Gaggle Components
Geese
Data Standards
Boss

Gaggle Microformat

Microformat for Gaggle data types

Microformats

A microformat is a way of encoding structured data in valid HTML using CSS classes to label data fields. For more information see microformats.org and bioformats.org. The Firegoose supports a microformat which can encode the gaggle data types.

Gaggle data is labeled as such by wrapping it in a div tag with the class gaggle-data. Inside that div, is an element that encodes the name of the piece of data and, optionally, a species and size element. Finally, another div specifies the exact type of gaggle data. As an example, we show a list.

Example


  <div class="gaggle-data">
   <p>name=<span class="gaggle-name">Copper response genes</span></p>
   <p>species=<span class="gaggle-species">Halobacterium sp. NRC-1</span></p>

   <p>(optional)size=<span class="gaggle-size">3</span></p>
   <div class="gaggle-namelist">
    <ol>
     <li>VNG0700G</li>
     <li>VNG0702H</li>
     <li>VNG1187G</li>
    </ol>
   </div>
  </div>

Anaerobically induced genes example.

Microformats in the Firegoose

When the browser opens a page, the Firegoose toolbar scans its contents for the presence of data encoded in the Gaggle microformat. If data elements are detected, they appear in the broadcast data menu on the toolbar and are available for broadcast to software or websites connected to the Gaggle framework.

Indirect references

For large data elements, we'd like to have a means of embedding a link to retreive the data on demand rather than embedding all the data in the page. A proposal for how this would look is here:

<div class="gaggle-data">
 <span class="gaggle-name">Expression</span>
 <span class="gaggle-description">copper time series data matrix</span>
 <span class="gaggle-species">Halobacterium sp. NRC-1</span>
 <span class="gaggle-size">2600x9</span>
 <span class="gaggle-type">indirect</span>
 <span class="gaggle-datatype">matrix</span>
 <span class="gaggle-url">http://www.mydomain.com/myapp/myprojects/123456789.tsv</span>
 <span class="gaggle-format">tsv</span>
</div>

Versioning

The first version of the Gaggle Microformat made no mention of versioning. Maybe we should add a version tag to allow future versions to coexist.

Reference

A complete set of examples is available as a reference.

About Microformats

A good discussion of microformats can be found in:

Microformats: the next (small) thing on the semantic Web?
R Khare - Internet Computing, IEEE, 2007
© 2006, Institute for Systems Biology, All Rights Reserved
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