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Proteomics Standards Initiative

Molecular Interaction XML Format 2.0

Documentation of changes from version 1.0 to 2.0

  1. id attributes
    1. The type of id attributes has been changed from xs:ID to xs:int. xs:ID requires that any id is unique in the file. This was incompatible with the denormalised form of MIF 1.0, where e.g. the same protein may be listed more than once.
      Ids are now defined to be arbibrary integers, unique to each <entry>.
      The type xs:int has been chosen to provide an easy mapping to standard data types, as it provides a limited range of integers, while xs:integer represents the mathmatical concept of integers with an unlimited value range.
    2. All major objects now have an id attribute, namely <experiment>, <interaction>, and all interactor and participant types.
  2. Method-related elements have been renamed for clarity:
    1. ParticipantDetection -> ParticipantIdentificationMethod
    2. InteractionDetection -> InteractionDetectionMethod
    3. FeatureDetection -> FeatureDetectionMethod
  3. Feature element
    1. renamed featureDescription -> featureType
    2. added a <names> element to featureType
    3. location:
      1. each feature now has a list of location elements, to allow representation of discontinuous features, e.g. structural domains.
      2. the location element has been restructured to allow fuzzy locations, and start/end ranges.
  4. namesType extended by addition of an optional list of aliases.
  5. created a new complex type confidenceType and inserted it in all previous occurrences of confidence elements.
  6. Ordered sequence of standard elements. New order is:
    1. names
    2. bibref
    3. xref
    4. other
    5. attributeList
  7. experimentDescription.bibref is now mandatory. Submissions are considered bibrefs.
  8. Negative interactions: Added a mandatory flag "negative" with default value false. If set to "true", it indicates that the interaction has explicitely been described as NOT being observed in the experiment.
  9. New element interaction.inferredInteractionList has been added to allow correct description of complex topology, with supporting experimental evidence.
  10. New element interaction.proteinExperimentalForm has been added to allow correct description of experimental form of proteins if one interaction is show as supported by multiple experiments.
  11. New interactor types have been added, together with the corresponding additions of participantTypes and participantRefs:
    1. DNA
    2. RNA
    3. Small molecule
Henning Hermjakob, 24-Aug-2004