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Editing strain metadata

Overview

EnteroBase allows editing by users of metadata for which they have editing permissions. Editing may be needed if the user has made mistakes in uploading metadata. Editing may also be needed for metadata associated with sort read archives (SRAs) that have been downloaded from NCBI, but for which metadata were absent, or inaccurate, even after the automated pre-processing by EnteroBase.

Editing permissions are automatically granted to:

• the owner of a strain, or their buddies, based on:

1. identical email address to the email address associated with SRA metadata
2. having uploaded short reads to EnteroBase
3. ownership rights that were explicitly granted by administrators/curators after receiving an email request

• Administrators and curators

To enter Edit Mode, login, and browse or Load Metadata from Query 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 desired information. The problematical fields are coloured red.

Desired information are :

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

If country and/or continent are inconsistent, modification is required to be done under a 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".