LexWiki User's Guide

Introduction

A PDF version of this guide is attached to this page.

LexWiki is an open source, high-capacity editor for distributed terminology development. Developed by Mayo Clinic with collaboration by the National Cancer Institute (NCI), the World Health Organization (WHO) and Stanford University, it is a synergistic effort for the development of a collaborative terminology authoring platform based on the integration of LexGrid and Semantic MediaWiki technologies. This version of LexWiki does not include Protégé components.

The features of LexWiki include:

• Browsing support
  • Hierarchy view with Category Tree extension
  • Concept-oriented view with Header tabs extension
  • Proposal browsing - all proposals listed by curation status and by categories with ontology browser
  • My Proposal browsing with MyWorkflow extension
• Authoring support
  • The LexWiki Protege Tab is used for loading contents into Wiki.
  • LexWiki Editor - semantic forms/Header Tabs: may propose change, new concept or concept removal
  • Change tracking and view changes
  • Proposal Commenting
  • Proposal Voting
  • Evidence attachment with citation and file upload

Scope

This document is intended for terminology content authors. It provides an overview of the browsing and authoring features that LexWiki supports.

Prerequisites

LexWiki is a Web-based application. You will need a web browser and the address (URL) of your LexWiki application. You will also need an account (username and password).

Authenticating

In order to use the authoring and workflow features of LexWiki, you will need to authenticate by clicking the login link at the top of the page and providing your username and password.

Browsing

This page explains ways to browse and search for terminology on the LexWiki.

Browsing Concepts

The LexWiki installer automatically loads a sub set of the BiomedGT terminology. When you view a newly installed LexWiki, you should see the following on the main page.

This is the terminology Tree View. You can drill down to more specific concepts by clicking the plus sign [+] which precedes to each concept.

Browsing Properties, Roles, and Associations

From the terminology Tree View, click the name of any concept. Once you select a concept, the wiki displays a detail page for that concept. For more information about the detail page, see #Examining Concept Details.

Searching for Concepts

The most efficient way to search is to use the search box at the top of the left navigation bar. The following topics explain how to set your search preferences, perform a simple search, and use the Autocomplete feature.

About the Go Button and Search Button

Below the search box, you will find two buttons: Go and Search.

• Click the Go button when you know that a category (concept) page exists and you know the exact name of the page. For example, if the full page name is Category:BGT Cytoskeletal Gene(B20918), type the full page name in the search box and click Go. Although this works best when you provide the exact page name, even entering an inexact name displays a results list with possible matches.
• Click the Search button for general searches where you enter a search term or use autocomplete. This displays a search results page.

Setting Your Search Preferences

You can set search preferences to control how your results are displayed and which namespaces you use for searching. To set preferences, follow these steps:

1. Log in to LexWiki.
2. Click the my preferences link in the the top right of the page.
   Your user profile page appears.
3. Click the Search tab.
4. Set your results display preferences by typing values in the three text boxes: Hits per page, Lines per hit, and Context per line.
5. Select namespaces for searching by selecting the appropriate boxes.
   We recommend checking at least Category, Relation, and Property. You may also want to add Proposal and Proposal Talk.
6. Click the Save button.
   A message confirms that your preferences have been saved.

Using a Simple Search Term

You perform a simple search when you simply enter a search term or phrase and run the search. To search using a term or phrase, follow these steps:

1. Click in the search box at the top of the left navigation bar.
2. Type a search term or phrase.
3. Click the Search button.
   The wiki displays a Search Results page.
4. To view details for a concept:
   • Click the concept name, or
   • Click the plus sign [+] preceding the concept name to drill down to child concepts.

     A category with a name preceded by a bracketed period . has no child concepts.}Once you select a concept, the wiki displays a detail page for that concept. For more information about the detail page, see #Examining Concept Details.

About Autocomplete

The Autocomplete feature enhances your searches by providing a list of suggested terms, based on what you type. To activate Autocomplete while entering search text, type some text and then press Ctrl + Spacebar (on Mac, this is Ctrl + Alt + Spacebar). When Autocomplete is active and working, you will see a red swirling circle while entering a search term.

Autocomplete recognizes namespaces for the available terminologies on the wiki. If you type a string without a namespace prefix, such as bed followed by Ctrl + Spacebar, the returned list displays concepts (categories) with a BGT prefix.

To restrict search results to a specific namespace, add the namespace prefix to your search text. For example, if you want to find a Semantic Type from the STY namespace such as the STY Cell concept (category), you would type the following:

STY followed by Ctrl + Spacebar

or

STY Ce followed by Ctrl+ Spacebar

Setting Up Autocomplete

Autocomplete is set up by default. As explained in #About Autocomplete, you can use this feature by pressing Ctrl + Spacebar while searching. If Autocomplete doesn't appear to be working, or if you would rather not press this keystroke during search, you can enable the Auto-triggered auto-completion setting in the following procedure.

Note that you may sometimes get faster results by using a simple search. For example, if you type lung (instead of lung as part of a phrase), then simple search might be the better choice.

To verify and/or change Autocomplete settings, follow these steps:

1. Log in to LexWiki.
2. Click the my preferences link in the the top right of the page.
   Your user profile page appears.
3. Click the Skin tab.
4. Select the OntoLiteSkin option if it is not already selected.
5. To enable Autocomplete without requiring a keystroke, do the following:
   1. Click the Misc tab.
   2. Check the Auto-triggered auto-completion box.
      If you select this setting, you don't need to press Ctrl + Spacebar to use Autocomplete. You can tell that this setting is enabled if you have not pressed the keystroke and a red swirling circle appears while you are entering a search term.
6. Click the Save button.
   A message confirms that your preferences have been saved.

Using Autocomplete

To search using Autocomplete, follow these steps:

1. Click in the search box at the top of the left navigation bar.
2. Type one or two characters.
   • If Autocomplete is set to work automatically, you will see a red swirling circle while entering the term.
   • If you do not see the red swirling circle, press Ctrl + Spacebar. To enable automatic use of Autocomplete, you need to change your settings as explained in #Setting Up Autocomplete.
3. (Optional) When the drop-down results list appears, do either of the following:
   • Select a term from the list to add it to the search box; or
   • Type additional characters to change the results appearing in the list.

     All BiomedGT concepts start with the letters BGT before the name, so type something such as *BGT Activ* to find _BGT Activity_ or other variations.
4. Do either of the following:
   • Click the Go button when you know that a category (concept) page exists and you know the exact name of the page. For example, if the full page name is Category:BGT Cytoskeletal Gene(B20918), type the full page name in the search box and click Go. Although this works best when you provide the exact page name, even entering an inexact name displays a results list with possible matches.
   • Click the Search button for general searches where you enter a search term or use Autocomplete.
5. Click the Search button.
   The wiki displays a Search Results page.
6. To view details for a concept:
   • Click the concept name, or
   • Click the plus sign [+] preceding the concept name to drill down to child concepts.

     A category with a name preceded by a bracketed period . has no child concepts.

If the list did not appear in step 4, check your Autocomplete settings.

Once you select a concept, the wiki displays a detail page for that concept. For more information about the detail page, refer to #Examining Concept Details.

Examining Concept Details

When you select a concept from a search results list, the wiki displays a detail page for that concept. The page name has the concept name and code (for example, Category: BGT Beckers Nevus(B4097) or Category:CTCAE Allergy/Immunology) and includes links to other concepts.

Each detail page includes the information described in the following table.

Authoring

This page explains how to submit proposals and participate in discussions. It also provides links to pages that provide help with editing.

Before You Begin

Before you can author content, you will need to authenticate.

About the Edit Toolbar

When writing and editing wiki pages, note the following points about the Edit toolbar:

• The toolbar includes icons for bold and italic.
• The toolbar includes a carriage return symbol for creating a line break in the middle of a paragraph.
• The toolbar does not include a button for adding bulleted lists. When you need a bulleted list item, type an asterisk (*) at the beginning of a line of text.
• The toolbar includes a signature icon labeled "Your signature with timestamp." Click the icon to append your user name and add a date/time stamp to your comment.

  The check box at the bottom of the text entry box enables you to switch between a syntax-highlighted and standard editor.

  If your signature is pre-pending rather than appending, make sure that this box is not checked.

A complete description of the Edit toolbar is available in the MediaWiki help.

Proposing Changes and Additions to Terminology

If you are authenticated, you can propose changes or additions to the terminology that LexWiki is hosting. For example, you might suggest changes to such information as preferred names, definitions, synonyms, associations, and parents. You can do this through either a structured or unstructured proposal.

About Structured Proposals

The more formal method of proposing changes and additions is through the submission of a structured proposal. This type of proposal requires that you complete a standardized submission form. You can save and edit the proposal using the same structured form. For more information, see #Submitting a Structured Proposal.

About Unstructured Proposals

Before proposing changes, a group of collaborators can start a discussion about the nature of the changes using a discussion page. They can also use this page to make recommendations to curators who may be integrating content from another terminology. A discussion page enables each contributor to add signed, date-stamped comments.

Examples of discussion page content:

• "You should consider creating the sibling concepts for this concept because we need them in order to..."
• "We recommend adding a new property X for this concept and all its children to represent Y (give definition and other relevant info)."

Creating a Structured Proposal

Prerequisite topic: #About Structured Proposals

To submit a structured proposal, follow these steps:

1. Find the concept for which you want to submit a proposal.
2. Select the concept in the search results list.
   The wiki displays the detail page for the concept.
3. Ensure that the second tab at the top of the page shows propose changes in red letters and not proposed changes in blue letters.
   If the tab shows proposed changes in blue letters, then someone has already submitted a proposal for this concept.
4. Click the propose changes tab at the top of the page.
   The LexWiki BGT Form page appears. The tab at the top of the page shows the word special. Note the four tabs: Meta, Lexical, Properties, and Associations.
5. Complete the fields for each tab using the VKC:Structured Proposal Form Reference section.

See Also: #Submitting Proposals

Creating an Unstructured Proposal

Prerequisite topic: #About Unstructured Proposals

To add or contribute to a proposal discussion, follow these steps:

1. Browse or search for the term that you want to discuss.
2. Click the discuss tab at the top of the category page for the selected term.
   If a discussion is already in progress, you will see previously entered comments on the discussion page. If no one has added comments, you will immediately see the page title, the Edit toolbar, and a box for typing text. Regardless, you can use the toolbar and text entry box to add your own comments.
3. Write and edit your comments in the text entry box:
   • Start each bulleted item with an asterisk (*).
   • Surround subheadings with equal signs

      ==heading==

   • Use the*Edit* toolbar to add formatting.
     For a complete description of the toolbar buttons, refer to the Edit toolbar MediaWiki page.
4. Append your signature to the comments by clicking the Your signature with timestamp button.
5. Click Save page.
   The most recent comments appear at the top of the page.

Submitting Proposals

Prerequisite topics:

• #Creating a Structured Proposal
• #Creating an Unstructured Proposal

When you are ready to submit a proposal for consideration, you can submit it as a package. The package can contain only one proposal or several proposals. Once you have submitted a proposal package, your package enters into a workflow process. The process has various stages, each with a status designation that identifies what process stage the package has reached:

• New
• Ready to Submit
• Submitted
• In Process
• Completed

Creating a Workflow Package

Prerequisite topic: #Submitting Proposals

If you are a registered user, you may click "My workflow" at the top of the page where you may browse and define "MyWorkflow" and browse "My Proposals". Collaborators can propose changes to an existing concepts or propose new child concepts. A logical grouping of the various proposals from a particular collaborator forms part of his/her workflow package. This can be submitted for curation en masse for curation to be incorporated into the existing ontological model. The status for the individual packages tracks the changes to the workflow status. The user can log in to Lexwiki at any point of time and be informed of the status of the workflow by clicking on the "My workflow" link at the top of the page. Post-curation, the workflow status can be set to one of Completed or Completed w/issues. The individual proposals can then be browsed to check whether they were accepted or rejected. For proposals that are accepted the wiki concept is updated or created accordingly.

To create a workflow package, follow these steps:

1. Click on the "My workflow" tab at the top of the page.
2. In the My Workflow Packages section, enter a name for the workflow package and click the Define Workflow Package button.
   The Add Workflow Request: Workflow:{Package Name} opens.
3. Select a Priority option.
4. Add a comment or instructions in the text entry box.
5. Follow these steps in both the Structured Proposals and Unstructured Proposals sections:
   1. Click Add another.
   2. Enter the proposal name in the Proposal field.
   3. Repeat steps a and b to add more proposals.
6. Click Save page.
   The WorkFlow:{Package Name} page updates to show details about the package that you just submitted. This page includes the following informtion:
   • Submitter: Your user name
   • Submission date: The submission date in numerical format
   • Priority: The priority level that you assigned
   • Proposal: Concepts included in the package
   • Package status: The current workflow status for the package
   • Facts about {Package Name}: A FactBox showing the workflow component, submission date, priority, and submitted name. The FactBox also provides a link to the RDF feed for the package.
   • Categories: Shows the current status of the package. The initial status is WorkFlow Pending Receipt.

Structured Proposal Form Reference

This page explains the fields used on each of the structured proposal form tabs.

Before You Begin: Understanding Common Features

Each of the tabs on the structured proposal form includes the features described in the following table.

Meta Tab

The Reason for Change field is a text field in which you can type the reason for the requested change. The following table lists change types and examples.

Lexical Tab

The Lexical tab displays lexical information about the selected concept. The following table describes each field.

Properties Tab

The Properties tab has only one field: Concept Property. Use this field to add any of the notation properties currently available in BiomedGT.

If you know which property you are looking for, do either of the following:

• Use Autocomplete to find the property. To use Autocomplete, type part of the property name, then press Ctrl + Spacebar.
• Use the NCI Thesaurus Browser to search for the concept and view a list of currently available properties. On the results page, scroll down to the*Information About This Concept* section.

Associations Tab

The Associations tab enables you to change or add relationships. The following table describes each field on this tab.

References Tab

The References tab enables you to add URIs to relevant Web sites, PubMed IDs, and ISBNs.