BiomedGT Help: Browsing and Searching

From BiomedGT

This page explains ways to browse and search for terminology on the BiomedGT Wiki. If you have suggestions for this page, please submit feedback.

Contents 1 Before You Begin 2 Browsing Concepts 3 Browsing Properties, Roles, and Associations 4 Searching for Concepts 4.1 About the Go Button and Search Button 4.2 Setting Your Search Preferences 4.3 Using a Simple Search Term 4.4 About Autocomplete 4.5 Setting Up Autocomplete 4.6 Using Autocomplete (General Users) 4.7 Using Autocomplete (CTCAE Project Only) 4.8 Examining Concept Details (General Users) 4.9 Examining Concept Details (CTCAE Project Only) 5 Need More Help? 6 Tell Us How We're Doing...

Before You Begin

Although you are welcome to browse and search this wiki, you need to register as a collaborator to perform certain tasks that are detailed on this page. If you want to propose additions or changes to current terminology, see Registration Process for Collaborators.

Browsing Concepts

Note: Concepts are called categories on the wiki pages. For the sake of familiarity, the help pages use concept.

To browse concepts, follow these steps:

1. Locate the terminologies section on the left navigation bar.
2. Click a terminology name (example: BiomedGT or CTCAE_Category).
3. If necessary, expand the root node by clicking the plus sign [+].
4. To drill down to details for a concept:

• Click the concept name.
• Click the plus sign [+] preceding the concept name to drill down to child concepts.
  Note: A concept 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.

Browsing Properties, Roles, and Associations

To browse properties, roles, and associations, follow these steps:

1. Locate the terminologies section on the left navigation bar.
2. Click a terminology name (example: BiomedGT or CTCAE_Category).
3. If necessary, expand the root node for properties, roles, or associations by clicking the plus sign [+].
4. Click the name of an item to view its details.

Searching for Concepts

Note: Concepts are called categories on the wiki pages. 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.

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

Note: You need a BiomedGT user account to perform this task. To request an account, see Registration Process for Collaborators.

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 the BiomedGT wiki.
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.
     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 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. When Autocomplete is active and working, you will see a red swirling circle while entering a search term.

Note: 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

Setting Up Autocomplete

Note: You need a BiomedGT user account to perform this task. To request an account, see Registration Process for Collaborators.

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 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.

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

1. Log in to the BiomedGT wiki.
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 (General Users)

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.
     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.
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.
     Note: 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, see Examining Concept Details.

Using Autocomplete (CTCAE Project Only)

Note: Since the new CTCAE SOC is the coding scheme for the second iteration, you can type CTCAE SOC as a search term (in caps or lowercase) and find the AE term within this namespace.

To search using Autocomplete, follow these steps:

1. Click in the search box at the top of the left navigation bar.
2. Type CTCAE SOC and the desired AE term (for example, Hypohidrosis).
   • 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.
4. Do either of the following:
   • Click the Go button to be directed to the AE term page.
   • Click the Search button to be directed to a search results page. At this page you can also click the link for the AE page to be directed to that page.

Note:

• In the auto-complete search, you may see icons next to the search results drop-down box. These indicate whether the search result is a property (P), category (C), or adverse event term (no icon).
• For CTCAE purposes, you may only need to search for the CTCAE SOC adverse event name. You can therefore disregard the items with an icon next to them.

Troubleshooting Tips:

• If you have problems searching for a word, try entering part of the word and then using Autocomplete. This should increase your search range.
• If you have any other problems with search, consult the Getting Help page.

Examining Concept Details (General Users)

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: 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: Click a property to link to a descriptive property page. Click an association (relationship) to link to a descriptive page for the related concept. Click the spyglass icon on the right of each property/association to search for concepts that have the same association. For example, clicking the icon to the right of BGT Disease Has Associated Anatomic Site BGT Integumentary System returns a list of all other concepts that have the associated anatomic site BGT Integumentary System. Click the RDF Feed link in the upper right area of the FactBox to view the details for the concept in XML/RDF format. To learn more about RDF, see the W3C RDF specification.

Examining Concept Details (CTCAE Project Only)

When you select a concept from a search results list, the wiki displays a table with all of the adverse events for the selected category. Properties are represented as grades, with their values shown as published.

Click the adverse event that you want to edit. The AE is represented by two tabs: Tabular and Factbox, each discussed in the following table.

Page Section	What it Shows
Tabular	Displays a table representing the adverse event and various grades. If you select an adverse event, a second table displays the Proposal Status (if any).
Factbox	Summarizes the selected concept, with links to more detailed information. Click the spyglass icon to the right of each property/association to search for concepts that have the same property and value combination. Click the RDF Feed link in the upper right area of the FactBox to view the details for the concept in XML/RDF format. To learn more about RDF, see the W3C RDF specification.

Need More Help?

• BiomedGT Help: Contributing Content
• BiomedGT Help: Contributing Content: Working with CTCAE Proposals (CTCAE Project Only)
• MediaWiki Help: Getting Help with Wiki Markup

Tell Us How We're Doing...

• BiomedGT Help: Feedback Page
• BiomedGT Help: Reporting a Bug or Requesting a Feature