From Proteopedia

Jump to: navigation, search


Two search methods

On the left toolbar present when viewing any page in Proteopedia is a standard wiki search box, similar to what you find in Wikipedia. The second search method is using Google to search Proteopedia with the search string " ...", where "..." stands for the term or combination of terms you are interested in. Why have two? Performing good searches is a hard task, and the standard wiki search feature often comes up short, so we wanted to provide another option.

Disadvantages of the wiki search box

Words of 3 or fewer characters in length are ignored and cannot be found, for example searching for MHC fails to find any page text matches, while doing the same search in the Google search box finds many. Words of 4 or more characters are found, e.g. hook, unless they are stop words (see Help:Stop Words).

Advantages of the wiki search box

Searching for the singular finds the plural, and vice versa. Searching for the lower case term finds the capitalized term, and vice versa. Examples:

  • Searching for enzyme (singular, not capitalized) finds Glycolysis Enzymes (plural, capitalized), a page where the singular does not occur. It also finds pages where only the plural (never the singular) term occurs in the text (and neither term in the title), e.g. Ouabain.
  • Searching for enzymes (plural, not capitalized) finds Insulin-Degrading Enzyme (singular, capitalized), an article in which the singular term does not occur. It also finds pages where only the singular (never the plural) term occurs in the text, but does not highlight the singular term in red under the page title, e.g. Butyrylcholinesterase.
  • Searching for Enzyme (capitalized) matches the article title SUMO conjugating enzyme Ubc9 (not capitalized), and the text in the page Tripeptidyl peptidase, which contains only the uncapitalized term.
  • Searching for CASP (all upper case) matches casp in 3af5, and Casp in 2vsp.
  • Searching for casp (all lower case) matches the article title CASP as well as CASP, Casp, and casp in page text.

You can put double quotes around a phrase to restrict hits to the phrase, rather than getting hits to all pages that include any word in the phrase. See more tips below.

You can exclude namespaces that you specify. For example, the automatically-generated Category: pages may flood your search results, but you can exclude those. See the namespace checkboxes at the bottom of the results from any search. Also, when logged in, you can set your default namespaces for wiki searches in my preferences (see link at the top of every page to my preferences).

Redirects are excluded from searches by default, and this cannot be changed in my preferences. However, the very last checkbox at the bottom of the search results page is List redirects. Check it and run the search again (using the button near the checkboxes) to see redirects.

What is a redirect? If you enter CRABP in the wiki search box and click Go, you will be redirected and arrive at the page Cellular retinoic acid-binding protein. Beneath the title, you will see Redirected from CRABP. Click on CRABP to see the page titled CRABP that redirects to Cellular retinoic acid-binding protein.

Disadvantages of the Google search

Recently created pages will not appear when searching using the Google search box because Google needs time to find and index new pages. Additionally, it is impossible to restrict your search to particular namespaces like you can with the wiki search.

Advantages of the Google search

Three-character length words, such as MHC, are found by Google but are not found by the wiki search box.

"Go" versus "Search"

In the wiki search box, using the button "Go" will take you directly to a page whose title exactly matches your search query, if it exists. Using the button "Search" will instead perform a search using your search query and take you to a page displaying the results.

Titles vs. Page Text

Search results are divided into two sections:

  • Article title matches
  • Page text matches

This makes it easy to find articles that have your search term in their titles.

Titles Alphabetically

You can display a list of article (page) titles that begin with a specified character or characters by using the Special:Prefixindex search mechanism.

  • Searching for "a" lists all page titles beginning with the letter A.
  • searching for "alpha" lists all page titles beginning with those characters.

Titles in italics are redirects to other pages. If you click a redirect, you will go to a page with a different title. Underneath the title you will see "Redirected from ...". Redirects provide alternative titles that users might look for, guiding them to the relevant page.

Note that this mechanism searches only one namespace at a time. You may need to search several namespaces.

A similar mechanism is offered by Special:Allpages.

Excluding PDB code-titled pages

The Page text matches section of your search results will usually be mostly pages that are title with a 4-character PDB code. These are automatically-generated "seeded" pages, and are the most numerous pages in Protopedia.

It is easy to restrict your search results to pages created by humans (which are never titled with a PDB code). At the very bottom of your search results are a group of checkboxes. Notice the line

Include only [ ] Seeded (Automatic) pages - [ ] only Human created pages

By checking "only human created pages" you will eliminate all the PDB code-titled pages in your results.

More powerful searching

Searching in Proteopedia works in the same way as does searching in Wikipedia, with the addition of some special operators to enhance "full text search".

Full Text Search Operators
* The asterisk serves as the truncation (or wildcard) operator.
+ A leading plus sign indicates that this word must be present in every page returned.
- A leading minus sign indicates that this word must not be present in any page returned.
" Double quotes at the beginning and end of a phrase, matches only pages that contain the complete phrase, as it was typed.
By default (when neither + nor - is specified) the word is optional, but the pages that contain it are rated higher.


Namespaces include pages in subcategories labeled Proteopedia:, Help:, User:, and so forth. To see all the pages within a namespace, go to Proteopedia:Namespaces.

Additional information

For additional information, please see:

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Karsten Theis, Eran Hodis, Jaime Prilusky

Personal tools