InterMine Items XML

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

Unfortunately, there is no document giving the formal specification for this format yet (please ping us on the mailing list or elsewhere if you need this). However, an example and some information is below

<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 is 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:

• bio/scripts/intermine_items_example.pl
• RedFly testing objects file at bio/sources/flymine/redfly/test/resources/RedFlyGFF3RecordHandlerTest.xml.

Datatypes

The data formats required for attributes in InterMine Items XML need proper documentation. However, for the most part they 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.

1. As the number of seconds since the Unix epoch.
2. In the string format ‘yyyy-MM-dd HH:mm:ss’, assuming UTC.
3. 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.

• Java Items API
• Perl Items API
• Python Items API