psimi25Source-class {RpsiXML} | R Documentation

## Class "psimi25Source"

### Description

A class representing data source compatible with PSI-MI 2.5 XML data exchange format

### Objects from the Class

Objects can be created by calls of the form `new("psimi25Source", ...)`

### Slots

`label`:
  Object of class `"character"`, a meaningful unique label of the database, does not necessarily have to be the identifier used in the PSI-MI files. The value is advised to be overwritten by the objects
`sourceDb`:
  Object of class `"character"`, the character string used in the PSI-MI files to identify the source database. The value must be overwritten by the object, depending on the database identifier used in the PSI-MI file.
`uniprotSymbol`:
  Object of class `"character"`, the identifier of UniProf reference in "primaryRef" or "secondaryRef" attributes of the interactors, telling the parser where to find UniProt symbol of the interactors. The value must be overwritten by the objects.
`parseExperiment`:
  Object of class `"function"`, the function to parse experiment from the PSI-MI 2.5 file. Except for special need this function should not be overwritten by the objects, since it parses the experiment node strictly according the PSI-MI standard
`parseInteractor`:
  Object of class `"function"`, the function to parse interactor from the PSI-MI 2.5 file. Except for special need this function should not be overwritten by the objects, since it parses the interactor node strictly according the PSI-MI standard
`parseComplex`:
  Object of class `"function"`, the function to parse complex from the PSI-MI 2.5 file. Except for special need this function should not be overwritten by the objects, since it parses the complex node strictly according the PSI-MI standard

### Methods

parseComplex
  `signature(x = "psimi25Source")`: parse complex node of PSI-MI 2.5 file
parseExperiment
  `signature(x = "psimi25Source")`: parse experiment node of PSI-MI 2.5 file
parseInteractor
  `signature(x = "psimi25Source")`: parse interactor node of PSI-MI 2.5 file
sourceDb
  `signature(x = "psimi25Source")`: returns the source database
uniprot
  `signature(x = "psimi25Source")`: returns the uniprot identifier of the PSI-MI 2.5 XML file

### Note

In case of a new data repository, you can first try creating a new object of the class with `label`, `sourceDb` and `uniprotSymbol` adjusted as needed. Try parsing a function with this new psimi25Source object. In case of warnings or errors, it may mean that the file provided is not strictly compatible with PSI-MI 2.5 data exchange format standard, please then contact the data provider.

By 02.06.08, six sources have been registered in the release version of `RpsiXML`: BIOGRID.PSIMI25, DIP.PSIMI25, HPRD.PSIMI25, INTACT.PSIMI25,, MINT.PSIMI25,MIPS.PSIMI25. Along the development we will implement more data sources under PSI-MI 25 standard.

### Author(s)

Jitao David Zhang <j.zhang@dkfz.de>

### See Also

`parsePsimi25Interaction`, `parsePsimi25Complex`, `psimi25XML2Graph`

### Examples

    showClass("psimi25Source")

[Package RpsiXML version 1.0.0 Index]