Upload¶

Prerequisites

This article requires that you understand how data is stored on SynDB, we recommend reading through the overview article if you are uncertain.

Uploading to SynDB is a multistep process, and requires understanding of the SynDB dataset model.

The process¶

Preparation¶

We recommend you to follow the guide in the exact sequence provided. This ensures the instructions are followed effectively and idiomatically.

Terms and conditions¶

You must accept the terms and conditions before uploading data. The terms include: - Statement that the data is not false or misleading - Redistribution rights - Data licensing agreement with the license of your choice, see guide to pick license; the default license is ODC-BY.

Data structuring¶

SynDB utilizes data standardization to facilitate uploads. Your imaging metrics must be in a tabular data format; for instance, .xlsx, .csv, or .parquet. Read more about the data structuring in the contributor's guide.

Once you enter the upload page, you will be prompted to log in to your SynDB account if you are not already; furthermore, you must verify your academic status by logging in to your institution's account.

The upload¶

You can upload data using the CLI or the GUI; including mixing the usage of both. We recommend that you only use the GUI for the first time.

1. Assign IDs, and correlate relations¶

Each SynDB unit requires a unique ID assigned before being uploaded to the platform. The GUI does this automatically, but not the CLI. When you have multiple SynDB tables under one dataset it is expected that these have some relations with each other.

Dataset integrity

As it may lead to undefined behaviour, it is disallowed to upload SynDB table data that are unrelated under the same dataset!

Meaning that you cannot upload a table of neurons and a table of synapses under the same dataset unless each synapse has a relation to a neuron from the respective table of neurons.

GUI¶

The GUI will automatically assign UUIDs to each SynDB unit. The relations are correlated based on the top-down hierarchy of the tables, you may find the latest version of the hierarchy in the source on GitHub.

CLI¶

TODO

2. Selecting or creating the SynDB dataset metadata¶

As mentioned, in the overview article, every dataset has a metadata defined by the data owner during the upload. You can either select an existing dataset or create a new one.

3. Confirm and upload¶

Before the upload starts you will be prompted to confirm the dataset and the data you are uploading. Once you confirm, the upload will start. Should be relatively quick.

Delete owned datasets¶

You may at any time delete datasets that you own. This will remove the dataset and all the data associated with it. The deletion is permanent and cannot be undone.