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guide.qmd
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guide.qmd
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---
title: "Step-by-step guide"
lightbox: true
---
### YODA
**YODA** is used as a secure data solution, where data generators can upload the filled templates.
::: {.callout-tip icon="false" appearence="simple"}
More information and a detailed ‘manual’ about YODA can be found on their [website](https://www.uu.nl/en/research/yoda/guide-to-yoda).
:::
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## Good to know
It is also possible to publish data straight from YODA.
:::
Data generators receive an email to register, after which they can access the dedicated [website](https://dgk.yoda.uu.nl/) for data upload.
The main folder is called **‘research-enanomapper’** with an **‘enm_filesharing’** and an optional **‘for_publication’** folder within. There is also a README.txt file giving extra information on file naming. This information is also available under the [**naming convention**](/naming.qmd) tab.
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Only MOMENTUM data generators, the responsible person from eNanomapper and data managers have access to this environment.
:::
#### Explanation of folder stucture
- The **enm_filesharing** is a dump folder that provides a collection place for Excel-based MOMENTUM data that will subsequently be transferred into the online database of eNanomapper. It has sub-folders corresponding to separate experiments. Templates should be uploaded into the fitting folder. If there is no fitting folder, one can simply create one (using lowercase letters and hyphens, if needed).
- Furthermore, the provision of descriptive metadata in Excel format about other types of data (e.g. microscopy, DNA sequencing etc.) is required. The metadata should contain a link to where these other data types are stored/will be made available (e.g. in YODA or another well-established repository).
- Data in other formats that is described by a template can be directly placed in this filesharing folder, according to experiment type, to make referencing easier. However, the data owner can choose to make these other files available in another repository as long as clear referencing in templates to linked files is achieved.
- The **for_publication** folder is intended for the minimum 'data packages'. Organising MOMENTUM data properly is part of good data management and therefore a key step. Where to store and publish these 'data bundles' however is up to the data owner - having the possibility to choose another standard, widely-accepted repository gives more freedom.
- This folder is rather empty still. Data generators are free to create sub-folders for their *intended publications* to keep data packages there.
### eNanomapper
"The eNanoMapper database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project."[^1]
[^1]: https://enanomapper.adma.ai/about/
#### How to use eNanomapper for Momemtum data
- Navigate to the [**template wizard**](https://enanomapper.adma.ai/projects/momentum/datatemplates/) of MOMENTUM.
- Find template corresponding to experiment and adjust variables in the wizard. After downloading, fill in Excel sheet. In case the layout does not fit the experimental output (/you wish to adjust template layout to fit your data), please create a template in the [**template designer**](https://enanomapper.adma.ai/templates) instead. Same applies to the metadata templates. Templates obtained from the wizard and changed after download are not suitable for the data transfer into eNanomapper.
- After downloading and filling in suitable templates according to your respective research, upload Excel files to the corresponding sub-folders (name as the template/experiment name). Naming convention is described under the [**corresponding tab**](/naming.qmd).
- If there is no sub-folder for a given template/experiment yet, please create it under the temp_filesharing folder.
- There are no sub-folders in the publication folder yet so create one for your paper if you decide to place data packages in YODA. There is an extra folder for data that will not be part of your publication. Please follow the same naming convention for traceability.
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## Template wizard
For a more elaborate walk-through, please consult the [user guide](https://enanomapper.adma.ai/assets/img/guide/guide.pdf) for the Template wizard.
:::
#### How to use the Template Designer
- You can see the different steps of designing your own template on the [**Template designer tab**](/designer.qmd).
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## Next step
When the folders are populated with data, the partner from eNanomapper can fetch this data and parse it into the eNanomapper database.
:::