iRefIndex Development

See iRefIndex Issues and Notes for details of ongoing work to improve the iRefIndex software.

Adding Sources to iRefIndex

1. Identify the location of the downloaded data.
2. Evaluate the form of the data:
   1. For PSI MI XML (Molecular Interaction XML) documents, check the version of the format employed by the data documents.
   2. For the specific version, review the format's schema and how the data uses the schema. For example, PSI MI XML permits the specification of interactors within interaction descriptions as well as in a separate interactor list.
3. Review existing, similar mapper definition files.

Evaluating the Data

The show_xml_paths.py script in the iRef_PSI_XML2RDBMS directory can be used to show the different element paths used in an XML data file to hold data items. For example:

python show_xml_paths.py --data /home/irefindex/data/MINT/2010-09-14/10023771.psi25.xml

The resulting list of paths indicates the places in the element hierarchy of a PSI-MI XML file where information is actually stored. For example:

entrySet/entry/experimentList/experimentDescription/attributeList/attribute
entrySet/entry/experimentList/experimentDescription/hostOrganismList/hostOrganism/names/fullName
entrySet/entry/experimentList/experimentDescription/hostOrganismList/hostOrganism/names/shortLabel
entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/alias
entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/fullName
entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel
entrySet/entry/experimentList/experimentDescription/names/fullName
entrySet/entry/experimentList/experimentDescription/names/shortLabel
entrySet/entry/interactionList/interaction/attributeList/attribute
entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/names/fullName
entrySet/entry/interactionList/interaction/confidenceList/confidence/unit/names/shortLabel
entrySet/entry/interactionList/interaction/confidenceList/confidence/value
entrySet/entry/interactionList/interaction/experimentList/experimentRef
entrySet/entry/interactionList/interaction/interactionType/names/fullName
entrySet/entry/interactionList/interaction/interactionType/names/shortLabel
entrySet/entry/interactionList/interaction/intraMolecular
entrySet/entry/interactionList/interaction/modelled
entrySet/entry/interactionList/interaction/names/shortLabel
entrySet/entry/interactionList/interaction/negative
entrySet/entry/interactionList/interaction/participantList/participant/biologicalRole/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/biologicalRole/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/experimentalPreparationList/experimentalPreparation/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/experimentalPreparationList/experimentalPreparation/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/experimentalRoleList/experimentalRole/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/experimentalRoleList/experimentalRole/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureRangeList/featureRange/endStatus/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureRangeList/featureRange/endStatus/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureRangeList/featureRange/isLink
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureRangeList/featureRange/startStatus/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureRangeList/featureRange/startStatus/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureType/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/featureType/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/featureList/feature/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/interactorRef
entrySet/entry/interactionList/interaction/participantList/participant/names/shortLabel
entrySet/entry/interactionList/interaction/participantList/participant/participantIdentificationMethodList/participantIdentificationMethod/names/alias
entrySet/entry/interactionList/interaction/participantList/participant/participantIdentificationMethodList/participantIdentificationMethod/names/fullName
entrySet/entry/interactionList/interaction/participantList/participant/participantIdentificationMethodList/participantIdentificationMethod/names/shortLabel
entrySet/entry/interactorList/interactor/attributeList/attribute
entrySet/entry/interactorList/interactor/interactorType/names/fullName
entrySet/entry/interactorList/interactor/interactorType/names/shortLabel
entrySet/entry/interactorList/interactor/names/alias
entrySet/entry/interactorList/interactor/names/fullName
entrySet/entry/interactorList/interactor/names/shortLabel
entrySet/entry/interactorList/interactor/organism/names/fullName
entrySet/entry/interactorList/interactor/organism/names/shortLabel
entrySet/entry/interactorList/interactor/sequence
entrySet/entry/source/attributeList/attribute
entrySet/entry/source/names/fullName
entrySet/entry/source/names/shortLabel

With this information, a suitable mapper file can be identified for the conversion of the XML-encoded data into tabular data to be stored in a database. In the above example, it is apparent that the experiment, interaction and interactor details reside alongside each other within each entry element:

entrySet/entry/experimentList/experimentDescription
entrySet/entry/interactionList/interaction
entrySet/entry/interactionList/interaction/participantList/participant
entrySet/entry/interactorList/interactor

In contrast, other PSI-MI XML files adopt a different structure which can be reduced to the following:

entrySet/entry/interactionList/interaction
entrySet/entry/interactionList/interaction/experimentList/experimentDescription
entrySet/entry/interactionList/interaction/participantList/participant

The different sources can be divided into a number of subformats as follows:

Subformat	Sources	Notes
Separate experiment, interaction, interactor lists	BioGRID, HPRD, IntAct, MINT, OPHID	BioGRID uses proteininteractor instead of interactor OPHID uses proteinParticipant, proteinInteractor
Interaction contains experiment; separate interactor list	DIP
Interaction contains experiment and interactor/participant	BIND Translation, CORUM, InnateDB, MPACT, MPPI	InnateDB provides apparently redundant lists of experiments and interactors MPPI uses proteinParticipant, proteinInteractor

Reviewing Mapper Files

The mapper files already in existence can be reviewed by using the show_xml_paths.py script together with one of these files which reside in the mapper subdirectory of the iRef_PSI_XML2RDBMS directory. For example:

python show_xml_paths.py --mapper mapper/Map25_CORUM.xml

The resulting output describes the structure of the data and how the mapper will attempt to interpret that data. For example (for CORUM):

Element experimentDescription ...
  Table int_name ...
    _euid ...
      <incremental>
    _idetlbl ...
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/alias
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/names/fullname
    _idetncat ...
      24
      25
      25
  Table int_xref ...
    _euid ...
      <incremental>
    _brefdb ...
      entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/primaryRef/@db
      entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/secondaryRef/@db
    _brefid ...
      entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/primaryRef/@id
      entry/interactionList/interaction/experimentList/experimentDescription/bibref/xref/secondaryRef/@id
    _brefct ...
      4
      5
  Table int_xref ...
    _euid ...
      <incremental>
    _idetdb ...
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@db
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@db
    _idetid ...
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/primaryRef/@id
      entry/interactionList/interaction/experimentList/experimentDescription/interactionDetectionMethod/xref/secondaryRef/@id
    _idetct ...
      6
      7
Element experimentList ...
  Table int_experiment ...
    _euidr ...
      _euid
    _iuider ...
      _iuid
Element interaction ...
  Table int_name ...
    _iuid ...
      <incremental>
    _iuiflnm ...
      entry/interactionList/interaction/names/fullName
    _iuiflnmct ...
      12
  Table int_source ...
    _iuid ...
      <incremental>
    _itp ...
      entry/interactionList/interaction/xref
    _isrc ...
      entry/interactionList/interaction/xref
    _ifle ...
      entry/interactionList/interaction/xref
  Table int_xref ...
    _iuid ...
      <incremental>
    _idb ...
      entry/interactionList/interaction/xref/primaryRef/@db
    _iref ...
      entry/interactionList/interaction/xref/primaryRef/@id
    _irefcat ...
      0
Element participant ...
  Table int_name ...
    _ouid ...
      <incremental>
    _olb ...
      entry/interactionList/interaction/participantList/participant/interactor/names/shortLabel
      entry/interactionList/interaction/participantList/participant/interactor/names/alias
      entry/interactionList/interaction/participantList/participant/interactor/names/fullName
    _olbct ...
      13
      14
      15
  Table int_object ...
    _ouid ...
      <incremental>
    _oltyp ...
      entry/interactionList/interaction/participantList/participant/interactor/interactorType/names/shortLabel
    _osrc ...
      entry/interactionList/interaction/participantList/participant/interactor/names
    _ofil ...
      entry/interactionList/interaction/participantList/participant/interactor/names
  Table int_sequence ...
    _ouid ...
      <incremental>
    _obsq ...
      entry/interactionList/interaction/participantList/participant/interactor/sequence
  Table int_xref ...
    _ouid ...
      <incremental>
    _odb ...
      entry/interactionList/interaction/participantList/participant/interactor/xref/primaryRef/@db
      entry/interactionList/interaction/participantList/participant/interactor/xref/secondaryRef/@db
    _orefid ...
      entry/interactionList/interaction/participantList/participant/interactor/xref/primaryRef/@id
      entry/interactionList/interaction/participantList/participant/interactor/xref/secondaryRef/@id
    _oicat ...
      2
      3
    _otax ...
      entry/interactionList/interaction/participantList/participant/interactor/organism/@ncbiTaxId
    _otp ...
      entry/interactionList/interaction/participantList/participant/interactor/xref/primaryRef/@refType
      entry/interactionList/interaction/participantList/participant/interactor/xref/secondaryRef/@refType
Element participantList ...
  Table int_source2object ...
    _iuidr ...
      _iuid
    _what ...
      entry/interactionList/interaction/participantList/participant/interactor/names
    _isrcr ...
      entry/interactionList/interaction/participantList/participant/interactor/names
    _ifler ...
      entry/interactionList/interaction/participantList/participant/interactor/names
    _refob ...
      _ouid

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