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Introduction

A PDF version of this guide is attached to this page

Template:Menu LexWiki

Introduction

An off-line version of this is available VKC:here.

LexWiki is an open source, high-capacity editor for distributed terminology development. Developed by Mayo Clinic with collaborations of 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.

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• 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

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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.

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

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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 VKC:Examining #Examining Concept Details.

Searching for Concepts

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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 VKC: use Autocompleteautocomplete. This displays a search results page.

Setting Your Search Preferences

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Info
1 #Authentication] to perform this task. title

You need to be

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[authenticated

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.

     Info
     title

     Note:

     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

     VKC:Examining

     #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.Note:

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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.

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STY followed by Ctrl + Spacebar

or

STY Ce followed by Ctrl+ Spacebar

Setting Up Autocomplete

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+ Spacebar

Setting Up Autocomplete

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Autocomplete is set up by default. As explained in VKC:About #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 step 6 of 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.

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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: #Click

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 VKC:Setting #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.

     Tip
     title

     Hint:

     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.
   • Click the Search button.
     The wiki displays a Search Results page.
   • 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. Note:

       Info
       title A category with a name preceded by a bracketed period [.] has no child concepts.

If the list did not appear in step 4, VKC: 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, see VKC:Examining 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.Note:

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

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