Annotation Tool Help
Introduction
The purpose of this document is to demontrate how to use the Online Annotation Tool to create a batch of temporary submissions. These temporary submissions will contain all annotation data but not metadata such as probe details, submitter details etc which are to be submitted using the relevant submission spreadsheet - either for ISH spreadsheet or IHC spreadsheet. This tool has been tested using IE7+Windows Vista and Firefox2.0+Windows Vista.
Logging in
- Trainee user
We recommend that an initial training session is undertaken by first-time users and that this should be carried out using the Annotation Tool we have housed on the TEST version of the website. Please note that annotations created on the TEST site cannot be uploaded to the GUDMAP database.
Log in to the TEST website http://www.gudmap.org/gudmap_test using username and password supplied by GUDMAP developers, and then click ‘Annotate’ button at the bottom of the database home page. On the ‘Adding annotation’ page which you will be taken to, there will be a new link named ‘View/Create lab batch annotation’ alongside the PI’s name. The interface identifies the PI associated with that username.
- Submitter
Once familiar with using the Annotation Tool on the TEST site, users should move to the version housed on the LIVE website and this must be used for all annotations that are intended for submission to the GUDMAP database. Once again, please note that annotations created on the TEST site cannot be uploaded to the GUDMAP database.
Log in to the LIVE website http://www.gudmap.org/gudmap/pages/database_homepage.html using username and password supplied by GUDMAP developers, and then click ‘Annotate’ button at the bottom of the database home page. On the ‘Adding annotation’ page which you will be taken to, there will be a new link named ‘View/Create lab batch annotation’ alongside the PI’s name. The interface identifies the PI associated with that username.
Creating and modifying a batch submission
On clicking the link ‘View/Create lab batch annotation’, the user will be taken to a new page where submissions can be added, deleted or modified.
- Click on a Temporary Batch ID to view an existing batch submission (Step 1 in the figure below).
Each batch submission lists multiple submissions with one submission per row.
- The first column is a checkbox column used to select submission.
- The second column displays temporary GUDMAP ID. This unique identifier is used to link a newly created online submission to a row in the ISH/IHC spreadsheet. A temporary GUDMAP ID will be allocated of the form 999999n.
- The third column displays the link ‘Edit annotation’. When the link is clicked, the annotation tree window will pop up.
- The user can create new empty submission by clicking the ‘New Submission’ link
- The user can delete submissions by selecting a list of submissions using the checkboxes, and clicking the ‘Delete Submission’ link .
- The user can copy/paste annotation from one submission to another. Choose the source submission by clicking on the checkbox beside the temporary gudmap id and click on the ‘Duplicate submission’ link. A new submission with duplicated annotation will then be created.
The user can annotate gene expression by clicking on the 'Edit Annotation’ link (Step 2 in the figure).
Annotating Gene Expression
In the anatomy tree window, the user will see a stage dropdown menu at the top of the page. Selecting a new stage will display/refresh the tree.
To annotate Expression Strength, the user must use the expression icons (present, present strong, not detected, etc) to the left of the anatomy tree.
- Select (left mouse click) terms on the tree and then click on one of the icons (e.g. present strong) to allocate this expression to an anatomical component. Click a term again to deselect it.
- Please note that multiple terms can be selected. Using the left mouse click selection, multiple terms can be annotated simultaneously.
- To undo annotation, click on the relevant node(s) and select the ‘Not Examined’ icon.
To annotate Expression Pattern & Location, the user must right click on an anatomical component. This brings up a popup window that allows users to add patterns, locations, and annotation notes (see figure below). This feature is only enabled after an Expression Strength has been assigned to the anatomical component. Single button mouse users can instead use ctrl+click to obtain the popup menu.
- The figure below shows users how to annotate Gene Expression with a Pattern & Location
- The figure below shows users how to add an Annotation Note
Please note the following:
- Patterns and Locations will only be available for terms annotated as Present.
- Only one submission (Temporary GUDMAP ID) can be annotated at a time.
- To annotate further submissions or to complete the batch, click the ‘Close’ button at the bottom of the anatomy tree window.
Notifying the Editorial Office of completing a batch of submissions
After the user finishes a batch, they should select all the completed entries in the table via the checkboxes and click ‘Complete batch’. In order to notify the GUDMAP Editorial Office, please email gudmap-editors@hgu.mrc.ac.uk. The user is then required to send the supplementary spreadsheet plus the original images to the FTP site or via other file sharing tools as for example yousendit.
- Please ensure the Temporary GUDMAP IDs appear in Column 0 of the supplementary spreadsheet. Help pages on how to fill in the spreadsheet can be found here.
FTP
Open your favourite FTP client and type the following:
• ftp> open ftpin.hgu.mrc.ac.uk
• ftp> name: anonymous
• ftp> password <your email_address>
• ftp> binary
• ftp> put <GUDMAP_HGU_110906_1428.tar.gz> incoming/
You will know your files have been sent when you get a FTP 'transfer complete' message. Once the files have been sent, please send us an email to notify us of the incoming files.
Email
Once files have been transferred, send an email to the GUDMAP Developers:
• gudmap-db@gudmap.org
Cc to the GUDMAP Editorial Office :
• gudmap-editors@hgu.mrc.ac.uk
In the Subject of the email please write:
• GUDMAP FTP UPLOAD
In the body of the email please state the following:
• The time you sent the file
• The name of the file
• The size of the file
• The number of completed entries (rows) in the spreadsheet
• Whether the entries refer to ISH or IHC data.
Ensure that you add the following attachment before sending:
• listings.txt (a list of the image filenames)
