Linking To WormBase

From WormBaseWiki
Jump to: navigation, search

It is easy to link to WormBase. You can link to HTML pages, text-only dumps, images, and XML pages.

Naming Conventions

All objects in WormBase have a name and a class. The name is a unique identifier which is usually, but not invariably, a human-readable name. The class describes the type of the object, such as "Sequence" or "Protein.

For example, the cell ADAR has a name of "ADAR" and a class of "Cell".

For historical reasons, the classes of objects are not always what you expect. While the class of a predicted gene such as ZK154.1 is "Predicted_gene", as you might expect, it is less obvious that the named gene zyg-1 has a class of "Locus". The [#Link_rules_table #Link rules table] at the bottom of this page lists some of the common classes.

If you are not sure, you can learn the name and class of a particular WormBase object by performing a search for the object. Once you find and display it, look at the URL at the top of the page. The URL will contain the arguments name= and class=. These are the name and class of the object.

Linking to an HTML Page

To link to a WormBase web page describing the object, create a link to

http://www.wormbase.org/db/get?name=X;class=Y

, where X and Y are replaced with the name and class of the object you wish to retrieve. For example:

  http://www.wormbase.org/db/get?name=WBGene00006763;class=Gene -- The unc-26 Gene page
  http://www.wormbase.org/db/get?name=unc;class=Gene_class -- The unc gene class page

Linking to XML

To link to an XML dump of the object, create a link to http://www.wormbase.org/db/misc/xml?name=X;class=Y, where X and Y are again replaced with the object name and class. For example:

  <a href="http://www.wormbase.org/db/misc/xml?name=WBGene00006988;class=Gene">WBGene00006988</a><br>
  <a href="http://www.wormbase.org/db/misc/xml?name=WBGene00006988;class=Gene">(try it)</a>

Linking to Text

To link to a text-only representation of the object, create a link to http://www.wormbase.org/db/misc/text?name=X;class=Y, where X and Y are again replaced with the object name and class. For example:

  <a href="http://www.wormbase.org/db/misc/text?name=WBGene00006988;class=Gene">WBGene00006988</a><br>
  <a href="http://www.wormbase.org/db/misc/text?name=WBGene00006988;class=Gene">(try it)</a>

Linking to a Physical Map

To link to an image of the C. elegans physical map and you know the contig name, create a link to http://www.wormbase.org/db/misc/epic?name=X;class=Map, where X is replaced with the contig of interest. To link to a particular clone on the map, link to: http://www.wormbase.org/db/misc/epic?name=X;class=Clone, where X is replaced with the name of the clone. For example:

  <a href="http://www.wormbase.org/db/misc/epic?name=F59E12;class=Clone">F59E12</a><br>
  <a href="http://www.wormbase.org/db/misc/epic?name=F59E12;class=Clone">(try it)</a>

Linking to the Genome

Create a URL like this one:

<a href="http://www.wormbase.org/db/seq/gbrowse?source=wormbase;name=F59E12.2">F59E12.2><br>
<a href="http://www.wormbase.org/db/seq/gbrowse?source=wormbase;name=F59E12.2">(try it)</a>

The "name=" argument can be filled with almost any landmark, including predicted gene names, locus names, cosmid names, and chromosome names. You can also combine a landmark specify a range such as II:1000..20000. This means to show chromosome II from positions 1000 to 20,000, inclusive.

Linking to an Image of the Genome

You can create an inline image of a portion of the genome using a URL like this one:

<img src="http://www.wormbase.org/db/seq/gbrowse_img?source=wormbase;name=mec-3;width=650">

This will produce the following 650-pixel wide image:

<img src="http://www.wormbase.org/db/seq/gbrowse_img?source=wormbase;name=mec-3;width=650">

There are many more options. You can turn on tracks, add your own tracks, and much more. See the gbrowse_img help page for details.

Linking to Genetic Maps

Create a link like this one:

<a href="http://www.wormbase.org/db/misc/epic?class=Map;name=III">III><br>
<a href="http://www.wormbase.org/db/misc/epic?class=Map;name=III">(try it)</a>

To link to a region of the map defined by a centimorgan interval, add the map_start and map_stop arguments:

<a href="http://www.wormbase.org/db/misc/epic?class=Map;name=III;map_start=3;map_stop=4">III:3..4><br>
<a href="http://www.wormbase.org/db/misc/epic?class=Map;name=III;map_start=3;map_stop=4">(try it)</a>

Linking to Acedb Format

To link to an ACEDB representation of the object suitable for loading into a local ACeDB database, create a link to http://www.wormbase.org/db/misc/acedb?name=X;class=Y, where X and Y are again replaced with the object name and class. For example:

  <a href="http://www.wormbase.org/db/misc/acedb?name=F59E12.2;class=Predicted_Gene">F59E12.2</a><br>
  <a href="http://www.wormbase.org/db/misc/acedb?name=F59E12.2;class=Predicted_Gene">(try it)</a>

Fetching Multiple Objects

You can fetch multiple objects by using wild cards in the name, where "*" replaces any character, and "?" replaces a single character. For example, to retrieve all RME cells in XML format, use:

  <a href="http://www.wormbase.org/db/misc/xml?name=RME*;class=Cell">All Cells</a><br>
  <a href="http://www.wormbase.org/db/misc/xml?name=RME*;class=Cell">(try it)</a>