 'Vital Sign Name',\n", " 'tags': ['Preferred Question Text'],\n", " 'sources': ['Project 5']}],\n", " 'definitions': [{'definition': \"A textual description of a person's vital signs measurement category.\",\n", " 'tags': [],\n", " 'sources': ['Project 5']}],\n", " 'sources': [{'sourceName': 'Project 5',\n", " 'imported': '2022-03-29T15:13:59.754Z'}],\n", " 'created': '2022-03-29T15:13:59.754Z',\n", " 'imported': '2022-03-29T15:13:59.754Z',\n", " 'changeNote': 'Update Name Source',\n", " 'registrationState': {'registrationStatus': 'Qualified',\n", " 'administrativeStatus': 'Org Approve'},\n", " 'classification': [{'stewardOrg': {'name': 'Project 5'},\n", " 'elements': [{'elements': [{'elements': [], 'name': 'Tier 1'}],\n", " 'name': 'Project 5 (COVID-19)'}]}],\n", " 'properties': [{'key': 'Tags/Keywords',\n", " 'value': 'Person, Diagnosis, Vital Signs',\n", " 'source': 'Project 5'},\n", " {'key': 'Project 5 Source', 'value': 'FDA, CDC', 'source': 'Project 5'}],\n", " 'ids': [],\n", " 'attachments': [],\n", " 'history': [],\n", " 'archived': False,\n", " 'views': 4473,\n", " 'referenceDocuments': [],\n", " 'dataSets': [],\n", " 'derivationRules': [],\n", " '__v': 30514,\n", " 'partOfBundles': ['w_QQb9XUq']}" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cdeId = \"GOr1OFJAKC\"\n", "\n", "base_url = 'https://cde.nlm.nih.gov/api'\n", "\n", "search_url = base_url + \"/de/\" + cdeId\n", "\n", "headers= {\n", " 'accept': 'application/json',\n", " 'Content-Type': 'application/json'\n", "}\n", "\n", "r = requests.get(search_url, headers=headers)\n", "results = r.json()\n", "results" ] }, { "cell_type": "code", "execution_count": 13, "id": "vKz7qWBUxgqd", "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 182 }, "id": "vKz7qWBUxgqd", "outputId": "62116a7f-fdb2-4b77-cadc-36e893f016aa" }, "outputs": [ { "data": { "application/vnd.google.colaboratory.intrinsic+json": { "type": "dataframe", "variable_name": "df_nih_cde" }, "text/html": [ "\n", "
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062432240ad66cd31638d50d4cdeTrueGOr1OFJAKC[{'designation': 'Vital Signs Type', 'tags': [...[{'definition': 'A textual description of a pe...[{'sourceName': 'Project 5', 'imported': '2022...2022-03-29T15:13:59.754Z2022-03-29T15:13:59.754ZUpdate Name Source...NIH CDE Repository Team[][{'name': 'Vital Signs Measurement', 'origin':...[][][]Value List[{'permissibleValue': 'Systolic blood pressure...QualifiedOrg Approve
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\n" ], "text/plain": [ " _id elementType nihEndorsed tinyId \\\n", "0 62432240ad66cd31638d50d4 cde True GOr1OFJAKC \n", "\n", " designations \\\n", "0 [{'designation': 'Vital Signs Type', 'tags': [... \n", "\n", " definitions \\\n", "0 [{'definition': 'A textual description of a pe... \n", "\n", " sources \\\n", "0 [{'sourceName': 'Project 5', 'imported': '2022... \n", "\n", " created imported changeNote \\\n", "0 2022-03-29T15:13:59.754Z 2022-03-29T15:13:59.754Z Update Name Source \n", "\n", " ... createdBy.username property.concepts \\\n", "0 ... NIH CDE Repository Team [] \n", "\n", " dataElementConcept.concepts objectClass.concepts \\\n", "0 [{'name': 'Vital Signs Measurement', 'origin':... [] \n", "\n", " valueDomain.identifiers valueDomain.ids valueDomain.datatype \\\n", "0 [] [] Value List \n", "\n", " valueDomain.permissibleValues \\\n", "0 [{'permissibleValue': 'Systolic blood pressure... \n", "\n", " registrationState.registrationStatus registrationState.administrativeStatus \n", "0 Qualified Org Approve \n", "\n", "[1 rows x 33 columns]" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Normalize the JSON\n", "df_nih_cde = pd.json_normalize(results)\n", "df_nih_cde" ] }, { "cell_type": "code", "execution_count": 14, "id": "QOmXHAoBzE_y", "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 165 }, "id": "QOmXHAoBzE_y", "outputId": "1f18d941-20f1-40a2-edad-3d3666d4554a" }, "outputs": [ { "data": { "application/vnd.google.colaboratory.intrinsic+json": { "type": "dataframe", "variable_name": "df_merged" }, "text/html": [ "\n", "
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study2CdeMappingIdstudyAccessioncdeIdnamecdePvIdpvLabelimmportTableNameimmportColumnNameimmportColumnValue_id...createdBy.usernameproperty.conceptsdataElementConcept.conceptsobjectClass.conceptsvalueDomain.identifiersvalueDomain.idsvalueDomain.datatypevalueDomain.permissibleValuesregistrationState.registrationStatusregistrationState.administrativeStatus
012592SDY87GOr1OFJAKCVital Signs TypeC81328Weightassessment_componentname_preferredWeight62432240ad66cd31638d50d4...NIH CDE Repository Team[][{'name': 'Vital Signs Measurement', 'origin':...[][][]Value List[{'permissibleValue': 'Systolic blood pressure...QualifiedOrg Approve
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\n" ], "text/plain": [ " study2CdeMappingId studyAccession cdeId name cdePvId \\\n", "0 12592 SDY87 GOr1OFJAKC Vital Signs Type C81328 \n", "\n", " pvLabel immportTableName immportColumnName immportColumnValue \\\n", "0 Weight assessment_component name_preferred Weight \n", "\n", " _id ... createdBy.username property.concepts \\\n", "0 62432240ad66cd31638d50d4 ... NIH CDE Repository Team [] \n", "\n", " dataElementConcept.concepts objectClass.concepts \\\n", "0 [{'name': 'Vital Signs Measurement', 'origin':... [] \n", "\n", " valueDomain.identifiers valueDomain.ids valueDomain.datatype \\\n", "0 [] [] Value List \n", "\n", " valueDomain.permissibleValues \\\n", "0 [{'permissibleValue': 'Systolic blood pressure... \n", "\n", " registrationState.registrationStatus registrationState.administrativeStatus \n", "0 Qualified Org Approve \n", "\n", "[1 rows x 42 columns]" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# filter the data from the ImmPort API to include only the row that corresponds to the CDE permissible value we are interested in (Weight) and join it with the results from the CDE API\n", "df_merged = pd.merge(df_immport_study_cde_sdy87[df_immport_study_cde_sdy87[\"cdePvId\"] == \"C81328\"], df_nih_cde, left_on='cdeId', right_on='tinyId', how='inner')\n", "df_merged" ] }, { "cell_type": "markdown", "id": "2SclYY80Yzmq", "metadata": { "id": "2SclYY80Yzmq" }, "source": [ "We can see that the NIH CDE repository API results provide us with lots of additional metadata about the CDE of interest. Perhaps we are interested in getting a list of all possbile permissible values for this CDE to investigate what other possible vital sign type values exist." ] }, { "cell_type": "code", "execution_count": 38, "id": "xmwpkf4t1DaK", "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 300 }, "id": "xmwpkf4t1DaK", "outputId": "147cd901-dd73-4459-b1ab-0889c84370b6" }, "outputs": [ { "data": { "application/vnd.google.colaboratory.intrinsic+json": { "summary": "{\n \"name\": \"pd\",\n \"rows\": 8,\n \"fields\": [\n {\n \"column\": \"permissibleValue\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 8,\n \"samples\": [\n \"Diastolic blood pressure\",\n \"Weight\",\n \"Systolic blood pressure\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"valueMeaningDefinition\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 8,\n \"samples\": [\n \"The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling C25299\",\n \"The weight of a subject C81328\",\n \"The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart C25298\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"conceptId\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 8,\n \"samples\": [\n \"C25299\",\n \"C81328\",\n \"C25298\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n },\n {\n \"column\": \"conceptSource\",\n \"properties\": {\n \"dtype\": \"category\",\n \"num_unique_values\": 1,\n \"samples\": [\n \"NCI Thesaurus\"\n ],\n \"semantic_type\": \"\",\n \"description\": \"\"\n }\n }\n ]\n}", "type": "dataframe" }, "text/html": [ "\n", "
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permissibleValuevalueMeaningDefinitionconceptIdconceptSource
0Systolic blood pressureThe maximum pressure exerted into the systemic...C25298NCI Thesaurus
1Diastolic blood pressureThe minimum pressure exerted into the systemic...C25299NCI Thesaurus
2Heart rateThe number of heartbeats per unit of time, usu...C49677NCI Thesaurus
3Respiratory rateThe rate of breathing (inhalation and exhalati...C49678NCI Thesaurus
4Body temperatureA measurement of the temperature of the body C...C174446NCI Thesaurus
5WeightThe weight of a subject C81328C81328NCI Thesaurus
6HeightThe vertical measurement or distance from the ...C164634NCI Thesaurus
7Oxygen SaturationThe measurement of the ratio of oxygenated hem...C60832NCI Thesaurus
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\n" ], "text/plain": [ " permissibleValue \\\n", "0 Systolic blood pressure \n", "1 Diastolic blood pressure \n", "2 Heart rate \n", "3 Respiratory rate \n", "4 Body temperature \n", "5 Weight \n", "6 Height \n", "7 Oxygen Saturation \n", "\n", " valueMeaningDefinition conceptId conceptSource \n", "0 The maximum pressure exerted into the systemic... C25298 NCI Thesaurus \n", "1 The minimum pressure exerted into the systemic... C25299 NCI Thesaurus \n", "2 The number of heartbeats per unit of time, usu... C49677 NCI Thesaurus \n", "3 The rate of breathing (inhalation and exhalati... C49678 NCI Thesaurus \n", "4 A measurement of the temperature of the body C... C174446 NCI Thesaurus \n", "5 The weight of a subject C81328 C81328 NCI Thesaurus \n", "6 The vertical measurement or distance from the ... C164634 NCI Thesaurus \n", "7 The measurement of the ratio of oxygenated hem... C60832 NCI Thesaurus " ] }, "execution_count": 38, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pd.read_json(json.dumps(df_merged[\"valueDomain.permissibleValues\"][0]))" ] }, { "cell_type": "markdown", "id": "q49TIyOL1aWV", "metadata": { "id": "q49TIyOL1aWV" }, "source": [ "Now we can see all the possible permissible values for this CDE from the NIH CDE repository metadata. We can see that each of these concepts comes from the NCI Thesaurus and that there exists a corresponding definition and concept ID for each of the permissible values." ] }, { "cell_type": "markdown", "id": "AJTPpWgDZbx1", "metadata": { "id": "AJTPpWgDZbx1" }, "source": [ "# Next Steps\n", "\n", "This same approach can be utilized to search for other CDE data within ImmPort and combine the results with data from other repositories that incorporate the use of CDEs, as adoption of CDEs increases." ] }, { "cell_type": "code", "execution_count": null, "id": "ehuilqSLZx5u", "metadata": { "id": "ehuilqSLZx5u" }, "outputs": [], "source": [] } ], "metadata": { "colab": { "provenance": [] }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.13.12" } }, "nbformat": 4, "nbformat_minor": 5 }