Editing strain metadata

Access control

Firstly, All the genome records downloaded from public databases, i.e. GenBank/SRA, can be viewed by all the users. However, there are strict access controls in EnteroBase for genome records uploaded by our users. By default, only the owner (the one who uploaded the data) and curators/administrators of the database have access to the genomic assemblies, metadata and genotypes prior to the release date. Owners can explicitly assign editing permissions to other users. See more about permissions here.

Furthermore, the user defined fields are private to their creator and curators/admin. Again, the creator can grant access to other users and the owner can chose to publicly publish their user defined fields, such that all other users can see and download the data.

The specific permissions granted to different users are listed in the table:

		Public	User uploads		User defined fields
		Released	Pre-release	Post-release	Private	Public
Curators & Admins		Edit & Download	Edit & Download	Edit & Download	Edit & Download	Edit & Download
Owner		Edit & Download	Edit & Download	Edit & Download	Edit & Download	Download
Buddies with edit rights		Edit & Download	Edit & Download	Edit & Download	Only visible when shared	Download
Buddies w/o edit rights		Download	Download in shared workspace	Download	Only visible when shared	Download
Other users		Download	View only	Download	Not visible	Download

Edit permissions

EnteroBase allows users with sufficent permissions to edit metadata. Users can correct mistakes in uploaded metadata or metadata associated with records downloaded from sequenced read archives (SRAs). Metadata maybe absent, or inaccurate, even after the automated pre-processing by EnteroBase. Editing permissions are automatically granted to:

• Administrators and curators
• the owner of a strain, or their buddies, if:

1. their EnteroBase email address matches the submitter’s email address in the SRA metadata
2. they have uploaded short reads to EnteroBase
3. ownership rights that were explicitly granted by administrators/curators after receiving an email request

To enter Edit Mode, login, and search strains using “Search Strains” and click on the Edit Mode checkbox. A popup window informs you that you are in Edit Mode and you need to click on OK. You have the rights to edit any row of metadata that contains a pencil icon in the second column from the left. If you need to edit metadata with no pencil, contact the administrators/curators to obtain permissions for individual Strain designations.

Editing Mode

In Edit Mode, for Strains where you have editing permission, a dark green pencil indicates adequate metadata while a red pencil indicates metadata which is lacking required information. The fields with errors are coloured red.

Required information include:

• Year of isolation
• Country, and continent of isolation
• Laboratory contact details

If country and/or continent are inconsistent, you will need to resolved this in the sub-window, which is opened by clicking the field Location.

Metadata can be changed by typing into the text boxes, or all metadata for a Strain can be edited after clicking the pencil icon. Editing changes are updated in the Edit Mode browser after clicking outside the text box, but can be reversed with Ctl+Z or a mouse right click on the cell with changed data. Yellow cells indicate data which has been edited. Saving edited data is not automatic! To save edited data, click on Save Edits icon or `Edit -> Save Edits`. To save only one row of edited data, right click and choose Save Edited Row.

Multiple replaces can be performed using `Edit -> Search and Replace`.

Downloading Metadata

Metadata -> Download Metadata will generate a tab delimited text file (can be imported into Excel) containing the metadata and an overview of the experimental data from the right part of the screen. If some entries are selected, only selected entries will be downloaded. If no entries are selected, you will need to specify how many are to be downloaded, starting from the top entry on the screen. Warning: downloading all entries can result in a file containing 10,000s of rows. `Metadata -> Download editable Metadata` will also generate a tab delimited text file, with the suffix “.txt”.

You are not able to download metadata of a private EnteroBase record unless you have been granted download permissions from the owner of the record.