PSI-MI XML 2.5 Formatted Downloads

The PSI MI format is a means of exchanging data on molecular interactions, maintained by the HUPO Proteomics Standards Initiative. For a diagram of the PSI 2.5 XML schema click here. BioGRID interactions are annotated with the terms described in the Experimental Evidence Codes section to distinguish between different types of evidence supporting an interaction. The BioGRID PSI MI 2.5 XML files primarily contain MI ontology terms to describe experimental methods and other interaction details; please see the BioGRID/MI mapping file which explains how the MI terms in the BioGRID PSI MI XML file were chosen.

The original BioGRID evidence code used for the annotation can also be found in the PSI MI XML file in the entrySet > entry > interactionList > interaction > attributeList > attribute XML tag with attribute name = BioGRID Evidence Code.

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How to Detect a PSI-MI 2.5 XML file

PSI-MI 2.5 XML files are denoted by the extension .psi25.txt or .psi25.zip

Interactions

Interaction IDs found in the entrySet > entry > interactionList > interaction XML tag as an XML attribute are a references which are meaningful only within the XML file. BioGRID interaction IDs which are found in the entrySet > entry > interactionList > interaction > xref > primaryRef XML tag are created when an interaction is curated (an interaction here being an interaction demonstrated between a pair of interactors with one evidence code in one publication). References to experiments used to support the interaction can be found in the entrySet > entry > interactionList > interaction > experimentList > experimentRef XML tag and the XML elements representing the experiments can be found in entrySet > entry > experimentList > experimentDescription.

References to XML elements for the interactors can be found in entrySet > entry > interactionList > interaction > participantList > participant > interactorRef, and the XML elements representing the interactors can be found in entrySet > entry > interactorList > interactor. Details of the interactor's role in the experiment are found in the following XML tags: entrySet > entry > interactionList > interaction > participantList > participant > participantIdentificationMethodList > participantIdentificationMethod, entrySet > entry > interactionList > interaction > participantList > participant > biologicalRole, entrySet > entry > interactionList > interaction > participantList > participant > experimentalRoleList > experimentalRole.

These are expressed in PSI MI terms mapped from BioGRID terms according to the BioGRID/MI mapping file.

Experiments

Each experiment contains a reference to the publication (entrySet > entry > experimentList > experimentDescription > bibref), the host organism used in the experiment (entrySet > entry > experimentList > experimentDescription > hostOrganismList > hostOrganism) and interaction detection method (entrySet > entry > experimentList > experimentDescription > interactionDetectionMethod). Interaction detection methods are given according to MI terms chosen using a mapping from BioGRID experimental codes. The original BioGRID evidence code can be found in entrySet > entry > interactionList > interaction > attributeList > attribute.

Interactors

Curation of all interactors in BioGRID are by reference to Entrez Gene identifiers. However, to allow maximum integration with other interaction databases which also use the PSI MI format the primaryRef of interactors in this XML file is a protein RefSeq ID the primaryXref(entrySet > entry > interactorList > interactor > xref > primaryRef), with the exception of interactors having multiple protein RefSeq IDs. Therefore, if the curated Entrez Gene ID has only one protein RefSeq, that RefSeq ID will be present as a primaryRef and the Entrez Gene ID will be present as a secondaryRef. If the curated Entrez Gene ID has multiple protein RefSeqs, those RefSeq IDs will be present as secondaryRefs and the Entrez Gene ID will be present as the primaryRef. Any curation referencing discontinued Entrez Gene IDs are re-pointed to the appropriate new ID, if possible, and the original ID used for annotation is listed as a secondaryRef; if a discontinued Entrez Gene ID is used as a primaryRef, an annotation can be found in the entrySet > entry > interactorList > interactor > xref > primaryRef > attributeList > attribute XML tag, with XML attribute name =“Discontinued” and contents “This interactor record has been discontinued in its source database”. The release date of the Entrez Gene data used to build the XML file can be found in the entrySet > entry > attributeList > attribute XML tag, with attribute name=”based on entrez gene downloaded on”.

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psi-mi_xml_version_2.5.txt · Last modified: 2016/10/13 22:59 (external edit)