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Release History: Alpha 1 - January 2008; Alpha 2 - June 2008; Beta 1 - December 2008; Beta 1 Patch - January 2009

The alpha version of the BiomedGT Wiki was moved to an NCI server for the Alpha 2 release in June 2008. Seven development iterations have been completed since then. Much of the work since June, 2008, has been related to supporting the CTCAE 4 update project (Common Terminology Criteria for Adverse Events). Refer to the section "Other Changes" section below for additional information. To see the CTCAE4 content in progress, follow the CTCAE_SOC link under terminologies on the BiomedGT wiki.

CTCAE is not using the workflow available to the rest of the BiomedGT Wiki.


New Features

  • My Workflow link at top right corner, (which users will see when logged in). MyWorkflow will help users keep track of changes they are making to the wiki. It organizes the user's proposal page links by proposal status (new change, new concept, pending receipt, in progress, completed, rejected with the date, or other users' proposals that the user has edited.) Unstructured proposals (Discussion pages) show up under "All Proposals". Users can also see the status of their proposal packages.

    The regular wiki feature "Recent Changes" is also helpful for finding what others have been working on.

  • References (Evidence Attachment): A new tab has been added to the proposal function so that a user can include a PMID, ISBN number and/or URL site. At the moment, these are being packaged into a note field for export to Protégé, where the Protégé editor will model the reference information appropriately in the ontology along with the concept.
  • Workflow Synchronization with Protégé: The workflow for adding proposals for changes to concepts and new child concepts is significantly enhanced. Round trip publishing of concept changes back to the wiki is in place, and works with NCI Protégé 1.3.


  • "Add a child concept" functionality has been added back (it was lost in an earlier iteration by mistake).
  • Concept Status is now more aligned with workflow. When a user suggests a change to a concept, the status now says "New Change". When a user suggests a new concept, the status says "New Concept". When a proposal is added to a package, it is no longer editable until the change has been processed by curators in Protégé and posted back to the wiki.
  • Displaying available proposal packages.There is now a button to list available packages, useful if you want to add or delete proposals to an existing package before you send it for curation in Protégé.
  • Proposal Package Status: Users can add change proposals to a package until ready to send to Protégé, and then they can change the status to Pending Receipt.
  • Discussion pages: If a user makes a comment on the Discussion page of a term, an unstructured proposal will be created that can also be included in workflow packages. If included in the workflow package, the Protégé editor will get a link back to the comment page. The status of a saved discussion page becomes "Submitted".
  • Searching: Autocomplete searching is improved: The searching now returns the most likely hits at the top of the list, which makes it easier to find what you are looking for quickly.
  • Wiki namespaces: There is a workflow update to accommodate retrieving proposals in Protégé from only one wiki namespace at a time. This is important if two different groups of domain experts are working on two different projects on the wiki.
  • Synchronization between BiomedGT wiki and Protégé - a number of changes have been made to improve the mapping between what is exported from the wiki and the BiomedGT file in Protégé.

Other Changes

CTCAE: A number of changes have been added to the wiki for the CTCAE Update project, which displays terms in a tabular format and allows for term and grade (property) editing. This update project has been active since July 2008. These changes apply only to the CTCAE project and do not affect the rest of the wiki. This project is not using the regular wiki workflow software.

  • Pilot proposal processing for CTCAE phase I
  • Leave a Comment implemented in Discussion page
  • CTCAE Category to MedDRA SOC (System Organ Class) - initial mapping
  • CTCAE Category name change to SOC (create CTCAE4)
  • Restrict editing of CTCAE3 during proposal processing
  • Extraction of proposals (AE terms) into Excel spreadsheet
  • Regroup proposals by SOC - PHP changes & Wiki template and properties
  • Hide edit tab for CTCAE users (check into SVN) to require data entry using forms
  • Unlock CTCAE3 for updates (lock and unlock several times)
  • Final CTCAE Proposal processing
  • Publish CTCAE4 to Wiki (draft 1) (CTCAE_SOC)
  • Create link from CTCAE4 terms to CTCAE3 terms so users can track proposals
  • Create dummy SOC and data entry form for new terms not associated with a SOC.

Other Information

  • Settings: Autocomplete can be used either automatically, or by typing some letters in the search window and Ctrl+Space. For the automatic function, log in, go into My Preferences, and under Misc, check "Automatically Enable Autocomplete." In the Preferences under searching, you may also want to check multiple article types of interest, for example, you can include Proposals in searching.
  • Searching Tips: If you want to search in a particular namespace, preface the search term with the namespace, for example, BGT, STY, CTCAE or CTCAE_SOC.
  • Passwords: When users email themselves a new password (option at bottom of login box), the wiki will automatically reset the password to a temporary password. The user will then be prompted to reset the password when after logging in with the temporary password. If the original user account was created without an email address, that user won't be able to use this feature, and will have to request another account.
  • How to use "Recent Changes": Users can change the number of recent changes, and the period visible in the User Preferences.

Known Issues

  • The clock on the production wiki is not set correctly. We don't know why. The server clock is set appropriately. We will continue to investigate. Therefore, if you're looking for the time of a recent change, it is recording 5 hours ahead. For instance if you make a change at 7:00 pm one day, it records in recent changes as occurring at 12:00 am the next day. (The insert name/date function in the discussion pages however is recording the correct time.)
  • All changes made in a proposal will not show up on the main concept page in red. For instance, if you propose to delete a synonym, it doesn't show on main page. If you make a comment in the proposal, it doesn't show on the main page. If you add a reference to the proposal it doesn't show up. Is this a bug or a feature? Comments are welcome.
  • Mail password: Sometimes shows an error even though it actually resets the password and emails it to the user. (However, if the username and password were created without addition of an email address, this function will not work.)

CORE Product Dependencies

This is dependent on Protégé 1.3 Release which contains the workflow modifications to work with this version of the BiomedGT Wiki.

Upcoming Changes

  • The CTCAE processing for the editing of CTCAE term grades is concluding and proposal processing will occur. A new version of CTCAE will be posted in the early spring.
  • NPO - Nanoparticle Ontology will be loaded into the wiki in February 2009
  • Radlex - RadLex 1.02 (or 2.0) will be loaded into the wiki in February 2009
  • Update of the BiomedGT terminology from the Dec 2008 baseline will replace the current version from mid 2008 during Feb 2009
  • CTCAE 3 Subject terms, the pre-coordinated version of CTCAE3 extracted from the NCI Thesaurus, will be removed from BiomedGT during Feb 2009. CTCAE3 will remain as part of the NCI Thesaurus at least until CTCAE4 is published as a standalone version. Mapping help between CTCAE3 and 4 is planned.

For more detail about bugs and enhancement requests, or to report bugs, go to the tracker and follow the appropriate link for BiomedGT wiki enhancement requests or bug reports.