Gaggle Components
Geese
Data Standards
Boss

Gaggle Embedded XML

Embedded XML for Gaggle data types

Firegoose can read Gaggle data types from web pages using embedded XML. Embedded XML overlaps almost exactly with microformats and the inclusion of both is meant to accomodate the preferences of data providers. The embedded XML can specify a Gaggle data type directly, or indirectly by linking to a URL from which the data can be acquired as needed.

Examples:

<div name="gaggle_xml" class="hidden">
  <gaggleData version="0.1">
    <namelist type="direct" name="Orf names" species="Halobacterium sp. NRC-1">
      VNG0536G	VNG0700G	VNG0702H	VNG1187G
    </namelist>
  </gaggleData>
</div>
**Note that the list elements are delimited by tabs.
<div name="gaggle_xml" class="hidden">
  <gaggleData version="0.1">
    <dataMatrix type="indirect"
                name="Microarray experiments"
                species="Halobacterium sp. NRC-1"
                url="http://www.mydomain.com/myapp/myprojects/123456789.tsv"/>
  </gaggleData>
</div>

further examples (click and view source).

Status

Embedded Gaggle XML is currently defined only for list and matrix types (direct and indirect). It is likely to remain so, unless other types are requested. A well-defined XML schema definition for Gaggle data type is something we should do and would probably replace this version of Embedded XML.

© 2006, Institute for Systems Biology, All Rights Reserved
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