diff --git a/notebooks/getting_started/exploring_clinical_data.ipynb b/notebooks/getting_started/exploring_clinical_data.ipynb
index d481c6a..92c3f0f 100644
--- a/notebooks/getting_started/exploring_clinical_data.ipynb
+++ b/notebooks/getting_started/exploring_clinical_data.ipynb
@@ -43,7 +43,7 @@
"---\n",
"Initial version: Jul 2024\n",
"\n",
- "Updated: Sep 2024"
+ "Updated: Feb 2025"
],
"metadata": {
"id": "RVHEoPZJgVbl"
@@ -65,7 +65,7 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {
"id": "k8B1uiZkYlHu"
},
@@ -89,9 +89,9 @@
{
"cell_type": "code",
"source": [
- "from idc_index import index\n",
+ "from idc_index import IDCClient\n",
"\n",
- "c = index.IDCClient()\n",
+ "c = IDCClient()\n",
"\n",
"c.fetch_index('clinical_index')\n",
"\n",
@@ -99,12 +99,12 @@
],
"metadata": {
"id": "ehb4MeuPYy4c",
- "outputId": "c7267c6e-9a3f-4378-86aa-9868c78cf5dc",
+ "outputId": "36e97296-465a-4e13-9dd5-6a423abf1a82",
"colab": {
"base_uri": "https://localhost:8080/"
}
},
- "execution_count": 2,
+ "execution_count": null,
"outputs": [
{
"output_type": "stream",
@@ -115,7 +115,8 @@
"table_name\n",
"short_table_name\n",
"column\n",
- "column_label\n"
+ "column_label\n",
+ "values\n"
]
}
]
@@ -157,7 +158,7 @@
"metadata": {
"id": "L6rMuMEHjiML"
},
- "execution_count": 3,
+ "execution_count": null,
"outputs": []
},
{
@@ -171,181 +172,60 @@
"height": 1000
},
"id": "X5jfORxlaQ-Q",
- "outputId": "76af1c40-a713-4639-a730-b7e82bf56414"
+ "outputId": "d4eadd7c-cdf9-4fa8-eca6-4c7ce0f86086"
},
- "execution_count": 4,
+ "execution_count": null,
"outputs": [
{
"output_type": "execute_result",
"data": {
"text/plain": [
- " collection_id \\\n",
- "0 rms_mutation_prediction \n",
- "1 rms_mutation_prediction \n",
- "2 rms_mutation_prediction \n",
- "3 rms_mutation_prediction \n",
- "4 rms_mutation_prediction \n",
- "5 rms_mutation_prediction \n",
- "6 rms_mutation_prediction \n",
- "7 rms_mutation_prediction \n",
- "8 rms_mutation_prediction \n",
- "9 rms_mutation_prediction \n",
- "10 rms_mutation_prediction \n",
- "11 rms_mutation_prediction \n",
- "12 rms_mutation_prediction \n",
- "13 rms_mutation_prediction \n",
- "14 rms_mutation_prediction \n",
- "15 rms_mutation_prediction \n",
- "16 rms_mutation_prediction \n",
- "17 rms_mutation_prediction \n",
- "18 rms_mutation_prediction \n",
- "19 rms_mutation_prediction \n",
- "20 rms_mutation_prediction \n",
- "21 rms_mutation_prediction \n",
- "22 rms_mutation_prediction \n",
- "23 rms_mutation_prediction \n",
- "24 rms_mutation_prediction \n",
- "25 rms_mutation_prediction \n",
- "26 rms_mutation_prediction \n",
- "27 rms_mutation_prediction \n",
- "28 rms_mutation_prediction \n",
- "29 rms_mutation_prediction \n",
- "30 rms_mutation_prediction \n",
- "31 rms_mutation_prediction \n",
- "32 rms_mutation_prediction \n",
- "33 rms_mutation_prediction \n",
- "34 rms_mutation_prediction \n",
- "35 rms_mutation_prediction \n",
- "36 rms_mutation_prediction \n",
- "37 rms_mutation_prediction \n",
- "38 rms_mutation_prediction \n",
- "\n",
- " table_name \\\n",
- "0 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "1 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "2 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "3 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "4 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "5 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "6 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "7 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "8 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "9 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "10 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "11 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "12 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "13 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "14 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "15 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "16 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "17 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "18 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "19 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "20 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "21 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "22 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "23 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "24 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "25 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "26 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "27 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "28 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "29 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "30 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "31 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "32 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "33 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "34 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "35 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "36 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "37 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "38 bigquery-public-data.idc_v19_clinical.rms_muta... \n",
- "\n",
- " short_table_name column \\\n",
- "0 rms_mutation_prediction_demographics source_batch \n",
- "1 rms_mutation_prediction_demographics race \n",
- "2 rms_mutation_prediction_demographics gender \n",
- "3 rms_mutation_prediction_demographics dicom_patient_id \n",
- "4 rms_mutation_prediction_demographics participant_id \n",
- "5 rms_mutation_prediction_diagnosis source_batch \n",
- "6 rms_mutation_prediction_diagnosis diagnosis_id \n",
- "7 rms_mutation_prediction_diagnosis disease_type \n",
- "8 rms_mutation_prediction_diagnosis primary_diagnosis \n",
- "9 rms_mutation_prediction_diagnosis primary_diagnosis_reference_source \n",
- "10 rms_mutation_prediction_diagnosis metastasis_at_diagnosis \n",
- "11 rms_mutation_prediction_diagnosis stage \n",
- "12 rms_mutation_prediction_diagnosis last_known_disease_status \n",
- "13 rms_mutation_prediction_diagnosis days_to_last_known_disease_status \n",
- "14 rms_mutation_prediction_diagnosis tissue_or_organ_of_origin \n",
- "15 rms_mutation_prediction_diagnosis progression_or_recurrence \n",
- "16 rms_mutation_prediction_diagnosis site_of_resection_or_biopsy \n",
- "17 rms_mutation_prediction_diagnosis dicom_patient_id \n",
- "18 rms_mutation_prediction_diagnosis participantparticipant_id \n",
- "19 rms_mutation_prediction_diagnosis primary_site \n",
- "20 rms_mutation_prediction_diagnosis days_to_recurrence \n",
- "21 rms_mutation_prediction_diagnosis days_to_last_followup \n",
- "22 rms_mutation_prediction_diagnosis age_at_diagnosis \n",
- "23 rms_mutation_prediction_sample source_batch \n",
- "24 rms_mutation_prediction_sample sample_type \n",
- "25 rms_mutation_prediction_sample histological_classification \n",
- "26 rms_mutation_prediction_sample tumor_grade \n",
- "27 rms_mutation_prediction_sample tumor_stage_clinical_t \n",
- "28 rms_mutation_prediction_sample tumor_stage_clinical_n \n",
- "29 rms_mutation_prediction_sample tumor_stage_clinical_m \n",
- "30 rms_mutation_prediction_sample tumor_morphology \n",
- "31 rms_mutation_prediction_sample tumor_incidence_type \n",
- "32 rms_mutation_prediction_sample sample_description \n",
- "33 rms_mutation_prediction_sample sample_tumor_status \n",
- "34 rms_mutation_prediction_sample dicom_patient_id \n",
- "35 rms_mutation_prediction_sample participantparticipant_id \n",
- "36 rms_mutation_prediction_sample sample_id \n",
- "37 rms_mutation_prediction_sample sample_anatomic_site \n",
- "38 rms_mutation_prediction_sample participant_age_at_collection \n",
- "\n",
- " column_label \n",
- "0 idc_provenance_source_batch \n",
- "1 race \n",
- "2 gender \n",
- "3 idc_provenance_dicom_patient_id \n",
- "4 participant_id \n",
- "5 idc_provenance_source_batch \n",
- "6 diagnosis_id \n",
- "7 disease_type \n",
- "8 primary_diagnosis \n",
- "9 primary_diagnosis_reference_source \n",
- "10 Metastasis_at_diagnosis \n",
- "11 Stage \n",
- "12 last_known_disease_status \n",
- "13 days_to_last_known_disease_status \n",
- "14 tissue_or_organ_of_origin \n",
- "15 progression_or_recurrence \n",
- "16 site_of_resection_or_biopsy \n",
- "17 idc_provenance_dicom_patient_id \n",
- "18 participant.participant_id \n",
- "19 primary_site \n",
- "20 days_to_recurrence \n",
- "21 days_to_last_followup \n",
- "22 age_at_diagnosis \n",
- "23 idc_provenance_source_batch \n",
- "24 sample_type \n",
- "25 Histological_Classification \n",
- "26 tumor_grade \n",
- "27 tumor_stage_clinical_t \n",
- "28 tumor_stage_clinical_n \n",
- "29 tumor_stage_clinical_m \n",
- "30 tumor_morphology \n",
- "31 tumor_incidence_type \n",
- "32 sample_description \n",
- "33 sample_tumor_status \n",
- "34 idc_provenance_dicom_patient_id \n",
- "35 participant.participant_id \n",
- "36 sample_id \n",
- "37 sample_anatomic_site \n",
- "38 participant_age_at_collection "
+ " collection_id ... values\n",
+ "0 rms_mutation_prediction ... [{'option_code': '0', 'option_description': No...\n",
+ "1 rms_mutation_prediction ... [{'option_code': '', 'option_description': Non...\n",
+ "2 rms_mutation_prediction ... [{'option_code': 'Female', 'option_description...\n",
+ "3 rms_mutation_prediction ... []\n",
+ "4 rms_mutation_prediction ... []\n",
+ "5 rms_mutation_prediction ... [{'option_code': '0', 'option_description': No...\n",
+ "6 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "7 rms_mutation_prediction ... [{'option_code': 'Soft Tissue Tumors and Sarco...\n",
+ "8 rms_mutation_prediction ... [{'option_code': 'Rhabdomyosarcoma', 'option_d...\n",
+ "9 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "10 rms_mutation_prediction ... [{'option_code': '', 'option_description': Non...\n",
+ "11 rms_mutation_prediction ... [{'option_code': '', 'option_description': Non...\n",
+ "12 rms_mutation_prediction ... [{'option_code': '', 'option_description': Non...\n",
+ "13 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "14 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "15 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "16 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "17 rms_mutation_prediction ... []\n",
+ "18 rms_mutation_prediction ... []\n",
+ "19 rms_mutation_prediction ... []\n",
+ "20 rms_mutation_prediction ... []\n",
+ "21 rms_mutation_prediction ... []\n",
+ "22 rms_mutation_prediction ... []\n",
+ "23 rms_mutation_prediction ... [{'option_code': '0', 'option_description': No...\n",
+ "24 rms_mutation_prediction ... [{'option_code': 'Tumor', 'option_description'...\n",
+ "25 rms_mutation_prediction ... [{'option_code': '', 'option_description': Non...\n",
+ "26 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "27 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "28 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "29 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "30 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "31 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "32 rms_mutation_prediction ... [{'option_code': '', 'option_description': None}]\n",
+ "33 rms_mutation_prediction ... [{'option_code': 'Tumor', 'option_description'...\n",
+ "34 rms_mutation_prediction ... []\n",
+ "35 rms_mutation_prediction ... []\n",
+ "36 rms_mutation_prediction ... []\n",
+ "37 rms_mutation_prediction ... []\n",
+ "38 rms_mutation_prediction ... []\n",
+ "\n",
+ "[39 rows x 6 columns]"
],
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