--- agentTools: projectIndex: https://docs.cancergenomicscloud.org/llms.txt --- # dbGaP Submission Form Suite ## Overview dbGaP Submission Form Suite is an app that allows you to easily import, map and prepare your data for import into the database of Genotypes and Phenotypes (dbGaP). ***The app does not submit any data to dbGaP, but allows you to prepare the proper submission format and accelerate the submission process, as shown below.*** [block:image] { "images": [ { "image": [ "https://files.readme.io/6035977-dbgap-process.png", "dbgap-process.png", 1760, 890, "#000000" ] } ] } [/block] The dbGaP Submission Form Suite is currently in its BETA stage. Please send any feedback or suggestions to . ### Access the dbGaP Submission Form Suite app To access the dbGaP Submission Form Suite app on the CGC, follow the steps below: 1. Log in to the CGC. 2. [Create](https://docs.cancergenomicscloud.org/docs/create-a-project) or [open](https://docs.cancergenomicscloud.org/docs/view-a-project) a project that you want to use for data manipulation with the app. If you don't already have the data in a project on the CGC, you can [upload](https://docs.cancergenomicscloud.org/docs/upload-to-the-cgc) it beforehand. Note that the data doesn't have to be in the same project from which you are launching the app. 3. Click the **Interactive Browsers** tab. Available interactive apps are displayed. 4. Scroll down to the **Custom interactive apps** section to find the **dbGaP Submission App** card. 5. On the dbGaP Submission App card, click **Open**. The app opens in a new tab. 6. Click **Yes** to allow the app to access your CGC resources. The app's landing screen is displayed and you can now start loading data The following options are available on the landing screen: * **dbGaP Form Creator**: Opens the dbGaP Submission Worksheet tab inside the app. * **Need Help**: Opens this guide. ### Load an input manifest file To load an input manifest file, select the **dbGaP Submission Worksheet** tab on the app's top navigation bar. This displays the manifest input selection screen. Supported file format for input manifest files is a single-sheet .xlsx file with column names in the first row. To load a manifest file, follow the steps below: [block:image] { "images": [ { "image": [ "https://files.readme.io/88003ee-dbgap-load-manifest.png", "dbgap-load-manifest.png", 1182, 713, "#000000" ] } ] } [/block] 1. Select the **Project** from which you want to load the file. Please wait until the folder list is populated as it might take several seconds with a larger number of folders. 2. Select the **Folder** within the project that contains the file you want to load. Available options are either the project's **root** folder, or the folders from the first level of folder structure. *Files that are located deeper inside the project's folder structure can't be loaded directly*. 3. Click **Select file**. A new window opens, displaying available files from the selected project folder. 4. Select the file you want to use as your manifest file and click **Pick file**. Once the file has been loaded, you can start the configuration and mapping process. 5. Click **Load Data**. The file structure and content is validated. If the validation is completed successfully, two additional panes are displayed: * **Uploaded File Content**: Contains a table showing the data present in the file. *You have the options to sort and filter data for preview purposes, but these actions won't affect the actual data in any way*. * **Uploaded File Summary**: Shows charts that represent the structure of uploaded data, as well as missing data from each of the columns present in the loaded file. 6. Click **Next**. You can now start mapping data. ### Step 1: Subject and Sample (SSM DS) In this step you need to select corresponding metafields of your input metadata spreadsheet for the following fields: * **Subject ID** *(required)*: Select the column that contains the unique IDs of study participants (subjects). Expected data type for the column is string. * **Sample ID** *(required)*: Select the column that contains IDs for each of the samples. A Sample ID is a biological aliquot from a person and is the primary key for the molecular data. Expected data type for the column is also string. [block:image] { "images": [ { "image": [ "https://files.readme.io/6961812-dbgap-step-1.png", "dbgap-step-1.png", 1029, 509, "#000000" ] } ] } [/block] Add any additional (optional) fields and their mapping: 1. Click **Add New Field**. The Add new optional field dialog opens. [block:image] { "images": [ { "image": [ "https://files.readme.io/08875b5-dbgap-optional-field.png", "dbgap-optional-field.png", 898, 611, "#000000" ] } ] } [/block] 2. Enter the information for the new field: * **Field name** *(required)*: Define the name for the field you are adding. * **Mapping column** *(required)*: Select the column in the manifest file which the new field will be mapped to. * **Field type**: Enter the value type of the field you want to add. For encoded fields, enter `encoded value`. * **Units**: Enter the measurement units for the values contained in the field. * **Values** *(for encoded fields only)*: Enter all unique value for the encoded field in the `value=description;value=description` format (separated by semicolons). For example, `1=Male;2=Female;UNK=Unknown`. * **Description**: Enter a text description that provides more details about the field. To refer to the structure of the loaded manifest file at any time while adding a new field, click **Explore loaded manifest**. 3\. Click **Submit**. A new optional field mapping is added. [block:image] { "images": [ { "image": [ "https://files.readme.io/a80b6b3-dbgap-optional-fields-list.png", "dbgap-optional-fields-list.png", 986, 458, "#000000" ] } ] } [/block] Once added, optional fields can be edited () or deleted (). Click **Next** to continue. ### Step 2: Sample Attributes DS In this step you need to select the following required attribute values: * **Sample ID** *(required)*: The column that contains IDs for each of the samples. A Sample ID is a biological aliquot from a person and is the primary key for the molecular data. Expected data type for this field is string. Add any [optional fields](#add-optional-fields). Click **Next** to continue. ### Step 3: Subject Consent DS In this step you need to link the consent information with Subject ID, by selecting columns for the following fields: * **Subject ID** *(required)*: Select the column that contains the unique IDs of study participants (subjects). Expected data type for this field is string. * **Consent** *(required)*: Select the column that contains the single consent value for each person using a value encoded in the DD. * **Consent encoded values**: Enter all unique values and descriptions of all encoded consent values in the following format: `value=description;value=description`. Note that these value-description pairs should be separated by semicolons. For example, `1=General Research Use (NPU);2=Health/Medical/Biomedical (GSO)`. Add any [optional fields](#add-optional-fields). Click **Next** to continue. ### Step 4: Subject Phenotypes DS In this step you need to link phenotypic data with Subject ID, by selecting columns for the following fields: * **Subject ID** *(required)*: Select the column that contains the unique IDs of study participants (subjects). Expected data type for this field is string. Add any [optional fields](#add-optional-fields). Click **Next** to continue. ### Step 5: Review and Export The final step allows you to review the mapped data and export it for submission to dbGaP. Before export, you can preview the data in the **Generated dbGaP Submission Document Preview** pane. [block:image] { "images": [ { "image": [ "https://files.readme.io/faf558a-dbgap-review-and-export.png", "dbgap-review-and-export.png", 1293, 921, "#000000" ] } ] } [/block] To export a file for submission to dbGaP, use the controls in the **Download Submission Document** pane by following the steps below: 1. In the **Submission file name** field enter the name for the exported file. 2. *(Optional)* Click **Add timestamp** to append the timestamp to the defined file name. 3. Click **Download Submission File**. The file is downloaded to your computer. To start the file loading and mapping process from the very beginning click **Reset all**. This will reset all loaded and mapping data and let you start the process again.