VIOLIN Account and Data Submission Tutorial
1. Register an account
Please register for an account if you haven't done so (Figure 1). Once registered, you will automatically be logged in and given access to the various features. These include: 1) changing your profile, 2) changing your password, 3) setting up an Email Alert system, 4) curating and submitting vaccine data through a web-based vaccine data submission system, and 5) if is proved, reviewing submitted vaccine data through a web-based vaccine data review system.
Figure 1. User registration. Items with "*" must be filled out. A registered user can update his/her profile after loging in.
2. Log in
If you have an account in VIOLIN, you can log in using the Log in page (a link is available to the left navigation panel, Figure 2). After loging in, you can access all the features described above. If you forget your password, click "Forgot password?" to reset your password. A new password will be sent to your registered Email address. If desired, you can change your password after you log in.
Figure 2. Enter Email address and password to log in.
3. Set up email alert
After loging in, you have the option of setting up your Email alert (Figure 3). Manuscripts that fit your search criteria from PubMed will be emailed to you periodically according to the frequency you select (daily, weekly, bi-weekly, or monthly).
Figure 3. Setup of the vaccine publication Email alert service after login.
4. To initiate data submission by selecting a pathogen
To submit vaccine data, first select the pathogen that you wish to work with (Figure 4). If the pathogen is not listed, you may enter the pathogen's name and add it to our database.
Figure 4. Pathogen name is first needed for data submission.
5. Main curation page
The main curation page contains four sections: 1) a horizontal menu bar, 2) a "Table of Contents" panel, 3) a main editing panel, and 4) a literature search panel (Figure 5A). The sizes of these panels may be adjusted by dragging the panel separators at the "borders". The web page design is a core of the web-based literature mining and curation system (Limix). A basic feature of the Limix system is that it contains a manual data edition system and a literature search/mining system on the same web screen. This feature allows registered users/curators to search the literature, copy/paste/edit literature information, submit, or review structured vaccine data all on the same web screen. Limix was first implemented in the Brucella Limix system in the Brucella Bioinforamtics Portal (BBP) and has first been described in the BBP publication (BMC Bioinformatics. 2006;7:347). The Limix system implemented in VIOLIN is an updated version that contains many new features including automatic reference extraction, version history and comparison, and an interactive data review capability. These new features are described below.
The menu bar contains the name of the current pathogen in the center of the menu bar. Many other features are included. Using the "Settings" menu, you are allowed to hide/show "Table of contents" panel (on the left of the screen) or the "Literature Search" panel (at the bottom of the screen) (Figure 5B). A pathogen page may also be assessed by clicking "Settings" and then clicking the corresponding command contained in the menu. Using the "Literature Search" menu, you may use PubMed, type a new URL, or select one of the VIOLIN literature search tools (Litesearch, Vaxquery, Vaxmech, and Vaxlert) (Figure 5C). The selected page (e.g., PubMed) will be shown on the bottom of the screen entitiled "Literature Search". To return to the VIOLIN home page, click "VIOLIN HOME". Using the "My Account" menu, you may access your account pages (My Email Account, My Profile, or My Password) (Figure 5D). You can log out of the VIOLIN system by clicking the "Logout" link.
The "Table of Contents" panel helps to navigate through information related to the pathogen selected. The size of the panel may be adjusted by dragging the panel separator. This panel can be hidden by clicking the "Hide Table of Contents panel" in the "Settings" menu in the menu bar.
The "Main Editing" panel at top right of the screen lists detailed information about general pathogen overview, vaccine-related genes, individual vaccines, and references. To unfold a section, click . If the function of any button/icon is in question, move the mouse cursor over to the appropriate button/icon, A short description of the function will appear. Corresponding links such as "Add a Pathogen Gene", "Add a Vaccine", "Add a Reference", etc may also be clicked. In addition to the "Main Editing Form", this panel contains links to other tabs, such as "Host Genes" and "Hosts". They are shown on the top left of the panel.
The Literature Search panel at the bottom of the screen allows searching different literature databases while working on main curation panel. To change to different literature searching programs, select a menu item from "Literature Search" menu. Options include PubMed or any literature search tool (Litesearch, Vaxquery, Vaxmech, or Vaxlert). A URL may also be entered by the user. In addition, the size of this panel may be adjusted by dragging the panel separator. This panel can be hidden by clicking a "Hide Literature Search Frame" in the "Settings" menu.
Figure 5. The main curation page (A) and the choices of the different menus are found at the top menu bar. These include Settings (B), Literature Search (C), and My Account (D).
6. Adding a New Reference
To add a new reference, click "[Add a Reference]" in the section of "Pathogen/Vaccine Related Reference". A Reference Submission Form will appear (Figure 6). Fill out the form and click submit. Once submitted, the reference will be listed under section of "Pathogen/Vaccine Related Reference". [Tip: If the PMID of a reference is available, enter the ID first and then click "Retrieve Detail Information from PubMed". The rest of form will be automatically filled out.] The information about PMID is Here.
Figure 6. A convenient reference submission system. A PubMed ID called PMID is needed only for citing a given reference.
7. Addition of a new vaccine
If it is desirealbe to add a reference before you add a new vaccine, refer the above section entitled "Adding a New Reference". To add a new vaccine, first click "[Add a Vaccine]" in the section of "Vaccine Information". An "Add Vaccine Information" form will appear (Figure 7). Fill out the form and insert reference tags by selecting the desired reference from the drop down menu and then click "Insert a Reference Tag". Click "Submit" after the form is complete. The vaccine will be listed in an alphabetic order in the section of "Vaccine Information". After completion of this step, additional information including gene engineering and host response may be entered by clicking corresponding links. [Tip: If the reference dose not appear in the drop down list but a PMID of the reference is available, the reference may be entered by typing (PMID:******) in the text area. The program will automatically retrieve the detail information and store it in the database.]
Figure 7. To add information about a new vaccine in VIOLIN, this form will automatically appear after clicking the "Add a Vaccine" (Figure 5A).
8. To Show Detailed Vaccine Information
Find a specific vaccine on the Main Editing Form. Click to unfold a section (Figure 8). The "Table of Contents" may also be used to navigate to the desired vaccine.
Figure 8. Detailed vaccine information can be "unfolded". The sign is for editing purpose, is for viewing the edition history and comparing versions.
9. Updating a Vaccine
To update a vaccine, find a specific vaccine as described in the section "To Show Detailed Vaccine Information". Click to unfold a section. Click to edit an item. A "pop up" dialog will open (Figure 9). Fill in the text area, and if needed insert reference tags. If desired, a short description may be entered in the "Edit Summary" line to explain the updates and the rationale for this action. Click "Save" to submit changes. [Tip: Use literature search panel to search/display reference information and copy & paste desired phrases/sentences to the textarea in the main curation panel.]
Figure 9. Updating an item of vaccine information.
10. Show Revision History and Compare Versions
The revision history and comparison of the versions of a particular subject can be verified by clicking . When two versions are selected and "Compare selected versions" is clicked, each version will be listed side by side with the differences highlighted.
Figure 10. Revision history and comparison of versions .
11. Review a Vaccine
The reviewing process uses an almost identical interface as the data submission process except that any item that has been updated now is labeled with a icon (Figure 11). Click this icon to approve any changes made to this item. Compare the revisions of a particular item by clicking . [Tip: You can also make necessary changes in a similar way as shown in the updating step after clicking the sign .] Acknowledgement of the acceptance of all changes is done by clicking the sign s found at the top on of the vaccine section. The results will be published immediately.
Figure 11. Review of updated vaccine information. Newly updated items are labeled with the icon. The same icon can be clicked to approve publication.
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