CMdictionary-class: Class that stores a Conceptmapper dictionary

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

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')

Example output

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

Onassis documentation built on Nov. 8, 2020, 8:18 p.m.