Version: Next

InterMine Items XML Overview

InterMine items XML is a generic format that encodes data the matches InterMine class definitions.

<items>
   <item id="0_1" class="NewFeature" implements="">
      <attribute name="identifier" value="feature2"/>
      <attribute name="confidence" value="0.8"/>
      <reference name="protein" ref_id="0_3"/> 
  </item>
  <item id="0_2" class="NewFeature" implements="">
      <attribute name="identifier" value="feature2"/>
      <attribute name="confidence" value="0.37"/>
      <reference name="protein" ref_id="0_3"/> 
  </item>
  <item id="0_3" class="Protein" implements="">
      <attribute name="primaryAccession" value="Q8I5D2" />
      <attribute name="extraData" value="proteinInfo"/>
      <collection name="features">
          <reference ref_id="0_1" />
          <reference ref_id="0_2" />
      </collection>
  </item>
</items>

Here, the root element is always <items>.

Within <items> each object has id within a separate <item> element.

Each <item> has an id with the format <NAMESPACE_SUBID>. For simple cases, the namespace can always be '0'. These IDs are used to signify connections between items within the item XML file - once the data is loaded into InterMine its own serial IDs are used instead and these Item XML ids disappear.

The child elements of an <item> are either

<attribute> - this has the name of the attribute (matching the defined class name) and a value
<reference> - where the property is a reference to some other item by its Items XML id.
<collection> - this is a collection of <reference>s

Example scripts used to generate InterMine Items XML can be found at intermine_items_example.pl.

Datatypes#

The data formats required for attributes in InterMine Items XML for the most part are fairly obvious and match internal Java types (e.g. strings are UTF-8, doubles are 64-bit IEEE 754 floating point).

One exception is the format required for Dates. InterMine allows this to be expressed in 3 different ways.

As the number of seconds since the Unix epoch.
In the string format 'yyyy-MM-dd HH:mm:ss', assuming UTC.
In the string format 'yyyy-MM-dd', assuming UTC.

If parsing fails for all these formats then InterMine will throw a RuntimeException.

APIs#

InterMine Items XML can either be generated directly in your favourite programming language, or there are a number of language-specific APIs that can generate it, and handle issues like Item XML allocation and referencing automatically.