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.
The following methods can be applied to CMdictionary instances
To show the available dictionary types use the function
The path of the created dictionary file
Reference to the java object representing the dictionary
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
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)
dict <- new('CMdictionary')
Loading required package: rJava Loading required package: OnassisJavaLibs Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed OnASSIs successfully loaded
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