CMdictionary-class {Onassis} | R Documentation

## Class that stores a Conceptmapper dictionary

### Description

CMdictionary is a class that wraps a Conceptmapper ccp-nlp Java dictionary. Its methods allow the creation of a dictionary from OBO ontologies in OBO or OWL format. Different options to build the dictionary are available.

### Details

The following methods can be applied to CMdictionary instances

`dict_location`
`dict_location<-`
`dictInfo`
`dictInfo<-`
`dictRef`
`dictRef<-`

To show the available dictionary types use the function `dictTypes`

### Slots

`dict_location`

  The path of the created dictionary file

`dictRef`

  Reference to the java object representing the dictionary

`dictInfo`

  Information about how dictionary has been created. It is a list with the following fields

  - Dictionary Type:The type of dictionary

    - OBOA dictionary that has been created by An OBO file

    - ENTREZEntrez genes dictionary

    - TARGETEntrez genes dictionary, Histone marks and Histone modifications

    - CMDICTA previously created dictionary file in the Conceptmapper XML format

  - SynonymType: The type of synonyms to consider when building the dictionary for Conceptmapper. For further detail http://owlcollab.github.io/oboformat/doc/obo-syntax.html

    - EXACT

    - BROAD

    - NARROW

    - RELATED

    - ALL

  - dictSource: The OBO/OWL dictionary file to convert to a Conceptmapper dictionary in case the type is OBO. The XML file in case the type is CMDICT

  - taxID The NCBI taxon identifier for species to create the Entrez gene dictionary (e.g 9606 for Mus musculus)

### Examples

    dict <- new('CMdictionary')

[Package Onassis version 1.6.1 Index]