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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:
This document is intended for terminology content authors. It provides an overview of the browsing and authoring features that LexWiki supports.
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).
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.
This page explains ways to browse and search for terminology on the LexWiki.
For the sake of familiarity, the help pages use concept. |
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.
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. |
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.
For the sake of familiarity, the help pages use concept. |
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.
Below the search box, you will find two buttons: Go and Search.
You need to be authenticated to perform this task. |
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:
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:
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. |
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.
If you want to use Autocomplete without pressing Ctrl + Spacebar, you can turn on an auto-triggered setting as described in steps 5 and 6 of #Setting Up Autocomplete. |
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
You need to be VKC:authenticated to perform this task. |
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:
To search using Autocomplete, follow these steps:
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.
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.
If the page name includes v1 in the title, a collaborator has submitted a proposal to modify the represented concept in some way.}If this is the case, concept details that are affected by the proposal are shown in red, bold text. |
Each detail page includes the information described in the following table.
Page Section |
What it Shows |
---|---|
Lexical |
Displays the concept code, preferred name, links for the coding scheme and coding scheme version, synonyms, and URI. |
Properties |
Displays the META CUI and relevant properties. |
Associations |
Displays associations for the selected concept. You can click association links to view more information about each one. |
FactBox |
Summarizes the selected concept, with links to more detailed information. Use the following methods to view specific information:
|
This page explains how to submit proposals and participate in discussions. It also provides links to pages that provide help with editing.
Before you can author content, you will need to authenticate.
When writing and editing wiki pages, note the following points about the Edit toolbar:
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.
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.
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.
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:
Be as specific as possible in your unstructured comments and recommendations. |
Prerequisite topic: #About Structured Proposals
To submit a structured proposal, follow these steps:
See Also: #Submitting Proposals
Prerequisite topic: #About Unstructured Proposals
To add or contribute to a proposal discussion, follow these steps:
==heading== |
Prerequisite topics:
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:
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:
This page explains the fields used on each of the structured proposal form tabs.
Each of the tabs on the structured proposal form includes the features described in the following table.
Feature |
Description |
|
---|---|---|
Watch this page |
Check box that marks a page so that you will receive e-mail notifications of any changes. This is especially useful when you are collaborating with others on a proposal.
|
|
Save page |
Saves the current proposal and displays the full proposal page. To resume editing, click the Edit tab at the top of the page. |
|
Show preview |
Shows an unsaved preview of the page. In the proposal context, instead of clicking Save page when viewing a preview, click the Edit tab at the top of the page to resume editing, then save the page. |
|
Show changes |
Not recommended; not currently useful in this context. |
|
Cancel |
Discards any unsaved changes. |
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.
Type of Change |
Examples |
---|---|
Data Correction |
|
Content Change or Enhancement |
|
Feature Change or Enhancement |
|
The Lexical tab displays lexical information about the selected concept. The following table describes each field.
Field Name |
Description |
|
---|---|---|
Concept Code |
Non-editable field used to display the concept code. |
|
Concept Category |
Concept Type property used only by BiomedGT curators. Possible values are listed here for informational purposes only:
|
|
Preferred Name |
Editable field. Remember that there can be only one preferred name. A preferred name should be explanatory and should help identify the context where possible (for example, Body Temperature rather than Temperature). |
|
Coding Scheme |
Refers to the terminology or subset in which the concept participates. The original coding scheme is non-editable, but you can add a second coding scheme where appropriate.
|
|
Synonyms |
Shows previously added synonyms and enables you to add or remove synonyms. |
|
Definition |
Used to add or modify the main definition. Definitions should provide defining information and should not include too much extraneous information. You can add extra information either as an AltDefinition or Editorial Note if desired.
|
|
AltDefinition |
Used to display a definition from an alternate source. |
|
Editorial Note |
Used to provide explanatory, scope, or other information.
|
|
Example |
Illustrates the concept. This is not currently published in BiomedGT but is used by curators for context. |
|
URI |
Non-editable field that displays the URI for the selected concept. |
The Properties tab has only one field: Concept Property. Use this field to add any of the notation properties currently available in BiomedGT.
There is currently no pick list for this field. |
If you know which property you are looking for, do either of the following:
The Associations tab enables you to change or add relationships. The following table describes each field on this tab.
Field Name |
Description |
|
---|---|---|
Parents |
Used to change, remove, or add a parent concept.
|
|
Associations |
Used to add relationships to other concepts (categories). This creates a link from one concept to another concept in the wiki.
|
The References tab enables you to add URIs to relevant Web sites, PubMed IDs, and ISBNs.
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