jupyter/Notebook02_studies.ipynb

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    "## FHIR for Research Workshop - Exercise 2\n",
    "\n",
    "## Learning Objectives and Key Concepts\n",
    "\n",
    "In this exercise, you will: \n",
    "\n",
    "- Apply Knowledge from previous exercises\n",
    "- Understand dbGaP extensions to ResearchStudy\n",
    "- Query for dbGaP asthma studies by title\n",
    "- Query for dbGaP studies by codes\n",
    "\n",
    "## Identify dbGaP Asthma datasets\n",
    "For this exercise we will search for studies/datasets in dbGaP related to asthma. \n",
    "\n",
    "## Motivation/Purpose\n",
    "To identify asthma studies from which data may be aggregated. Consent codes will be listed to see if the data from different studies may be used for a particular research purpose\n",
    "\n",
    " ### Icons in this Guide\n",
    " 📘 A link to a useful external reference related to the section the icon appears in  \n",
    "\n",
    " 🖐 A hands-on section where you will code something or interact with the server  \n",
    " \n",
    " \n",
    "Acknowledging use of code snippets from [NIH FHIR training](https://github.com/NIH-ODSS/fhir-exercises/tree/main/Python) Exercise 0.\n",
    "\n",
    "## Step 1:  Set up a FHIR Client\n",
    "\n",
    "Obtain our NCBI API Key and set up a client to make requests, handle pagination etc."
   ]
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   "source": [
    "import json\n",
    "import os\n",
    "from dbgap_fhir import DbGapFHIR\n",
    "import pandas as pd\n",
    "\n",
    "FHIR_SERVER = \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1\"\n",
    "API_KEY_PATH = \"~/.keys/ncbi_api_key.txt\"\n",
    "\n",
    "with open(os.path.expanduser(API_KEY_PATH)) as f:\n",
    "    api_key = f.read()\n",
    "\n",
    "mf = DbGapFHIR(FHIR_SERVER, api_key=api_key)"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "## Step 2:  Explore ResearchStudy resource with dbGaP extensions\n",
    "\n",
    "To help understand what a Research Study resource looks like in dbGaP on FHIR we'll run the following query for a single study and list the whole resource. 'Resource' is a generic term for the real world entities that FHIR can represent. For this query the resource is a ResearchStudy.\n",
    "\n",
    "This helps see that some of the data we want to extract from the resource are held in extensions to the FHIR model."
   ]
  },
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   "execution_count": 2,
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    {
     "name": "stdout",
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     "text": [
      "Total  Resources: 1\n",
      "Total  Bytes: 9383\n",
      "Total  Pages: 1\n",
      "Time elapsed 0.2249 seconds\n",
      "# of studies:1\n",
      "Study id: phs001156\n",
      "Study title: The EVE Asthma Genetics Consortium: Building Upon GWAS\n",
      "Full resource\n",
      "{\n",
      "   \"resourceType\": \"ResearchStudy\",\n",
      "   \"id\": \"phs001156\",\n",
      "   \"meta\": {\n",
      "      \"versionId\": \"1\",\n",
      "      \"lastUpdated\": \"2022-02-14T01:59:54.353-05:00\",\n",
      "      \"source\": \"#LLcpbzxw95eFPBGW\",\n",
      "      \"security\": [\n",
      "         {\n",
      "            \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-SecurityStudyConsent\",\n",
      "            \"code\": \"public\",\n",
      "            \"display\": \"public\"\n",
      "         }\n",
      "      ]\n",
      "   },\n",
      "   \"extension\": [\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyOverviewUrl\",\n",
      "         \"valueUrl\": \"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001156.v2.p1\"\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ReleaseDate\",\n",
      "         \"valueDate\": \"2018-05-08\"\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyConsents\",\n",
      "         \"extension\": [\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyConsents-StudyConsent\",\n",
      "               \"valueCoding\": {\n",
      "                  \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/ResearchStudy-StudyConsents-StudyConsent\",\n",
      "                  \"code\": \"phs001156.v2.p1 - 1\",\n",
      "                  \"display\": \"GRU-NPU\"\n",
      "               }\n",
      "            }\n",
      "         ]\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content\",\n",
      "         \"extension\": [\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumPhenotypeDatasets\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 4,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumMolecularDatasets\",\n",
      "               \"valueCount\": {\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumVariables\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 19,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumAnalyses\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 4,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSubjects\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 296,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSamples\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 296,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSubStudies\",\n",
      "               \"valueCount\": {\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            }\n",
      "         ]\n",
      "      }\n",
      "   ],\n",
      "   \"identifier\": [\n",
      "      {\n",
      "         \"type\": {\n",
      "            \"coding\": [\n",
      "               {\n",
      "                  \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-DbGaPStudyIdentifier\",\n",
      "                  \"code\": \"dbgap_study_id\",\n",
      "                  \"display\": \"dbgap_study_id\"\n",
      "               }\n",
      "            ]\n",
      "         },\n",
      "         \"value\": \"phs001156.v2.p1\"\n",
      "      }\n",
      "   ],\n",
      "   \"title\": \"The EVE Asthma Genetics Consortium: Building Upon GWAS\",\n",
      "   \"status\": \"completed\",\n",
      "   \"category\": [\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/ResearchStudy-StudyDesign\",\n",
      "               \"code\": \"Case-Control\",\n",
      "               \"display\": \"Case-Control\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Case-Control\"\n",
      "      }\n",
      "   ],\n",
      "   \"focus\": [\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"urn:oid:2.16.840.1.113883.6.177\",\n",
      "               \"code\": \"D001249\",\n",
      "               \"display\": \"Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma\"\n",
      "      }\n",
      "   ],\n",
      "   \"condition\": [\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"urn:oid:2.16.840.1.113883.6.177\",\n",
      "               \"code\": \"D001249\",\n",
      "               \"display\": \"Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D001249 entry term: Asthma, Bronchial\",\n",
      "               \"display\": \"Asthma, Bronchial\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma, Bronchial\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D001249 entry term: Asthmas\",\n",
      "               \"display\": \"Asthmas\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthmas\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D001249 entry term: Bronchial Asthma\",\n",
      "               \"display\": \"Bronchial Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Bronchial Asthma\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://uts.nlm.nih.gov/metathesaurus.html\",\n",
      "               \"code\": \"C0004096\",\n",
      "               \"display\": \"Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma\"\n",
      "      }\n",
      "   ],\n",
      "   \"keyword\": [\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"urn:oid:2.16.840.1.113883.6.177\",\n",
      "               \"code\": \"D001249\",\n",
      "               \"display\": \"Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D001249 entry term: Asthma, Bronchial\",\n",
      "               \"display\": \"Asthma, Bronchial\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma, Bronchial\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D001249 entry term: Asthmas\",\n",
      "               \"display\": \"Asthmas\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthmas\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D001249 entry term: Bronchial Asthma\",\n",
      "               \"display\": \"Bronchial Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Bronchial Asthma\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://uts.nlm.nih.gov/metathesaurus.html\",\n",
      "               \"code\": \"C0004096\",\n",
      "               \"display\": \"Asthma\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Asthma\"\n",
      "      }\n",
      "   ],\n",
      "   \"description\": \"\\nThe EVE Asthma Genetics Consortium comprises U.S. investigators who have conducted genome-wide association studies (GWAS) of asthma; the main objective is to combine results of individual studies to increase the overall power to identify loci for asthma and asthma-associated traits. The consortium includes investigators at 9 U.S. institutions with GWAS results for &gt;10,000 individuals representing European American, African American, African Caribbean, U.S. Hispanic, and Mexican populations and includes the following studies:  - The Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE) - The Genetic Research on Asthma in the African Diaspora (GRAAD) Study - The Genetics of Asthma in Latino Americans (GALA 1) Study - The Childhood Asthma Management Program (CAMP) - The Childhood Asthma Research and Education (CARE) Network - The Children&#39;s Health Study (CHS) - Mexico City Childhood Asthma Study (MCCAS) - The Chicago Asthma Genetics Study (CAG)* - The National Heart, Lung, and Blood Institute Collaborative Studies of the Genetics of Asthma (CSGA)* - The Severe Asthma Research Program (SARP)*  (*CAG, CSGA, and SARP are part of the NHLBI-supported SNP Typing for Association with Multiple Phenotypes from Existing Epidemiologic Data (STAMPEED) consortium.) \\n\\nFor the GWAS, we developed a common set of &gt;1 million genotyped and imputed SNPs from the EVE Asthma Genetics Consortium to be tested for association with asthma and associated phenotypes in all samples and combined p-values for a grand meta-analysis for asthma gene discovery. A subset of 296 individuals representing African American, European American, and Latino ancestry were selected for whole genome sequencing.\\n\\nThe broad goals of this project were to characterize the genetic architecture of asthma and associated quantitative phenotypes (e.g., lung function, total serum IgE) in ethnically diverse populations from the U.S., Mexico, Puerto Rico, and Barbados.\\n\",\n",
      "   \"enrollment\": [\n",
      "      {\n",
      "         \"reference\": \"Group/phs001156.v2.p1-all-subjects\"\n",
      "      }\n",
      "   ],\n",
      "   \"sponsor\": {\n",
      "      \"reference\": \"Organization/NHLBI\",\n",
      "      \"type\": \"Organization\",\n",
      "      \"display\": \"National Heart, Lung, and Blood Institute\"\n",
      "   }\n",
      "}\n",
      "________________________________________\n"
     ]
    }
   ],
   "source": [
    "documents = mf.run_query(\"ResearchStudy?_id=phs001156\")\n",
    "print(\"# of studies:{}\".format(len(documents)))\n",
    "\n",
    "for s in documents:\n",
    "\n",
    "    print(\"Study id: {}\".format(s[\"id\"]))\n",
    "    print(\"Study title: {}\".format(s[\"title\"]))\n",
    "    print(\"Full resource\")\n",
    "    print(json.dumps(s, indent=3))\n",
    "    print(\"_\" * 40)"
   ]
  },
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    "Note that extensions include\n",
    "\n",
    "- A link to the study description e.g. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001156.v2.p1\n",
    "- Study release date\n",
    "- List groups of subjects within the study for which the subjects consented to spexcific uses of their data\n",
    "- Summary counts of various kinds - subjects, samples, variables, etc.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8817a96d",
   "metadata": {},
   "source": [
    "### Query for a different study"
   ]
  },
  {
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total  Resources: 1\n",
      "Total  Bytes: 31231\n",
      "Total  Pages: 1\n",
      "Time elapsed 0.1004 seconds\n",
      "# of studies:1\n",
      "Study id: phs001222\n",
      "Study title: CCDG - Whole Genome Sequencing in Type 1 Diabetes (T1DGC)\n",
      "Full resource\n",
      "{\n",
      "   \"resourceType\": \"ResearchStudy\",\n",
      "   \"id\": \"phs001222\",\n",
      "   \"meta\": {\n",
      "      \"versionId\": \"1\",\n",
      "      \"lastUpdated\": \"2022-02-14T01:58:59.250-05:00\",\n",
      "      \"source\": \"#YQ5VqwQ7veThKjIm\",\n",
      "      \"security\": [\n",
      "         {\n",
      "            \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/DbGaPConcept-SecurityStudyConsent\",\n",
      "            \"code\": \"public\",\n",
      "            \"display\": \"public\"\n",
      "         }\n",
      "      ]\n",
      "   },\n",
      "   \"extension\": [\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyOverviewUrl\",\n",
      "         \"valueUrl\": \"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001222.v1.p1\"\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ReleaseDate\",\n",
      "         \"valueDate\": \"2020-06-25\"\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyConsents\",\n",
      "         \"extension\": [\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyConsents-StudyConsent\",\n",
      "               \"valueCoding\": {\n",
      "                  \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/ResearchStudy-StudyConsents-StudyConsent\",\n",
      "                  \"code\": \"phs001222.v1.p1 - 1\",\n",
      "                  \"display\": \"DS-DRC-IRB-NPU\"\n",
      "               }\n",
      "            }\n",
      "         ]\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content\",\n",
      "         \"extension\": [\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumPhenotypeDatasets\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 4,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumMolecularDatasets\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 1,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumVariables\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 13,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSubjects\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 1414,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSamples\",\n",
      "               \"valueCount\": {\n",
      "                  \"value\": 1414,\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSubStudies\",\n",
      "               \"valueCount\": {\n",
      "                  \"system\": \"http://unitsofmeasure.org\",\n",
      "                  \"code\": \"1\"\n",
      "               }\n",
      "            }\n",
      "         ]\n",
      "      },\n",
      "      {\n",
      "         \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ComputedAncestry\",\n",
      "         \"extension\": [\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ComputedAncestry-AncestryCount\",\n",
      "               \"extension\": [\n",
      "                  {\n",
      "                     \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ComputedAncestry-AncestryCount-Ancestry\",\n",
      "                     \"valueCodeableConcept\": {\n",
      "                        \"coding\": [\n",
      "                           {\n",
      "                              \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/CodeSystem/ResearchStudy-ComputedAncestry-AncestryCount-Ancestry\",\n",
      "                              \"code\": \"EUR\"\n",
      "                           }\n",
      "                        ]\n",
      "                     }\n",
      "                  },\n",
      "                  {\n",
      "                     \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ComputedAncestry-AncestryCount-Count\",\n",
      "                     \"valueCount\": {\n",
      "                        \"value\": 17,\n",
      "                        \"system\": \"http://unitsofmeasure.org\",\n",
      "                        \"code\": \"1\"\n",
      "                     }\n",
      "                  }\n",
      "               ]\n",
      "            },\n",
      "            {\n",
      "               \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ComputedAncestry-AncestryCount\",\n",
      "               \"extension\": [\n",
      "                  {\n",
      "                     \"url\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-ComputedAncestry-AncestryCount-Ancestry\",\n",
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      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Autoimmune Diabetes\",\n",
      "               \"display\": \"Autoimmune Diabetes\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Autoimmune Diabetes\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Brittle Diabetes Mellitus\",\n",
      "               \"display\": \"Brittle Diabetes Mellitus\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Brittle Diabetes Mellitus\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Brittle\",\n",
      "               \"display\": \"Diabetes Mellitus, Brittle\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Brittle\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Insulin Dependent\",\n",
      "               \"display\": \"Diabetes Mellitus, Insulin Dependent\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Insulin Dependent\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Insulin-Dependent, 1\",\n",
      "               \"display\": \"Diabetes Mellitus, Insulin-Dependent, 1\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Insulin-Dependent, 1\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Juvenile Onset\",\n",
      "               \"display\": \"Diabetes Mellitus, Juvenile Onset\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Juvenile Onset\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Juvenile-Onset\",\n",
      "               \"display\": \"Diabetes Mellitus, Juvenile-Onset\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Juvenile-Onset\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Ketosis Prone\",\n",
      "               \"display\": \"Diabetes Mellitus, Ketosis Prone\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Ketosis Prone\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Ketosis-Prone\",\n",
      "               \"display\": \"Diabetes Mellitus, Ketosis-Prone\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Ketosis-Prone\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Sudden Onset\",\n",
      "               \"display\": \"Diabetes Mellitus, Sudden Onset\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Sudden Onset\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Sudden-Onset\",\n",
      "               \"display\": \"Diabetes Mellitus, Sudden-Onset\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Sudden-Onset\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Type 1\",\n",
      "               \"display\": \"Diabetes Mellitus, Type 1\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Type 1\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes Mellitus, Type I\",\n",
      "               \"display\": \"Diabetes Mellitus, Type I\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Type I\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes, Autoimmune\",\n",
      "               \"display\": \"Diabetes, Autoimmune\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes, Autoimmune\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes, Juvenile-Onset\",\n",
      "               \"display\": \"Diabetes, Juvenile-Onset\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes, Juvenile-Onset\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Diabetes, Type 1\",\n",
      "               \"display\": \"Diabetes, Type 1\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes, Type 1\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: IDDM\",\n",
      "               \"display\": \"IDDM\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"IDDM\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Insulin Dependent Diabetes Mellitus 1\",\n",
      "               \"display\": \"Insulin Dependent Diabetes Mellitus 1\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Insulin Dependent Diabetes Mellitus 1\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Insulin-Dependent Diabetes Mellitus 1\",\n",
      "               \"display\": \"Insulin-Dependent Diabetes Mellitus 1\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Insulin-Dependent Diabetes Mellitus 1\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Juvenile Onset Diabetes\",\n",
      "               \"display\": \"Juvenile Onset Diabetes\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Juvenile Onset Diabetes\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Juvenile-Onset Diabetes\",\n",
      "               \"display\": \"Juvenile-Onset Diabetes\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Juvenile-Onset Diabetes\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Juvenile-Onset Diabetes Mellitus\",\n",
      "               \"display\": \"Juvenile-Onset Diabetes Mellitus\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Juvenile-Onset Diabetes Mellitus\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Ketosis-Prone Diabetes Mellitus\",\n",
      "               \"display\": \"Ketosis-Prone Diabetes Mellitus\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Ketosis-Prone Diabetes Mellitus\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Sudden-Onset Diabetes Mellitus\",\n",
      "               \"display\": \"Sudden-Onset Diabetes Mellitus\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Sudden-Onset Diabetes Mellitus\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Type 1 Diabetes\",\n",
      "               \"display\": \"Type 1 Diabetes\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Type 1 Diabetes\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/NamingSystem/MeshEntryTerm\",\n",
      "               \"code\": \"D003922 entry term: Type 1 Diabetes Mellitus\",\n",
      "               \"display\": \"Type 1 Diabetes Mellitus\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Type 1 Diabetes Mellitus\"\n",
      "      },\n",
      "      {\n",
      "         \"coding\": [\n",
      "            {\n",
      "               \"system\": \"https://uts.nlm.nih.gov/metathesaurus.html\",\n",
      "               \"code\": \"C0011854\",\n",
      "               \"display\": \"Diabetes Mellitus, Type 1\"\n",
      "            }\n",
      "         ],\n",
      "         \"text\": \"Diabetes Mellitus, Type 1\"\n",
      "      }\n",
      "   ],\n",
      "   \"description\": \"\\nThe Type 1 Diabetes Genetics Consortium (T1DGC) was established to collect resources (biological samples and data) and conduct research to better understand the genetic basis of type 1 diabetes (T1D). Collection was initiated by ascertaining affected sib-pair families (both parents, two affected siblings and, when available, an unaffected sibling), collected from five geographic regions through four recruitment networks (Asia-Pacific, Europe, North America, United Kingdom). In addition, the T1DGC collected trio families (both parents and affected child) and cases and controls from low-prevalence populations (African-American, with four grandparents self-reporting as African ancestry; Mexican-American, with four grandparents self-reporting as ancestry from Mexico). The T1DGC also served as a repository for contributed collections from other studies, all meeting the broad data-sharing policy of the T1DGC, for inclusion in the genetic studies. These collections include T1D case samples ascertained from the UK Genetic Resource Investigating Diabetes (UK GRID) cohort, SEARCH for Diabetes in Youth (SEARCH), The Genetics of Kidneys in Diabetes (GoKinD), and control samples obtained from the British 1958 Birth Cohort, the UK National Blood Services collection, CLEAR (Consortium for the Longitudinal Evaluation of African-Americans with Early Rheumatoid Arthritis), the New York Cancer Project (NYCP), and other cohorts. For the NHGRI-funded Centers for Common Disease Genomics (CCDG) project, participants with T1D and ancestry-matched controls were identified through the T1DGC, either through direct ascertainment or by contribution from other sources to the T1DGC. As the CCDG has focused initially on non-Caucasian populations for whole genome sequencing, T1DGC participants of African, Mexican and Asian ancestry (targeting ~1200 cases and ~1200 controls in each ancestral group) and a small group of participants of Northern European ancestry (~100 cases, ~100 controls) were to be contributed to the study. Whole genome sequencing of T1DGC samples would be conducted at Washington University McDonnell Genome Institute and based upon matching case-control status within an ancestry group and prioritization by the CCDG.\\n\",\n",
      "   \"enrollment\": [\n",
      "      {\n",
      "         \"reference\": \"Group/phs001222.v1.p1-all-subjects\"\n",
      "      }\n",
      "   ],\n",
      "   \"sponsor\": {\n",
      "      \"reference\": \"Organization/NHGRI\",\n",
      "      \"type\": \"Organization\",\n",
      "      \"display\": \"National Human Genome Research Institute\"\n",
      "   }\n",
      "}\n",
      "________________________________________\n"
     ]
    }
   ],
   "source": [
    "documents = mf.run_query(\"ResearchStudy?_id=phs001222\")\n",
    "print(\"# of studies:{}\".format(len(documents)))\n",
    "\n",
    "for s in documents:\n",
    "\n",
    "    print(\"Study id: {}\".format(s[\"id\"]))\n",
    "    print(\"Study title: {}\".format(s[\"title\"]))\n",
    "    print(\"Full resource\")\n",
    "    print(json.dumps(s, indent=3))\n",
    "    print(\"_\" * 40)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ed5acfb4",
   "metadata": {},
   "source": [
    "## Step 3:  Query for asthma studies\n",
    "\n",
    "With the information above we can now run our query for studies with the word asthma in the title. We rely on standard FHIR query syntax for this. According to the FHIR standard the search will be case insensitive."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "dcde8fe5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total  Resources: 28\n",
      "Total  Bytes: 380133\n",
      "Total  Pages: 1\n",
      "Time elapsed 2.9568 seconds\n",
      "# of studies:28\n",
      "Study id: phs000166\n",
      "Study title: SNP Health Association Resource (SHARe) Asthma Resource Project (SHARP)\n",
      "Study id: phs000233\n",
      "Study title: Genome Wide Association Study of Asthma\n",
      "Study id: phs000355\n",
      "Study title: Genome Wide Association for Asthma and Lung Function\n",
      "Study id: phs000422\n",
      "Study title: NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Asthma)\n",
      "Study id: phs000886\n",
      "Study title: An Omics View of Asthma through Monozygotic Twins\n",
      "Study id: phs001009\n",
      "Study title: Determinants of Asthma Following RSV Bronchiolitis in Early Life\n",
      "Study id: phs001216\n",
      "Study title: A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma\n",
      "Study id: phs001156\n",
      "Study title: The EVE Asthma Genetics Consortium: Building Upon GWAS\n",
      "Study id: phs001123\n",
      "Study title: Consortium on Asthma among African-ancestry Populations in the Americas\n",
      "Study id: phs001812\n",
      "Study title: Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma\n",
      "Study id: phs001180\n",
      "Study title: Genes-Environments and Admixture in Latino Asthmatics (GALA II) Study\n",
      "Study id: phs000921\n",
      "Study title: NHLBI TOPMed: Study of African Americans, Asthma, Genes and Environment (SAGE)\n",
      "Study id: phs001274\n",
      "Study title: Genes-environments and Admixture in Latino Asthmatics (GALA II) GWAS Study\n",
      "Study id: phs001143\n",
      "Study title: NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados\n",
      "Study id: phs002224\n",
      "Study title: Sputum RNA-Seq from Asthmatic Patients for Microbes and Genes\n",
      "Study id: phs000920\n",
      "Study title: NHLBI TOPMed - NHGRI CCDG: Genes-Environments and Admixture in Latino Asthmatics (GALA II)\n",
      "Study id: phs001726\n",
      "Study title: NHLBI TOPMed: Childhood Asthma Management Program (CAMP)\n",
      "Study id: phs000988\n",
      "Study title: NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica\n",
      "Study id: phs001446\n",
      "Study title: NHLBI TOPMed: Severe Asthma Research Program (SARP)\n",
      "Study id: phs001602\n",
      "Study title: NHLBI TOPMed: Children&#39;s Health Study (CHS) Integrative Genetic Approaches to Gene-Air Pollution Interactions in Asthma (GAP)\n",
      "Study id: phs001603\n",
      "Study title: NHLBI TOPMed: Children&#39;s Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)\n",
      "Study id: phs001605\n",
      "Study title: NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)\n",
      "Study id: phs001467\n",
      "Study title: NHLBI TOPMed: Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE)\n",
      "Study id: phs001661\n",
      "Study title: NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)\n",
      "Study id: phs001727\n",
      "Study title: NHLBI TOPMed: Pathways to Immunologically Mediated Asthma (PIMA)\n",
      "Study id: phs001732\n",
      "Study title: NHLBI TOPMed: TReating Children to Prevent EXacerbations of Asthma (TREXA)\n",
      "Study id: phs001730\n",
      "Study title: NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)\n",
      "Study id: phs001542\n",
      "Study title: NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)\n"
     ]
    }
   ],
   "source": [
    "documents = mf.run_query(\"ResearchStudy?title:contains=asthma\")\n",
    "\n",
    "print(\"# of studies:{}\".format(len(documents)))\n",
    "\n",
    "for s in documents:\n",
    "\n",
    "    print(\"Study id: {}\".format(s[\"id\"]))\n",
    "    print(\"Study title: {}\".format(s[\"title\"]))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "69fca622",
   "metadata": {},
   "source": [
    "#### FHIR summary queries\n",
    "A FHIR query to obtain summary results for a query can be submitted as follows."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "d0b41f75",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total  Resources: 1\n",
      "Total  Bytes: 364\n",
      "Total  Pages: 1\n",
      "Time elapsed 0.0861 seconds\n"
     ]
    }
   ],
   "source": [
    "counts = mf.run_query(\"ResearchStudy?title:contains=asthma&_summary=count\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dedee977",
   "metadata": {},
   "source": [
    "In this case a single resource is returned by the run_query function.\n",
    "\n",
    "We can use an additional convenience function (prettyprint) from the ODSS FHIR training to format the result of the query as indented json. The prettyprint function is imported from the DbGapFHIR module."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "69c7857d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[\n",
      "   {\n",
      "      \"resourceType\": \"Bundle\",\n",
      "      \"id\": \"7ca1f357-a193-4a22-9b54-482bdb1063e2\",\n",
      "      \"meta\": {\n",
      "         \"lastUpdated\": \"2023-07-20T17:13:13.507-04:00\",\n",
      "         \"tag\": [\n",
      "            {\n",
      "               \"system\": \"http://terminology.hl7.org/CodeSystem/v3-ObservationValue\",\n",
      "               \"code\": \"SUBSETTED\",\n",
      "               \"display\": \"Resource encoded in summary mode\"\n",
      "            }\n",
      "         ]\n",
      "      },\n",
      "      \"type\": \"searchset\",\n",
      "      \"total\": 28\n",
      "   }\n",
      "]\n"
     ]
    }
   ],
   "source": [
    "from dbgap_fhir import prettyprint\n",
    "\n",
    "prettyprint(counts)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4626e150",
   "metadata": {},
   "source": [
    "## Step 4:  Extracting information about the studies\n",
    "We'll define a function for convenience. Because so many of the study details are in extensions, and there are extensions within extensions, the following function helps us deal with an extension at any level."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ee72f575",
   "metadata": {},
   "outputs": [],
   "source": [
    "# for a given resource find the extension identified by a given url\n",
    "# The assumption is that there is only one such extension within a given resource\n",
    "# For the dbGaP ResearchStudy resource that is true\n",
    "def getExtension(resource, uri):\n",
    "    exts = [d for d in resource[\"extension\"] if d[\"url\"] == uri]\n",
    "    if len(exts) > 0:\n",
    "        return exts[0]\n",
    "    else:\n",
    "        return None"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0aad2534",
   "metadata": {},
   "source": [
    "We can now use the function above to find the extensions for\n",
    "* the number of subjects in the study\n",
    "* the consent groups within the study\n",
    "\n",
    "The following extracts these details and puts them into a dataframe."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "896947f8",
   "metadata": {},
   "outputs": [],
   "source": [
    "def studies_to_df(documents, verbose=False):\n",
    "    studies = []\n",
    "    for s in documents:\n",
    "\n",
    "        if verbose:\n",
    "            print(s[\"id\"])\n",
    "            print(s[\"title\"])\n",
    "        # use our function to find the \"study content\" extension\n",
    "        content = getExtension(\n",
    "            s,\n",
    "            \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content\",\n",
    "        )\n",
    "        # use our function again to find the \"number of subjects\" extension nested within the content extension\n",
    "        subject_ext = getExtension(\n",
    "            content,\n",
    "            \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-Content-NumSubjects\",\n",
    "        )\n",
    "        # print(subject_ext)\n",
    "        # Handle the fact that not all studies may have this extension\n",
    "        if subject_ext != None and \"value\" in subject_ext[\"valueCount\"]:\n",
    "            subject_count = subject_ext[\"valueCount\"][\"value\"]\n",
    "        else:\n",
    "            subject_count = 0\n",
    "\n",
    "        # Now find the extension containing the study consents\n",
    "        consent_ext = getExtension(\n",
    "            s,\n",
    "            \"https://dbgap-api.ncbi.nlm.nih.gov/fhir/x1/StructureDefinition/ResearchStudy-StudyConsents\",\n",
    "        )\n",
    "        # extract the display name for each consent group and print them\n",
    "        if consent_ext != None:\n",
    "            consents = [\n",
    "                d[\"valueCoding\"][\"display\"] for d in consent_ext[\"extension\"]\n",
    "            ]\n",
    "            if verbose:\n",
    "                print(consents)\n",
    "        else:\n",
    "            consents = []\n",
    "\n",
    "        # focus\n",
    "        if \"focus\" in s:\n",
    "            focus = s[\"focus\"][0][\"text\"]\n",
    "            if \"coding\" in s[\"focus\"][0]:\n",
    "                focus_code = s[\"focus\"][0][\"coding\"][0][\"code\"]\n",
    "            else:\n",
    "                focus_code = \"\"\n",
    "        else:\n",
    "            focus = \"\"\n",
    "            focus_code = \"\"\n",
    "        # Add the relevant details to our list of studies\n",
    "        study = {\n",
    "            \"id\": s[\"id\"],\n",
    "            \"title\": s[\"title\"],\n",
    "            \"num_subjects\": subject_count,\n",
    "            \"focus\": focus,\n",
    "            \"focus_mesh\": focus_code,\n",
    "            \"consents\": consents,\n",
    "        }\n",
    "        studies.append(study)\n",
    "        if verbose:\n",
    "            print(\"_\" * 40)\n",
    "        df = pd.DataFrame(studies)\n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "e54bc5da",
   "metadata": {},
   "outputs": [],
   "source": [
    "df = studies_to_df(documents)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "306ece6c",
   "metadata": {},
   "source": [
    "## Step 5:  Show the study data in a Dataframe\n",
    "\n",
    "We can then put our list of studies into a DataFrame for display.\n",
    "\n",
    "We're listing the consent so we can see if any of the studies could potentially be used in the Computable Cohort Representation asthma exercise."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "4be7abab",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>title</th>\n",
       "      <th>num_subjects</th>\n",
       "      <th>focus</th>\n",
       "      <th>focus_mesh</th>\n",
       "      <th>consents</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>phs000166</td>\n",
       "      <td>SNP Health Association Resource (SHARe) Asthma Resource Project (SHARP)</td>\n",
       "      <td>4046</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[NRUP, ARR]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>phs000233</td>\n",
       "      <td>Genome Wide Association Study of Asthma</td>\n",
       "      <td>0</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[Analysis]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>phs000355</td>\n",
       "      <td>Genome Wide Association for Asthma and Lung Function</td>\n",
       "      <td>0</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[Analysis]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>phs000422</td>\n",
       "      <td>NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Asthma)</td>\n",
       "      <td>191</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>phs000886</td>\n",
       "      <td>An Omics View of Asthma through Monozygotic Twins</td>\n",
       "      <td>74</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>phs000920</td>\n",
       "      <td>NHLBI TOPMed - NHGRI CCDG: Genes-Environments and Admixture in Latino Asthmatics (GALA II)</td>\n",
       "      <td>4860</td>\n",
       "      <td>Lung Diseases</td>\n",
       "      <td>D008171</td>\n",
       "      <td>[DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>phs000921</td>\n",
       "      <td>NHLBI TOPMed: Study of African Americans, Asthma, Genes and Environment (SAGE)</td>\n",
       "      <td>2106</td>\n",
       "      <td>Lung Diseases</td>\n",
       "      <td>D008171</td>\n",
       "      <td>[DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>phs000988</td>\n",
       "      <td>NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica</td>\n",
       "      <td>4230</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, DS-ASTHMA-IRB-MDS-RD]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>phs001009</td>\n",
       "      <td>Determinants of Asthma Following RSV Bronchiolitis in Early Life</td>\n",
       "      <td>178</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, DS-AAR-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>phs001123</td>\n",
       "      <td>Consortium on Asthma among African-ancestry Populations in the Americas</td>\n",
       "      <td>14548</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, GRU-IRB, HMB, DS-LD, HMB-IRB-NPU, DS-FDO-IRB-NPU, HMB-IRB, DS-FDO-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>phs001143</td>\n",
       "      <td>NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados</td>\n",
       "      <td>1527</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>phs001156</td>\n",
       "      <td>The EVE Asthma Genetics Consortium: Building Upon GWAS</td>\n",
       "      <td>296</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>phs001180</td>\n",
       "      <td>Genes-Environments and Admixture in Latino Asthmatics (GALA II) Study</td>\n",
       "      <td>4458</td>\n",
       "      <td>Lung Diseases</td>\n",
       "      <td>D008171</td>\n",
       "      <td>[NRUP, DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>phs001216</td>\n",
       "      <td>A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma</td>\n",
       "      <td>447</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-PUB-NPU-MDS-GSO-RD]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>phs001274</td>\n",
       "      <td>Genes-environments and Admixture in Latino Asthmatics (GALA II) GWAS Study</td>\n",
       "      <td>4427</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>phs001446</td>\n",
       "      <td>NHLBI TOPMed: Severe Asthma Research Program (SARP)</td>\n",
       "      <td>1882</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>phs001467</td>\n",
       "      <td>NHLBI TOPMed: Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE)</td>\n",
       "      <td>4857</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, HMB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>phs001542</td>\n",
       "      <td>NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)</td>\n",
       "      <td>1024</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>phs001602</td>\n",
       "      <td>NHLBI TOPMed: Children&amp;#39;s Health Study (CHS) Integrative Genetic Approaches to Gene-Air Pollution Interactions in Asthma (GAP)</td>\n",
       "      <td>7</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>phs001603</td>\n",
       "      <td>NHLBI TOPMed: Children&amp;#39;s Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)</td>\n",
       "      <td>160</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>phs001605</td>\n",
       "      <td>NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)</td>\n",
       "      <td>292</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>phs001661</td>\n",
       "      <td>NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)</td>\n",
       "      <td>5464</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-GSO]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>phs001726</td>\n",
       "      <td>NHLBI TOPMed: Childhood Asthma Management Program (CAMP)</td>\n",
       "      <td>2640</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[NRUP, DS-AST-COPD]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>phs001727</td>\n",
       "      <td>NHLBI TOPMed: Pathways to Immunologically Mediated Asthma (PIMA)</td>\n",
       "      <td>73</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>phs001730</td>\n",
       "      <td>NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)</td>\n",
       "      <td>41</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>phs001732</td>\n",
       "      <td>NHLBI TOPMed: TReating Children to Prevent EXacerbations of Asthma (TREXA)</td>\n",
       "      <td>89</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>phs001812</td>\n",
       "      <td>Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma</td>\n",
       "      <td>115</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, GRU-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>phs002224</td>\n",
       "      <td>Sputum RNA-Seq from Asthmatic Patients for Microbes and Genes</td>\n",
       "      <td>116</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           id  \\\n",
       "0   phs000166   \n",
       "1   phs000233   \n",
       "2   phs000355   \n",
       "3   phs000422   \n",
       "4   phs000886   \n",
       "15  phs000920   \n",
       "11  phs000921   \n",
       "17  phs000988   \n",
       "5   phs001009   \n",
       "8   phs001123   \n",
       "13  phs001143   \n",
       "7   phs001156   \n",
       "10  phs001180   \n",
       "6   phs001216   \n",
       "12  phs001274   \n",
       "18  phs001446   \n",
       "22  phs001467   \n",
       "27  phs001542   \n",
       "19  phs001602   \n",
       "20  phs001603   \n",
       "21  phs001605   \n",
       "23  phs001661   \n",
       "16  phs001726   \n",
       "24  phs001727   \n",
       "26  phs001730   \n",
       "25  phs001732   \n",
       "9   phs001812   \n",
       "14  phs002224   \n",
       "\n",
       "                                                                                                                                title  \\\n",
       "0   SNP Health Association Resource (SHARe) Asthma Resource Project (SHARP)                                                             \n",
       "1   Genome Wide Association Study of Asthma                                                                                             \n",
       "2   Genome Wide Association for Asthma and Lung Function                                                                                \n",
       "3   NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Asthma)                                                                        \n",
       "4   An Omics View of Asthma through Monozygotic Twins                                                                                   \n",
       "15  NHLBI TOPMed - NHGRI CCDG: Genes-Environments and Admixture in Latino Asthmatics (GALA II)                                          \n",
       "11  NHLBI TOPMed: Study of African Americans, Asthma, Genes and Environment (SAGE)                                                      \n",
       "17  NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica                                                                      \n",
       "5   Determinants of Asthma Following RSV Bronchiolitis in Early Life                                                                    \n",
       "8   Consortium on Asthma among African-ancestry Populations in the Americas                                                             \n",
       "13  NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados                                                                   \n",
       "7   The EVE Asthma Genetics Consortium: Building Upon GWAS                                                                              \n",
       "10  Genes-Environments and Admixture in Latino Asthmatics (GALA II) Study                                                               \n",
       "6   A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma                                       \n",
       "12  Genes-environments and Admixture in Latino Asthmatics (GALA II) GWAS Study                                                          \n",
       "18  NHLBI TOPMed: Severe Asthma Research Program (SARP)                                                                                 \n",
       "22  NHLBI TOPMed: Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE)                              \n",
       "27  NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)                                                                         \n",
       "19  NHLBI TOPMed: Children&#39;s Health Study (CHS) Integrative Genetic Approaches to Gene-Air Pollution Interactions in Asthma (GAP)   \n",
       "20  NHLBI TOPMed: Children&#39;s Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)                   \n",
       "21  NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)                                                             \n",
       "23  NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)                                                       \n",
       "16  NHLBI TOPMed: Childhood Asthma Management Program (CAMP)                                                                            \n",
       "24  NHLBI TOPMed: Pathways to Immunologically Mediated Asthma (PIMA)                                                                    \n",
       "26  NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)                                                                              \n",
       "25  NHLBI TOPMed: TReating Children to Prevent EXacerbations of Asthma (TREXA)                                                          \n",
       "9   Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma                                                          \n",
       "14  Sputum RNA-Seq from Asthmatic Patients for Microbes and Genes                                                                       \n",
       "\n",
       "    num_subjects          focus focus_mesh  \\\n",
       "0   4046                                     \n",
       "1   0             Asthma         D001249     \n",
       "2   0             Asthma         D001249     \n",
       "3   191           Asthma         D001249     \n",
       "4   74            Asthma         D001249     \n",
       "15  4860          Lung Diseases  D008171     \n",
       "11  2106          Lung Diseases  D008171     \n",
       "17  4230          Asthma         D001249     \n",
       "5   178           Asthma         D001249     \n",
       "8   14548         Asthma         D001249     \n",
       "13  1527          Asthma         D001249     \n",
       "7   296           Asthma         D001249     \n",
       "10  4458          Lung Diseases  D008171     \n",
       "6   447           Asthma         D001249     \n",
       "12  4427          Asthma         D001249     \n",
       "18  1882          Asthma         D001249     \n",
       "22  4857          Asthma         D001249     \n",
       "27  1024          Asthma         D001249     \n",
       "19  7             Asthma         D001249     \n",
       "20  160           Asthma         D001249     \n",
       "21  292           Asthma         D001249     \n",
       "23  5464          Asthma         D001249     \n",
       "16  2640                                     \n",
       "24  73            Asthma         D001249     \n",
       "26  41            Asthma         D001249     \n",
       "25  89            Asthma         D001249     \n",
       "9   115           Asthma         D001249     \n",
       "14  116                                      \n",
       "\n",
       "                                                                         consents  \n",
       "0   [NRUP, ARR]                                                                    \n",
       "1   [Analysis]                                                                     \n",
       "2   [Analysis]                                                                     \n",
       "3   [GRU]                                                                          \n",
       "4   [GRU]                                                                          \n",
       "15  [DS-LD-IRB-COL]                                                                \n",
       "11  [DS-LD-IRB-COL]                                                                \n",
       "17  [NRUP, DS-ASTHMA-IRB-MDS-RD]                                                   \n",
       "5   [NRUP, DS-AAR-IRB]                                                             \n",
       "8   [NRUP, GRU-IRB, HMB, DS-LD, HMB-IRB-NPU, DS-FDO-IRB-NPU, HMB-IRB, DS-FDO-IRB]  \n",
       "13  [NRUP, GRU-IRB]                                                                \n",
       "7   [GRU-NPU]                                                                      \n",
       "10  [NRUP, DS-LD-IRB-COL]                                                          \n",
       "6   [DS-ASTHMA-IRB-PUB-NPU-MDS-GSO-RD]                                             \n",
       "12  [DS-LD-IRB-COL]                                                                \n",
       "18  [GRU]                                                                          \n",
       "22  [NRUP, HMB-COL]                                                                \n",
       "27  [DS-LD-IRB-COL]                                                                \n",
       "19  [GRU]                                                                          \n",
       "20  [GRU]                                                                          \n",
       "21  [DS-ASTHMA-IRB-COL]                                                            \n",
       "23  [DS-ASTHMA-GSO]                                                                \n",
       "16  [NRUP, DS-AST-COPD]                                                            \n",
       "24  [DS-ASTHMA-IRB-COL]                                                            \n",
       "26  [DS-ASTHMA-IRB-COL]                                                            \n",
       "25  [DS-ASTHMA-IRB-COL]                                                            \n",
       "9   [NRUP, GRU-IRB-COL]                                                            \n",
       "14  [GRU]                                                                          "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.set_option(\"display.max_colwidth\", 0)\n",
    "df.sort_values(by=[\"id\"], inplace=True)\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "36856639",
   "metadata": {},
   "source": [
    "## Step 6 -  Query on focus of study, by code\n",
    "\n",
    "The MESH code for Asthma\n",
    "\n",
    "Note that this returns studies that were not retrieved where the word asthma was in the title."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "6a944de0",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total  Resources: 25\n",
      "Total  Bytes: 332675\n",
      "Time elapsed 2.9763 seconds\n"
     ]
    }
   ],
   "source": [
    "documents = mf.run_query(\"ResearchStudy?focus=D001249\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "60677634",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>title</th>\n",
       "      <th>num_subjects</th>\n",
       "      <th>focus</th>\n",
       "      <th>focus_mesh</th>\n",
       "      <th>consents</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>phs001542</td>\n",
       "      <td>NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)</td>\n",
       "      <td>1024</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>phs001732</td>\n",
       "      <td>NHLBI TOPMed: TReating Children to Prevent EXacerbations of Asthma (TREXA)</td>\n",
       "      <td>89</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>phs001730</td>\n",
       "      <td>NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)</td>\n",
       "      <td>41</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>phs001729</td>\n",
       "      <td>NHLBI TOPMed: Characterizing the Response to a Leukotriene Receptor Antagonist and an Inhaled Corticosteroid (CLIC)</td>\n",
       "      <td>19</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>phs001728</td>\n",
       "      <td>NHLBI TOPMed: Best ADd-on Therapy Giving Effective Response (BADGER)</td>\n",
       "      <td>50</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>phs001727</td>\n",
       "      <td>NHLBI TOPMed: Pathways to Immunologically Mediated Asthma (PIMA)</td>\n",
       "      <td>73</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>phs001661</td>\n",
       "      <td>NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)</td>\n",
       "      <td>5464</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-GSO]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>phs001467</td>\n",
       "      <td>NHLBI TOPMed: Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE)</td>\n",
       "      <td>4857</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, HMB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>phs001605</td>\n",
       "      <td>NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)</td>\n",
       "      <td>292</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>phs001604</td>\n",
       "      <td>NHLBI TOPMed: Children&amp;#39;s Health Study (CHS) Effects of Air Pollution on the Development of Obesity in Children (Meta-AIR)</td>\n",
       "      <td>56</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>phs001603</td>\n",
       "      <td>NHLBI TOPMed: Children&amp;#39;s Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)</td>\n",
       "      <td>160</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>phs001602</td>\n",
       "      <td>NHLBI TOPMed: Children&amp;#39;s Health Study (CHS) Integrative Genetic Approaches to Gene-Air Pollution Interactions in Asthma (GAP)</td>\n",
       "      <td>7</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>phs001446</td>\n",
       "      <td>NHLBI TOPMed: Severe Asthma Research Program (SARP)</td>\n",
       "      <td>1882</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>phs000988</td>\n",
       "      <td>NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica</td>\n",
       "      <td>4230</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, DS-ASTHMA-IRB-MDS-RD]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>phs001143</td>\n",
       "      <td>NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados</td>\n",
       "      <td>1527</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>phs001274</td>\n",
       "      <td>Genes-environments and Admixture in Latino Asthmatics (GALA II) GWAS Study</td>\n",
       "      <td>4427</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-LD-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>phs001812</td>\n",
       "      <td>Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma</td>\n",
       "      <td>115</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, GRU-IRB-COL]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>phs001123</td>\n",
       "      <td>Consortium on Asthma among African-ancestry Populations in the Americas</td>\n",
       "      <td>14548</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, GRU-IRB, HMB, DS-LD, HMB-IRB-NPU, DS-FDO-IRB-NPU, HMB-IRB, DS-FDO-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>phs001156</td>\n",
       "      <td>The EVE Asthma Genetics Consortium: Building Upon GWAS</td>\n",
       "      <td>296</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>phs001216</td>\n",
       "      <td>A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma</td>\n",
       "      <td>447</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[DS-ASTHMA-IRB-PUB-NPU-MDS-GSO-RD]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>phs001009</td>\n",
       "      <td>Determinants of Asthma Following RSV Bronchiolitis in Early Life</td>\n",
       "      <td>178</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[NRUP, DS-AAR-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>phs000886</td>\n",
       "      <td>An Omics View of Asthma through Monozygotic Twins</td>\n",
       "      <td>74</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>phs000422</td>\n",
       "      <td>NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Asthma)</td>\n",
       "      <td>191</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>phs000355</td>\n",
       "      <td>Genome Wide Association for Asthma and Lung Function</td>\n",
       "      <td>0</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[Analysis]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>phs000233</td>\n",
       "      <td>Genome Wide Association Study of Asthma</td>\n",
       "      <td>0</td>\n",
       "      <td>Asthma</td>\n",
       "      <td>D001249</td>\n",
       "      <td>[Analysis]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           id  \\\n",
       "0   phs001542   \n",
       "1   phs001732   \n",
       "2   phs001730   \n",
       "3   phs001729   \n",
       "4   phs001728   \n",
       "5   phs001727   \n",
       "6   phs001661   \n",
       "7   phs001467   \n",
       "8   phs001605   \n",
       "9   phs001604   \n",
       "10  phs001603   \n",
       "11  phs001602   \n",
       "12  phs001446   \n",
       "13  phs000988   \n",
       "14  phs001143   \n",
       "15  phs001274   \n",
       "16  phs001812   \n",
       "17  phs001123   \n",
       "18  phs001156   \n",
       "19  phs001216   \n",
       "20  phs001009   \n",
       "21  phs000886   \n",
       "22  phs000422   \n",
       "23  phs000355   \n",
       "24  phs000233   \n",
       "\n",
       "                                                                                                                                title  \\\n",
       "0   NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)                                                                         \n",
       "1   NHLBI TOPMed: TReating Children to Prevent EXacerbations of Asthma (TREXA)                                                          \n",
       "2   NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)                                                                              \n",
       "3   NHLBI TOPMed: Characterizing the Response to a Leukotriene Receptor Antagonist and an Inhaled Corticosteroid (CLIC)                 \n",
       "4   NHLBI TOPMed: Best ADd-on Therapy Giving Effective Response (BADGER)                                                                \n",
       "5   NHLBI TOPMed: Pathways to Immunologically Mediated Asthma (PIMA)                                                                    \n",
       "6   NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)                                                       \n",
       "7   NHLBI TOPMed: Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE)                              \n",
       "8   NHLBI TOPMed: Chicago Initiative to Raise Asthma Health Equity (CHIRAH)                                                             \n",
       "9   NHLBI TOPMed: Children&#39;s Health Study (CHS) Effects of Air Pollution on the Development of Obesity in Children (Meta-AIR)       \n",
       "10  NHLBI TOPMed: Children&#39;s Health Study (CHS) Integrative Genomics and Environmental Research of Asthma (IGERA)                   \n",
       "11  NHLBI TOPMed: Children&#39;s Health Study (CHS) Integrative Genetic Approaches to Gene-Air Pollution Interactions in Asthma (GAP)   \n",
       "12  NHLBI TOPMed: Severe Asthma Research Program (SARP)                                                                                 \n",
       "13  NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica                                                                      \n",
       "14  NHLBI TOPMed: The Genetics and Epidemiology of Asthma in Barbados                                                                   \n",
       "15  Genes-environments and Admixture in Latino Asthmatics (GALA II) GWAS Study                                                          \n",
       "16  Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma                                                          \n",
       "17  Consortium on Asthma among African-ancestry Populations in the Americas                                                             \n",
       "18  The EVE Asthma Genetics Consortium: Building Upon GWAS                                                                              \n",
       "19  A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma                                       \n",
       "20  Determinants of Asthma Following RSV Bronchiolitis in Early Life                                                                    \n",
       "21  An Omics View of Asthma through Monozygotic Twins                                                                                   \n",
       "22  NHLBI GO-ESP: Lung Cohorts Exome Sequencing Project (Asthma)                                                                        \n",
       "23  Genome Wide Association for Asthma and Lung Function                                                                                \n",
       "24  Genome Wide Association Study of Asthma                                                                                             \n",
       "\n",
       "    num_subjects   focus focus_mesh  \\\n",
       "0   1024          Asthma  D001249     \n",
       "1   89            Asthma  D001249     \n",
       "2   41            Asthma  D001249     \n",
       "3   19            Asthma  D001249     \n",
       "4   50            Asthma  D001249     \n",
       "5   73            Asthma  D001249     \n",
       "6   5464          Asthma  D001249     \n",
       "7   4857          Asthma  D001249     \n",
       "8   292           Asthma  D001249     \n",
       "9   56            Asthma  D001249     \n",
       "10  160           Asthma  D001249     \n",
       "11  7             Asthma  D001249     \n",
       "12  1882          Asthma  D001249     \n",
       "13  4230          Asthma  D001249     \n",
       "14  1527          Asthma  D001249     \n",
       "15  4427          Asthma  D001249     \n",
       "16  115           Asthma  D001249     \n",
       "17  14548         Asthma  D001249     \n",
       "18  296           Asthma  D001249     \n",
       "19  447           Asthma  D001249     \n",
       "20  178           Asthma  D001249     \n",
       "21  74            Asthma  D001249     \n",
       "22  191           Asthma  D001249     \n",
       "23  0             Asthma  D001249     \n",
       "24  0             Asthma  D001249     \n",
       "\n",
       "                                                                         consents  \n",
       "0   [DS-LD-IRB-COL]                                                                \n",
       "1   [DS-ASTHMA-IRB-COL]                                                            \n",
       "2   [DS-ASTHMA-IRB-COL]                                                            \n",
       "3   [DS-ASTHMA-IRB-COL]                                                            \n",
       "4   [DS-ASTHMA-IRB-COL]                                                            \n",
       "5   [DS-ASTHMA-IRB-COL]                                                            \n",
       "6   [DS-ASTHMA-GSO]                                                                \n",
       "7   [NRUP, HMB-COL]                                                                \n",
       "8   [DS-ASTHMA-IRB-COL]                                                            \n",
       "9   [GRU]                                                                          \n",
       "10  [GRU]                                                                          \n",
       "11  [GRU]                                                                          \n",
       "12  [GRU]                                                                          \n",
       "13  [NRUP, DS-ASTHMA-IRB-MDS-RD]                                                   \n",
       "14  [NRUP, GRU-IRB]                                                                \n",
       "15  [DS-LD-IRB-COL]                                                                \n",
       "16  [NRUP, GRU-IRB-COL]                                                            \n",
       "17  [NRUP, GRU-IRB, HMB, DS-LD, HMB-IRB-NPU, DS-FDO-IRB-NPU, HMB-IRB, DS-FDO-IRB]  \n",
       "18  [GRU-NPU]                                                                      \n",
       "19  [DS-ASTHMA-IRB-PUB-NPU-MDS-GSO-RD]                                             \n",
       "20  [NRUP, DS-AAR-IRB]                                                             \n",
       "21  [GRU]                                                                          \n",
       "22  [GRU]                                                                          \n",
       "23  [Analysis]                                                                     \n",
       "24  [Analysis]                                                                     "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "studies_to_df(documents)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c1961c3f",
   "metadata": {},
   "source": [
    "## Step 7 - Query for studies sponsored by a particular NIH Institute\n",
    "\n",
    "We can query on the sponsor parameter to find studies for a given NIH institute."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "2943ce58",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total  Resources: 39\n",
      "Total  Bytes: 804259\n",
      "Time elapsed 3.0077 seconds\n"
     ]
    }
   ],
   "source": [
    "ic_studies = mf.run_query(\"ResearchStudy?sponsor=NIA\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "e134ee09",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>title</th>\n",
       "      <th>num_subjects</th>\n",
       "      <th>focus</th>\n",
       "      <th>focus_mesh</th>\n",
       "      <th>consents</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>phs002610</td>\n",
       "      <td>Maintenance of Genome Sequence Integrity in Long- and Short-lived Rodent Species</td>\n",
       "      <td>2</td>\n",
       "      <td>Longevity</td>\n",
       "      <td>D008136</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>phs002411</td>\n",
       "      <td>Genome Instability in Mammary Cells of Pathogenic BRCA1/2 Mutation Carriers</td>\n",
       "      <td>16</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[DS-BRCA-PUB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>phs002361</td>\n",
       "      <td>Genomics and Epigenomics of the Elderly Response to Pneumococcal Vaccines</td>\n",
       "      <td>2</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>phs002202</td>\n",
       "      <td>A New High-Throughput Sequencing-Based Technology to Study Heterochromatin Structure</td>\n",
       "      <td>2</td>\n",
       "      <td>Healthy Volunteers</td>\n",
       "      <td>D064368</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>phs000397</td>\n",
       "      <td>NIA Long Life Family Study (LLFS)</td>\n",
       "      <td>4997</td>\n",
       "      <td>Longevity</td>\n",
       "      <td>D008136</td>\n",
       "      <td>[NRUP, GRU-IRB, GRU-IRB-NPU, DS-LARHC-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>phs001916</td>\n",
       "      <td>Pilot Sequencing Study of Peripheral Blood Mononuclear Cells in Human Aging</td>\n",
       "      <td>20</td>\n",
       "      <td>Healthy Aging</td>\n",
       "      <td></td>\n",
       "      <td>[GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>phs001963</td>\n",
       "      <td>DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia</td>\n",
       "      <td>6907</td>\n",
       "      <td>Lewy Body Disease</td>\n",
       "      <td>D020961</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>phs001956</td>\n",
       "      <td>Genome Instability in Liver Stem and Mature Cells</td>\n",
       "      <td>15</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[HMB-PUB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>phs001808</td>\n",
       "      <td>Landscape of Somatic Mutations in B Lymphocytes Across Human Lifespan</td>\n",
       "      <td>14</td>\n",
       "      <td>Aging</td>\n",
       "      <td>D000375</td>\n",
       "      <td>[DS-AGR1-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>phs001779</td>\n",
       "      <td>CIDR-NIA Whole Exome Analysis of Ehlers-Danlos Syndrome</td>\n",
       "      <td>153</td>\n",
       "      <td>Ehlers-Danlos syndrome type 3</td>\n",
       "      <td>C0268337</td>\n",
       "      <td>[NRUP, DS-HCT-IRB-COL-GSO-RD]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>phs000786</td>\n",
       "      <td>RPGEH WGS Pilot Study</td>\n",
       "      <td>4</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[HMB-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>phs000674</td>\n",
       "      <td>Resource for Genetic Epidemiology Research on Aging (GERA)</td>\n",
       "      <td>78419</td>\n",
       "      <td>Aging</td>\n",
       "      <td>D000375</td>\n",
       "      <td>[HMB-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>phs000788</td>\n",
       "      <td>Research Program on Genes, Environment and Health (RPGEH)</td>\n",
       "      <td>78423</td>\n",
       "      <td>Aging</td>\n",
       "      <td>D000375</td>\n",
       "      <td>[NRUP, HMB-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>phs001470</td>\n",
       "      <td>Study of Women&amp;#39;s Health Across the Nation (SWAN) Repository</td>\n",
       "      <td>1463</td>\n",
       "      <td>Menopause</td>\n",
       "      <td>D008593</td>\n",
       "      <td>[NRUP, HMB-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>phs001462</td>\n",
       "      <td>NABEC NeuroChip Genotyping</td>\n",
       "      <td>270</td>\n",
       "      <td>Molecular Probe Techniques</td>\n",
       "      <td>D015336</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>phs001354</td>\n",
       "      <td>NABEC Total RNA Sequencing of Human Cerebral Frontal Cortex</td>\n",
       "      <td>276</td>\n",
       "      <td>Healthy Volunteers</td>\n",
       "      <td>D064368</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>phs001353</td>\n",
       "      <td>NABEC mRNA Sequencing of Human Cerebral Frontal Cortex</td>\n",
       "      <td>69</td>\n",
       "      <td>Healthy Volunteers</td>\n",
       "      <td>D064368</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>phs001301</td>\n",
       "      <td>NABEC Exome Sequencing of Human Cerebral Frontal Cortex</td>\n",
       "      <td>343</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>phs001302</td>\n",
       "      <td>NABEC CAGE Sequencing of Human Cerebral Frontal Cortex</td>\n",
       "      <td>142</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>phs001300</td>\n",
       "      <td>NABEC: North American Brain Expression Consortium</td>\n",
       "      <td>432</td>\n",
       "      <td>Gene Expression Profiling</td>\n",
       "      <td>D020869</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>phs001209</td>\n",
       "      <td>MIDCIRS Reveals Antibody Diversification in Young Children with Malaria</td>\n",
       "      <td>22</td>\n",
       "      <td>Malaria</td>\n",
       "      <td>D008288</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>phs000572</td>\n",
       "      <td>Alzheimer&amp;#39;s Disease Sequencing Project (ADSP)</td>\n",
       "      <td>15630</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[HMB-IRB, HMB-IRB-NPU, DS-ALZ-IRB, DS-ALZ-IRB-NPU, DS-ND-IRB, DS-ND-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>phs001157</td>\n",
       "      <td>Wisconsin Longitudinal Study on Aging</td>\n",
       "      <td>9027</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>[NRUP, GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>phs000249</td>\n",
       "      <td>NABEC: Genome-Wide Genotyping</td>\n",
       "      <td>382</td>\n",
       "      <td>Healthy Volunteers</td>\n",
       "      <td>D064368</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>phs000745</td>\n",
       "      <td>RNAseq analysis of posterior cingulate astrocytes in Alzheimer&amp;#39;s disease</td>\n",
       "      <td>20</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>phs000313</td>\n",
       "      <td>SardiNIA Medical Sequencing Discovery Project</td>\n",
       "      <td>2105</td>\n",
       "      <td>Cardiovascular Diseases</td>\n",
       "      <td>D002318</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>phs000726</td>\n",
       "      <td>Genome-Wide Association Study of Myasthenia Gravis</td>\n",
       "      <td>972</td>\n",
       "      <td>Myasthenia Gravis</td>\n",
       "      <td>D009157</td>\n",
       "      <td>[GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>phs000428</td>\n",
       "      <td>Health and Retirement Study (HRS)</td>\n",
       "      <td>15620</td>\n",
       "      <td>Aging</td>\n",
       "      <td>D000375</td>\n",
       "      <td>[NRUP, NPR]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>phs000215</td>\n",
       "      <td>Genome-Wide Association Analysis of Biomarkers in the InCHIANTI and BLSA</td>\n",
       "      <td>0</td>\n",
       "      <td>Nutritional and Metabolic Diseases</td>\n",
       "      <td>D009750</td>\n",
       "      <td>[]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>phs000584</td>\n",
       "      <td>The Longevity Genes Project</td>\n",
       "      <td>2140</td>\n",
       "      <td>Longevity</td>\n",
       "      <td>D008136</td>\n",
       "      <td>[NRUP, GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>phs000496</td>\n",
       "      <td>Columbia University Study of Caribbean Hispanics and Late Onset Alzheimer&amp;#39;s disease</td>\n",
       "      <td>3139</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>phs000168</td>\n",
       "      <td>NIA - Late Onset Alzheimer&amp;#39;s Disease and National Cell Repository for Alzheimer&amp;#39;s Disease Family Study: Genome-Wide Association Study for Susceptibility Loci</td>\n",
       "      <td>5220</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRUP, GRU, NPU, DS-ALZ, DS-ALZ-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>phs000451</td>\n",
       "      <td>NHLBI and NIA The New England Centenarian Study (NECS)</td>\n",
       "      <td>2</td>\n",
       "      <td>Aged, 80 and over</td>\n",
       "      <td>D000369</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>phs000378</td>\n",
       "      <td>Indianapolis-Ibadan, Nigeria Comparative Epidemiological Study of Dementia</td>\n",
       "      <td>1251</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>phs000372</td>\n",
       "      <td>ADGC Genome Wide Association Study</td>\n",
       "      <td>6065</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[ADR]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>phs000338</td>\n",
       "      <td>National Institute on Aging (NIA) SardiNIA Study</td>\n",
       "      <td>0</td>\n",
       "      <td>Cardiovascular Diseases</td>\n",
       "      <td>D002318</td>\n",
       "      <td>[Genotype_Analysis]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>phs000138</td>\n",
       "      <td>GWAS for Genetic Determinants of Bone Fragility</td>\n",
       "      <td>1493</td>\n",
       "      <td>Osteoporosis</td>\n",
       "      <td>D010024</td>\n",
       "      <td>[NRUP, GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>phs000169</td>\n",
       "      <td>Whole Genome Association Study of Visceral Adiposity in the HABC Study</td>\n",
       "      <td>2802</td>\n",
       "      <td>Obesity</td>\n",
       "      <td>D009765</td>\n",
       "      <td>[NRUP, GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>phs000160</td>\n",
       "      <td>Genetics Consortium for Late Onset of Alzheimer&amp;#39;s Disease (LOAD CIDR Project)</td>\n",
       "      <td>2398</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRU, GRU, NPU, ALZ, ALZ_NPU]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           id  \\\n",
       "0   phs002610   \n",
       "1   phs002411   \n",
       "2   phs002361   \n",
       "3   phs002202   \n",
       "4   phs000397   \n",
       "5   phs001916   \n",
       "6   phs001963   \n",
       "7   phs001956   \n",
       "8   phs001808   \n",
       "9   phs001779   \n",
       "10  phs000786   \n",
       "11  phs000674   \n",
       "12  phs000788   \n",
       "13  phs001470   \n",
       "14  phs001462   \n",
       "15  phs001354   \n",
       "16  phs001353   \n",
       "17  phs001301   \n",
       "18  phs001302   \n",
       "19  phs001300   \n",
       "20  phs001209   \n",
       "21  phs000572   \n",
       "22  phs001157   \n",
       "23  phs000249   \n",
       "24  phs000745   \n",
       "25  phs000313   \n",
       "26  phs000726   \n",
       "27  phs000428   \n",
       "28  phs000215   \n",
       "29  phs000584   \n",
       "30  phs000496   \n",
       "31  phs000168   \n",
       "32  phs000451   \n",
       "33  phs000378   \n",
       "34  phs000372   \n",
       "35  phs000338   \n",
       "36  phs000138   \n",
       "37  phs000169   \n",
       "38  phs000160   \n",
       "\n",
       "                                                                                                                                                                    title  \\\n",
       "0   Maintenance of Genome Sequence Integrity in Long- and Short-lived Rodent Species                                                                                        \n",
       "1   Genome Instability in Mammary Cells of Pathogenic BRCA1/2 Mutation Carriers                                                                                             \n",
       "2   Genomics and Epigenomics of the Elderly Response to Pneumococcal Vaccines                                                                                               \n",
       "3   A New High-Throughput Sequencing-Based Technology to Study Heterochromatin Structure                                                                                    \n",
       "4   NIA Long Life Family Study (LLFS)                                                                                                                                       \n",
       "5   Pilot Sequencing Study of Peripheral Blood Mononuclear Cells in Human Aging                                                                                             \n",
       "6   DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia                                                                                                     \n",
       "7   Genome Instability in Liver Stem and Mature Cells                                                                                                                       \n",
       "8   Landscape of Somatic Mutations in B Lymphocytes Across Human Lifespan                                                                                                   \n",
       "9   CIDR-NIA Whole Exome Analysis of Ehlers-Danlos Syndrome                                                                                                                 \n",
       "10  RPGEH WGS Pilot Study                                                                                                                                                   \n",
       "11  Resource for Genetic Epidemiology Research on Aging (GERA)                                                                                                              \n",
       "12  Research Program on Genes, Environment and Health (RPGEH)                                                                                                               \n",
       "13  Study of Women&#39;s Health Across the Nation (SWAN) Repository                                                                                                         \n",
       "14  NABEC NeuroChip Genotyping                                                                                                                                              \n",
       "15  NABEC Total RNA Sequencing of Human Cerebral Frontal Cortex                                                                                                             \n",
       "16  NABEC mRNA Sequencing of Human Cerebral Frontal Cortex                                                                                                                  \n",
       "17  NABEC Exome Sequencing of Human Cerebral Frontal Cortex                                                                                                                 \n",
       "18  NABEC CAGE Sequencing of Human Cerebral Frontal Cortex                                                                                                                  \n",
       "19  NABEC: North American Brain Expression Consortium                                                                                                                       \n",
       "20  MIDCIRS Reveals Antibody Diversification in Young Children with Malaria                                                                                                 \n",
       "21  Alzheimer&#39;s Disease Sequencing Project (ADSP)                                                                                                                       \n",
       "22  Wisconsin Longitudinal Study on Aging                                                                                                                                   \n",
       "23  NABEC: Genome-Wide Genotyping                                                                                                                                           \n",
       "24  RNAseq analysis of posterior cingulate astrocytes in Alzheimer&#39;s disease                                                                                            \n",
       "25  SardiNIA Medical Sequencing Discovery Project                                                                                                                           \n",
       "26  Genome-Wide Association Study of Myasthenia Gravis                                                                                                                      \n",
       "27  Health and Retirement Study (HRS)                                                                                                                                       \n",
       "28  Genome-Wide Association Analysis of Biomarkers in the InCHIANTI and BLSA                                                                                                \n",
       "29  The Longevity Genes Project                                                                                                                                             \n",
       "30  Columbia University Study of Caribbean Hispanics and Late Onset Alzheimer&#39;s disease                                                                                 \n",
       "31  NIA - Late Onset Alzheimer&#39;s Disease and National Cell Repository for Alzheimer&#39;s Disease Family Study: Genome-Wide Association Study for Susceptibility Loci   \n",
       "32  NHLBI and NIA The New England Centenarian Study (NECS)                                                                                                                  \n",
       "33  Indianapolis-Ibadan, Nigeria Comparative Epidemiological Study of Dementia                                                                                              \n",
       "34  ADGC Genome Wide Association Study                                                                                                                                      \n",
       "35  National Institute on Aging (NIA) SardiNIA Study                                                                                                                        \n",
       "36  GWAS for Genetic Determinants of Bone Fragility                                                                                                                         \n",
       "37  Whole Genome Association Study of Visceral Adiposity in the HABC Study                                                                                                  \n",
       "38  Genetics Consortium for Late Onset of Alzheimer&#39;s Disease (LOAD CIDR Project)                                                                                       \n",
       "\n",
       "    num_subjects                               focus focus_mesh  \\\n",
       "0   2             Longevity                           D008136     \n",
       "1   16                                                            \n",
       "2   2                                                             \n",
       "3   2             Healthy Volunteers                  D064368     \n",
       "4   4997          Longevity                           D008136     \n",
       "5   20            Healthy Aging                                   \n",
       "6   6907          Lewy Body Disease                   D020961     \n",
       "7   15                                                            \n",
       "8   14            Aging                               D000375     \n",
       "9   153           Ehlers-Danlos syndrome type 3       C0268337    \n",
       "10  4                                                             \n",
       "11  78419         Aging                               D000375     \n",
       "12  78423         Aging                               D000375     \n",
       "13  1463          Menopause                           D008593     \n",
       "14  270           Molecular Probe Techniques          D015336     \n",
       "15  276           Healthy Volunteers                  D064368     \n",
       "16  69            Healthy Volunteers                  D064368     \n",
       "17  343                                                           \n",
       "18  142                                                           \n",
       "19  432           Gene Expression Profiling           D020869     \n",
       "20  22            Malaria                             D008288     \n",
       "21  15630         Alzheimer Disease                   D000544     \n",
       "22  9027                                                          \n",
       "23  382           Healthy Volunteers                  D064368     \n",
       "24  20            Alzheimer Disease                   D000544     \n",
       "25  2105          Cardiovascular Diseases             D002318     \n",
       "26  972           Myasthenia Gravis                   D009157     \n",
       "27  15620         Aging                               D000375     \n",
       "28  0             Nutritional and Metabolic Diseases  D009750     \n",
       "29  2140          Longevity                           D008136     \n",
       "30  3139          Alzheimer Disease                   D000544     \n",
       "31  5220          Alzheimer Disease                   D000544     \n",
       "32  2             Aged, 80 and over                   D000369     \n",
       "33  1251          Alzheimer Disease                   D000544     \n",
       "34  6065          Alzheimer Disease                   D000544     \n",
       "35  0             Cardiovascular Diseases             D002318     \n",
       "36  1493          Osteoporosis                        D010024     \n",
       "37  2802          Obesity                             D009765     \n",
       "38  2398          Alzheimer Disease                   D000544     \n",
       "\n",
       "                                                                        consents  \n",
       "0   [GRU]                                                                         \n",
       "1   [DS-BRCA-PUB-NPU]                                                             \n",
       "2   [GRU]                                                                         \n",
       "3   [GRU]                                                                         \n",
       "4   [NRUP, GRU-IRB, GRU-IRB-NPU, DS-LARHC-IRB-NPU]                                \n",
       "5   [GRU-IRB]                                                                     \n",
       "6   [GRU]                                                                         \n",
       "7   [HMB-PUB-NPU]                                                                 \n",
       "8   [DS-AGR1-NPU]                                                                 \n",
       "9   [NRUP, DS-HCT-IRB-COL-GSO-RD]                                                 \n",
       "10  [HMB-IRB-NPU]                                                                 \n",
       "11  [HMB-IRB-NPU]                                                                 \n",
       "12  [NRUP, HMB-IRB-NPU]                                                           \n",
       "13  [NRUP, HMB-IRB-NPU]                                                           \n",
       "14  [GRU]                                                                         \n",
       "15  [GRU]                                                                         \n",
       "16  [GRU]                                                                         \n",
       "17  [GRU]                                                                         \n",
       "18  [GRU]                                                                         \n",
       "19  [GRU]                                                                         \n",
       "20  [GRU]                                                                         \n",
       "21  [HMB-IRB, HMB-IRB-NPU, DS-ALZ-IRB, DS-ALZ-IRB-NPU, DS-ND-IRB, DS-ND-IRB-NPU]  \n",
       "22  [NRUP, GRU]                                                                   \n",
       "23  [GRU]                                                                         \n",
       "24  [GRU]                                                                         \n",
       "25  [NRUP, GRU-IRB]                                                               \n",
       "26  [GRU-IRB]                                                                     \n",
       "27  [NRUP, NPR]                                                                   \n",
       "28  []                                                                            \n",
       "29  [NRUP, GRU]                                                                   \n",
       "30  [NRUP, GRU-IRB]                                                               \n",
       "31  [NRUP, GRU, NPU, DS-ALZ, DS-ALZ-NPU]                                          \n",
       "32  [GRU]                                                                         \n",
       "33  [NRUP, GRU-IRB]                                                               \n",
       "34  [ADR]                                                                         \n",
       "35  [Genotype_Analysis]                                                           \n",
       "36  [NRUP, GRU]                                                                   \n",
       "37  [NRUP, GRU]                                                                   \n",
       "38  [NRU, GRU, NPU, ALZ, ALZ_NPU]                                                 "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "studies_to_df(ic_studies)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7dfde31b",
   "metadata": {},
   "source": [
    "## Step 8 - Query for studies with a particular disease focus\n",
    "\n",
    "We can query on the focus parameter to find studies which were focussed on a particular disease. The disease codes used are Mesh terms.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "61932c40",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total  Resources: 9\n",
      "Total  Bytes: 348787\n",
      "Time elapsed 0.2566 seconds\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>title</th>\n",
       "      <th>num_subjects</th>\n",
       "      <th>focus</th>\n",
       "      <th>focus_mesh</th>\n",
       "      <th>consents</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>phs000572</td>\n",
       "      <td>Alzheimer&amp;#39;s Disease Sequencing Project (ADSP)</td>\n",
       "      <td>15630</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[HMB-IRB, HMB-IRB-NPU, DS-ALZ-IRB, DS-ALZ-IRB-NPU, DS-ND-IRB, DS-ND-IRB-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>phs000745</td>\n",
       "      <td>RNAseq analysis of posterior cingulate astrocytes in Alzheimer&amp;#39;s disease</td>\n",
       "      <td>20</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>phs000727</td>\n",
       "      <td>miRNA Profiles in Serum and CSF of Parkinson&amp;#39;s and Alzheimer&amp;#39;s Patients</td>\n",
       "      <td>211</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[GRU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>phs000496</td>\n",
       "      <td>Columbia University Study of Caribbean Hispanics and Late Onset Alzheimer&amp;#39;s disease</td>\n",
       "      <td>3139</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>phs000168</td>\n",
       "      <td>NIA - Late Onset Alzheimer&amp;#39;s Disease and National Cell Repository for Alzheimer&amp;#39;s Disease Family Study: Genome-Wide Association Study for Susceptibility Loci</td>\n",
       "      <td>5220</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRUP, GRU, NPU, DS-ALZ, DS-ALZ-NPU]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>phs000378</td>\n",
       "      <td>Indianapolis-Ibadan, Nigeria Comparative Epidemiological Study of Dementia</td>\n",
       "      <td>1251</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRUP, GRU-IRB]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>phs000372</td>\n",
       "      <td>ADGC Genome Wide Association Study</td>\n",
       "      <td>6065</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[ADR]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>phs000219</td>\n",
       "      <td>GenADA/LONG/Imaging (Genetic Alzheimer&amp;#39;s Disease Associations)</td>\n",
       "      <td>1718</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[GBA]</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>phs000160</td>\n",
       "      <td>Genetics Consortium for Late Onset of Alzheimer&amp;#39;s Disease (LOAD CIDR Project)</td>\n",
       "      <td>2398</td>\n",
       "      <td>Alzheimer Disease</td>\n",
       "      <td>D000544</td>\n",
       "      <td>[NRU, GRU, NPU, ALZ, ALZ_NPU]</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          id  \\\n",
       "0  phs000572   \n",
       "1  phs000745   \n",
       "2  phs000727   \n",
       "3  phs000496   \n",
       "4  phs000168   \n",
       "5  phs000378   \n",
       "6  phs000372   \n",
       "7  phs000219   \n",
       "8  phs000160   \n",
       "\n",
       "                                                                                                                                                                   title  \\\n",
       "0  Alzheimer&#39;s Disease Sequencing Project (ADSP)                                                                                                                       \n",
       "1  RNAseq analysis of posterior cingulate astrocytes in Alzheimer&#39;s disease                                                                                            \n",
       "2  miRNA Profiles in Serum and CSF of Parkinson&#39;s and Alzheimer&#39;s Patients                                                                                         \n",
       "3  Columbia University Study of Caribbean Hispanics and Late Onset Alzheimer&#39;s disease                                                                                 \n",
       "4  NIA - Late Onset Alzheimer&#39;s Disease and National Cell Repository for Alzheimer&#39;s Disease Family Study: Genome-Wide Association Study for Susceptibility Loci   \n",
       "5  Indianapolis-Ibadan, Nigeria Comparative Epidemiological Study of Dementia                                                                                              \n",
       "6  ADGC Genome Wide Association Study                                                                                                                                      \n",
       "7  GenADA/LONG/Imaging (Genetic Alzheimer&#39;s Disease Associations)                                                                                                      \n",
       "8  Genetics Consortium for Late Onset of Alzheimer&#39;s Disease (LOAD CIDR Project)                                                                                       \n",
       "\n",
       "   num_subjects              focus focus_mesh  \\\n",
       "0  15630         Alzheimer Disease  D000544     \n",
       "1  20            Alzheimer Disease  D000544     \n",
       "2  211           Alzheimer Disease  D000544     \n",
       "3  3139          Alzheimer Disease  D000544     \n",
       "4  5220          Alzheimer Disease  D000544     \n",
       "5  1251          Alzheimer Disease  D000544     \n",
       "6  6065          Alzheimer Disease  D000544     \n",
       "7  1718          Alzheimer Disease  D000544     \n",
       "8  2398          Alzheimer Disease  D000544     \n",
       "\n",
       "                                                                       consents  \n",
       "0  [HMB-IRB, HMB-IRB-NPU, DS-ALZ-IRB, DS-ALZ-IRB-NPU, DS-ND-IRB, DS-ND-IRB-NPU]  \n",
       "1  [GRU]                                                                         \n",
       "2  [GRU]                                                                         \n",
       "3  [NRUP, GRU-IRB]                                                               \n",
       "4  [NRUP, GRU, NPU, DS-ALZ, DS-ALZ-NPU]                                          \n",
       "5  [NRUP, GRU-IRB]                                                               \n",
       "6  [ADR]                                                                         \n",
       "7  [GBA]                                                                         \n",
       "8  [NRU, GRU, NPU, ALZ, ALZ_NPU]                                                 "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "az_studies = mf.run_query(\"ResearchStudy?focus=D000544\")\n",
    "studies_to_df(az_studies)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "66c06037",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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