User guide for working with Cell metadata and expression #177
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MikhailAf
commented
Jan 22, 2026
MikhailAf
commented
| Each cell record belongs to a Cell Group, which represents a single cell table (group). | ||
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| ## Cell metadata and Cell expression in ODM | ||
| Cell metadata can be imported into ODM using the `job` endpoints and [import_ODM_data script](../../tools/odm-sdk/terminal/study/uploading-study.md). |
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Looks like we have to add examples on the mentioned page to show how cells and expression data for cells could be imported using script, wdyt?
| "groupAccession": "GSF1234567" | ||
| } | ||
| ``` | ||
| Learn more about [uploading data to ODM via API here](../doc-odm-user-guide/import-data-using-api.md). |
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Maybe we should add to this mentioned page also information about importing cell data, to keep information about all entities on the same page, wdyt?
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| Note that Cell metadata will be linked to the nearest metadata group mentioned above in the script. | ||
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| Learn more about [uploading data to ODM using the script here](../doc-odm-user-guide/import-data-using-python-script.md). |
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Don't we mention this page a lot of times? :)
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| #### Common rules | ||
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| To link Cell metadata to other metadata groups use the following endpoints: |
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Let's also mention that these endpoints can be found in the integrationCurator section
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| Fail conditions: | ||
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| * There is no Sample Source/Library/Preparation ID in Sample/Library/Preparation metadata group. |
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Are you sure that we can import such groups that do not contain values in required columns? I'm not sure but I didn't check
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| * There is no Sample Source/Library/Preparation ID in Sample/Library/Preparation metadata group. | ||
| * There are no matches between `batch` in Cell metadata and Sample Source/Library/Preparation IDs. | ||
| * Cell metadata group is already linked to another metadata group. |
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One cell group can be linked to different metadata groups, it's possible when user uses these endpoints (not odm import data command)
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| ### Linking Cell expression to Cell metadata | ||
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| To link Cell expression to Cell metadata group use the following endpoint: |
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Let's please also mention here section where this endpoint can be found
| threshold, cell type, or cluster) relative to a defined reference group or the total cell population | ||
| (`countAvailable`) defined by study, samples, library, or preparation metadata. | ||
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| Path: POST `/api/v1/as-curator/omics/cells/analytics/cell-ratio` |
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Let's mention where in swagger it can be found (in integrationCurator)
| You use it when you want quick “what does this gene look like in these cells?” metrics: | ||
| mean/median, spread, quantiles, min/max, and a histogram-style density summary. | ||
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| Path: POST `/api/v1/as-curator/omics/cells/analytics/gene-summary` |
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Let's mention where in swagger it can be found (in integrationCurator)
| a `Case` group and a `Control` group. It returns per-gene metrics that quantify how strongly expression | ||
| differs between the two groups, including **fold change** and **Mann–Whitney U test** results. | ||
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| Path: POST `/api/v1/as-curator/omics/cells/analytics/differential-expression` |
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Let's mention where in swagger it can be found (in integrationCurator)
