CMdictionary: 'CMdictionary'

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

Constructor method for creating instances of class CMdictionary-class. The created Conceptmapper dictionary will be stored as an XML file in the file system.

Usage

CMdictionary(inputFileOrDb = NULL, dictType = "OBO",
  outputDir = tempdir(), synonymType = "EXACT", taxID = 0,
  outputDirOp = TRUE)

Arguments

inputFileOrDb	The local OBO/OWL ontology to be converted into an XML Conceptmapper dictionary or the URL of a OBO/OWL file. If inputFileOrdb is NA and the dicType parameter is not the generic OBO then the method tries to download the corresponding dictionary from the available repositories. For ENTREZ and TARGET dictionary types a file named gene_info.gz will be automatically downloaded from ftp://ncbi.nlm.nih.gov/gene/data/gene_info.gz if a valid path is not provided by the user. Alternatively the name of an annotation package of the type Org.xx.eg.db from Bioconductor can be used. In this case the gene unique identifiers and their alternative identifiers will be retrieved from the annotation database without the need of downloading a gene_info file.
dictType	the type of input dictionary OBO A dictionary that has been created by An OBO file ENTREZ Entrez genes dictionary TARGET Entrez genes dictionary, Histone marks and Histone modifications CMDICT A previously created dictionary file in the Conceptmapper XML format
outputDir	the directory where the XML conceptmapper dictionary will be stored. Defaults to the tmp system's directory
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. Default: EXACT EXACT ALL
taxID	the taxonomy identifier of the organism when the dictionary type is ENTREZ or TARGET. If 0 all the taxonomies will be included in the new dictionary.
outputDirOp	set to TRUE to clean the directory before creating the dictionary

Value

An object of type CMdictionary-class that can be used to annotate text with the EntityFinder.

Examples

## Not run: 
#' ##This might take some time to download the dictionary
dict <- CMdictionary(dictType = 'TARGET', inputFileOrDb='org.Hs.eg.db')

dict_file <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
dictionary <- CMdictionary(dictType='OBO', inputFileOrDb=dict_file)

## End(Not run)

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