The section Import Data in ODM has been updated #60
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…ns and screenshots
…ns and screenshots
…ns and screenshots
…ns and screenshots
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In addition to the mentioned changes, could you please pay special attention to the final section "Important Considerations for Data Import"? I rephrased some of the text, but I want to make sure it is clear and accurate. Also, the name of the section should be Data Import in ODM, not "on" |
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| This will open a dialogue box that prompts you to select a local TSV file. | ||
| * A new window will pop up. Click **Select tsv file...** and choose your file. | ||
| * Once your file is recognized, click **Import**. Refer to the section [Supported files](https://docs.google.com/document/d/1uF3g11QO3PfyhsSY7u0CPozn0LPRsoblnI2djZydvIs/edit?usp=sharing) to explore details on metadata requirements (e.g., **Sample Source ID** is a mandatory column) |
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I believe we need to add some internal link to the section somewhere inside our user guide, it shouldn't be some google doc, we agreed to keep all instructions and information only in the user guide. Could you please fix this link?
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I mean that we need to do as e.g. here: https://github.com/genestack/user-docs/pull/60/files#diff-81b6cd4037411eff6f8046e8ece401b7dba1131cc5abd5ffbd1e2a7f5c419528R94
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| ## Import Data [BETA] | ||
| ## Import Libraries and preparations |
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Probably Preparations instead of preparations?
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| #### NOTE | ||
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| <figcaption>Click on the option <strong>+More</strong> to add Libraries and/or preparation metadata</figcaption> |
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preparations or Preparations?
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| You can find a detailed description of the supported file formats [Tabular data](supported-formats.md#format-label). | ||
| Both types of files are linked to the samples metadata file (from the Samples tab) via the **SampleSource ID** column. Ensure this column is included in all files to maintain the link between sample metadata, libraries, and preparations. |
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Sample Source ID column, not SampleSource ID
| - **Local Computer**: Select the file located on your computer. Please note: this option is only available if your ODM version is coupled with AWS S3 storage (provided by default). If this option isn’t functioning properly, please get in touch with Genestack’s customer care team. | ||
| - **External Link**: Upload the file by supplying a link to the file’s location. Keep in mind that while this option is intended to support any external location, in its BETA version, it only supports links from AWS S3 storage. If you encounter any issues with this feature, please reach out to Genestack’s customer care team. | ||
| * **Default Linking**: By default, the data is linked with the Samples file using the **Sample Source ID** column. To ensure proper linking, make sure your file includes a column called **Sample Source ID** with the same IDs used in the Sample Metadata table uploaded previously (see section "Import Samples Metadata"). | ||
| * **Custom Linking**: Alternatively you can select a different column to link the **experimental** data, such as **Sample Name**, **Date**, etc. This provides flexibility in how data is associated, but it is recommended to include the **SampleSourceID** column for consistent referencing and linking samples metadata files with additional data types like libraries and preparations. Read the [Supported format files](https://docs.google.com/document/d/1uF3g11QO3PfyhsSY7u0CPozn0LPRsoblnI2djZydvIs/edit?usp=sharing) section for more information. |
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Please, rename SampleSourceID to Sample Source ID, also please, replace link to some google doc with some internal link from the user guide
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| After the upload completes, the corresponding data will be visible in the ‘Data’ tab. All files are grouped by the chosen ‘Data Class’ parameter on the left panel, which includes attached files as well. | ||
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| <figcaption>The selected files will be scanned, and if the format is accepted and the columns contain the reference names to be linked, the files will be indexed and the experimental data will be searchable</figcaption> | ||
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| After uploading, you can populate the corresponding file metadata, including the necessary details. Please note that each uploaded data file has five mandatory read-only fields that do not belong to your template: |
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Could you please remove this part: "that do not belong to your template", because these attributes are from template? since we work with this file anyway
| * Select the entity to which your data will be linked. For example, when uploading a transcriptomics file with gene expression measurements for each sample, link the data to the relevant samples. Specify the ID column from the Samples (or Library, Preparation) tab that will be used to match the samples (or libraries, preparations) in the uploaded file. | ||
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| !!! note | ||
| You need to have sample information (metadata) uploaded in the **Samples** tab to enable data import. If no libraries or preparations are associated with the study, **Sample** will be the only available option. |
| !!! note | ||
| You need to have sample information (metadata) uploaded in the **Samples** tab to enable data import. If no libraries or preparations are associated with the study, **Sample** will be the only available option. | ||
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| * **Libraries and Preparations**: Libraries and preparations are connected to the samples via the **SampleSource ID** column. Ensure this column is included in all relevant files to maintain the linkage between sample metadata, libraries, and preparations. |
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SampleSource ID -> Sample Source ID
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Please, remove also in scope of this PR all old images that have been replaced and are nor used anymore |
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| ## Import experimental Data and attach files | ||
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| In addition to the samples, libraries, and preparations metadata described above, you can upload experimental data that is linked to your study via sample metadata and libraries/preparations. You can also supplement your study by attaching related research materials like PDFs, XLSX, DOCX, PPTX files, images, and more. Please note, the contents of these attached files won't be indexed or made searchable. | ||
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| **Data Type (Data Class)**: Identify the data type you want to upload. Multiple types are supported: |
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probably new data class "Document" also can be added to the list
| <figcaption>Click on the Data tab to access options for uploading experimental data and attaching additional files</figcaption> | ||
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optional: screenshot can be updated to shew current list of available data classes
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| If your file includes more than one measurement per Sample (Library or Preparation), e.g., Fold Change and P-value, the system will automatically recognize it based on the following criteria: | ||
| * Click "Next." This will open a window where you can select a file containing experimental data from your local computer or a cloud-based storage system (such as AWS). |
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Since we can import data from different sources (e.g. minio, aws s3, etc) it will be better to call it "external storage", let's please rephrase?
| - Presence of Measurement Separator Symbol: Every column must include a measurement separator. | ||
| - Consistency of Measurement Types: All samples (libraries or preparations) must have the same types of measurements in the file. For example, if you have three samples and each has measurements for Intensity and Quality Pass, your file should have six columns named: ‘Sample1.Intensity’, ‘Sample1.QualityPass’, ‘Sample2.Intensity’, ‘Sample2.QualityPass’, ‘Sample3.Intensity’, ‘Sample3.QualityPass’. | ||
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| <figcaption>Select the source for the experimental data. Experimental data can be imported from your local computer or a cloud-based storage system (such as AWS)</figcaption> |
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Since we can import data from different sources (e.g. minio, aws s3, etc) it will be better to call it "external storage", let's please rephrase?
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| After uploading, you can populate the corresponding file metadata, including the necessary details. Please note that each uploaded data file has five mandatory read-only fields that do not belong to your template: | ||
| After uploading, you can populate the corresponding file metadata, including the necessary details. Please note that each uploaded data file has five mandatory read-only fields: | ||
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| - Genestack:accession |
| * You can attach any format files such as PDF, PNG, etc. | ||
| * Click **Select file...**. Select the file from your local computer | ||
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Screenshot should be updates since we've added data classed to attachments also
| * Click **Select file...**. Select the file from your local computer | ||
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| <figcaption>The files will be uploaded (upload time will depend on the size of the files). Your files will be displayed in the Data tab under <strong>Attached Files</strong>.</figcaption> |
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Text should be updates since we've added data classed to attachments also
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| <figcaption>The files will be uploaded (upload time will depend on the size of the files). Your files will be displayed in the Data tab under <strong>Attached Files</strong>.</figcaption> | ||
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| Once the files are selected, the upload will begin and the files will be attached. Available data will be displayed in the Data tab by type: **Experimental** (e.g., bulk transcriptomics) and **Attached files** (e.g., manuscripts, reports). |
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Attachments will be displayed under chosen data type, could you please update this text.
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| Once the files are selected, the upload will begin and the files will be attached. Available data will be displayed in the Data tab by type: **Experimental** (e.g., bulk transcriptomics) and **Attached files** (e.g., manuscripts, reports). | ||
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Attachments will be displayed under chosen data type, could you please update this screenshot.
| Once the files are selected, the upload will begin and the files will be attached. Available data will be displayed in the Data tab by type: **Experimental** (e.g., bulk transcriptomics) and **Attached files** (e.g., manuscripts, reports). | ||
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| <figcaption>Once attached or linked, files will be shown on the Data tab under their specific category, e.g., <strong>bulk transcriptomics</strong> for experimental data and a manuscript (PDF format) for attached files</figcaption> |
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Attachments will be displayed under chosen data type, could you please update this text.
The section Import Data in ODM has been updated, and new screenshots and sections have been added.