User / Data Editing / Uploading

Uploading Data to Scifeon

Last updated on 27-Aug-2018 by Frej Nøhr Larsen
Frej Nøhr Larsen

Bioinformatician
larsen@scifeon.com

Uploading to Scifeon

Scifeon is, at its heart, an interactive database. The easiest way to load data into the database, is to directly upload files containing the data.

This can be accomplished with a few clicks through the Scifeon user interface.

The above video shows the process of uploading a file: From selecting a locally stored data sheet, to viewing the contents in Scifeon:

The main upload page is accessed from the frontpage by clicking the arrow-looking icon in the navigation menu to the left. An Excel spreadsheet containing the data selected for upload is then dragged onto the dropzone area in Scifeon.

This should produce a preview of the entities that will be transfered to the Scifeon database. These are then uploaded when the upload button is clicked.

Once the files are done uploading, you can enter the entity view pages for the newly created entities.

Upload Plugins

This is not the only place to upload files: dropzones are also present on some entities - experiments for instance. This can be seen in the video below where result sets are uploaded to an experiment.

This video shows the entity page of a FACS experiment. To the left, a custom element has been added. This element contains a dropzone for uploading results files.

Dragging an element to the dropzone opens a pop-up window similar to the previously discussed upload page with a preview of the new entities.

Clicking the upload button creates the new entities in the database as results of the FACS experiment.

File Formats

Experimental data is often saved as spreadsheets in Microsoft Excel or similar programs and they come in a wide variety of formats and styles.

This means that not all data formats can be directly uploaded to Scifeon.

For a format to be uploadable, it has to have a matching data loader. Scifeon has several data loaders capable of reading different formats, but in case your specific file format cannot be uploaded, there is the possibility of writing your own data loader.

Otherwise the file can simply be uploaded as a file element as shown in the image below:

This simply saves a raw copy of the file to the experiment without creating any entities in the database. The file can then later be downloaded from the same page.