biopax: Biopax example data set

In rBiopaxParser: Parses BioPax files and represents them in R

Description

A dataset containing two regulatory pathways encoded in Biopax Level 2 and parsed in via readBiopax().

Another dataset containing pathways encoded in Biopax Level 2 and parsed in via readBiopax().

Format

An example biopax model parsed in via readBiopax.

An example biopax model parsed in via readBiopax.

Examples

data(biopaxexample)
biopax
data(biopaxLevel3Example)
biopax

Example output

Loading required package: data.table
Summary of the biopax object:
            Length Class                             Mode     
namespaces  5      SimplifiedXMLNamespaceDefinitions character
ns_rdf      1      -none-                            character
ns_owl      1      -none-                            character
ns_bp       1      -none-                            character
file        1      -none-                            character
biopaxlevel 1      -none-                            numeric  
dt          6      biopax_df                         list     

Internal data:
$namespaces
                                               rdf 
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
                                                bp 
"http://www.biopax.org/release/biopax-level2.owl#" 
                                              rdfs 
           "http://www.w3.org/2000/01/rdf-schema#" 
                                               owl 
                  "http://www.w3.org/2002/07/owl#" 
                                               xsd 
               "http://www.w3.org/2001/XMLSchema#" 
attr(,"class")
[1] "SimplifiedXMLNamespaceDefinitions" "XMLNamespaceDefinitions"          

$ns_rdf
[1] "rdf"

$ns_owl
[1] "owl"

$ns_bp
[1] "bp"

$file
[1] "docu/vignette/exampledata.owl"

$biopaxlevel
[1] 2

$dt
                         class                 id          property
  1:                 bioSource       Homo_sapiens              NAME
  2:                 bioSource       Homo_sapiens        TAXON-XREF
  3:           unificationXref NCBI_taxonomy_9606                DB
  4:           unificationXref NCBI_taxonomy_9606                ID
  5:                dataSource example_DataSource              NAME
 ---                                                               
919: physicalEntityParticipant     ex_x_101435_30 CELLULAR-LOCATION
920:       sequenceParticipant   ex_x_101860_5907   PHYSICAL-ENTITY
921:       sequenceParticipant   ex_x_101860_5907 CELLULAR-LOCATION
922:       sequenceParticipant   ex_x_101441_5569   PHYSICAL-ENTITY
923:       sequenceParticipant   ex_x_101441_5569 CELLULAR-LOCATION
     property_attr                     property_attr_value       property_value
  1:  rdf:datatype http://www.w3.org/2001/XMLSchema#string         Homo sapiens
  2:  rdf:resource                     #NCBI_taxonomy_9606                     
  3:  rdf:datatype http://www.w3.org/2001/XMLSchema#string        NCBI_taxonomy
  4:  rdf:datatype http://www.w3.org/2001/XMLSchema#string                 9606
  5:  rdf:datatype http://www.w3.org/2001/XMLSchema#string example biopax model
 ---                                                                           
919:  rdf:resource                          #transmembrane                     
920:  rdf:resource                            #ex_m_101860                     
921:  rdf:resource                              #cytoplasm                     
922:  rdf:resource                            #ex_m_101441                     
923:  rdf:resource                                #nucleus                     

Dimension of internal data.table:  923,6 

Summary of parsed internal data.table 
    class                id              property         property_attr     
 Length:923         Length:923         Length:923         Length:923        
 Class :character   Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character   Mode  :character  
 property_attr_value property_value    
 Length:923          Length:923        
 Class :character    Class :character  
 Mode  :character    Mode  :character  
Summary of the biopax object:
            Length Class                             Mode     
namespaces  5      SimplifiedXMLNamespaceDefinitions character
ns_rdf      1      -none-                            character
ns_owl      1      -none-                            character
ns_bp       1      -none-                            character
file        1      -none-                            character
biopaxlevel 1      -none-                            numeric  
dt          6      biopax_df                         list     

Internal data:
$namespaces
                                               rdf 
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
                                                bp 
"http://www.biopax.org/release/biopax-level2.owl#" 
                                              rdfs 
           "http://www.w3.org/2000/01/rdf-schema#" 
                                               owl 
                  "http://www.w3.org/2002/07/owl#" 
                                               xsd 
               "http://www.w3.org/2001/XMLSchema#" 
attr(,"class")
[1] "SimplifiedXMLNamespaceDefinitions" "XMLNamespaceDefinitions"          

$ns_rdf
[1] "rdf"

$ns_owl
[1] "owl"

$ns_bp
[1] "bp"

$file
[1] "docu/vignette/exampledata.owl"

$biopaxlevel
[1] 2

$dt
                         class                 id          property
  1:                 bioSource       Homo_sapiens              NAME
  2:                 bioSource       Homo_sapiens        TAXON-XREF
  3:           unificationXref NCBI_taxonomy_9606                DB
  4:           unificationXref NCBI_taxonomy_9606                ID
  5:                dataSource example_DataSource              NAME
 ---                                                               
919: physicalEntityParticipant     ex_x_101435_30 CELLULAR-LOCATION
920:       sequenceParticipant   ex_x_101860_5907   PHYSICAL-ENTITY
921:       sequenceParticipant   ex_x_101860_5907 CELLULAR-LOCATION
922:       sequenceParticipant   ex_x_101441_5569   PHYSICAL-ENTITY
923:       sequenceParticipant   ex_x_101441_5569 CELLULAR-LOCATION
     property_attr                     property_attr_value       property_value
  1:  rdf:datatype http://www.w3.org/2001/XMLSchema#string         Homo sapiens
  2:  rdf:resource                     #NCBI_taxonomy_9606                     
  3:  rdf:datatype http://www.w3.org/2001/XMLSchema#string        NCBI_taxonomy
  4:  rdf:datatype http://www.w3.org/2001/XMLSchema#string                 9606
  5:  rdf:datatype http://www.w3.org/2001/XMLSchema#string example biopax model
 ---                                                                           
919:  rdf:resource                          #transmembrane                     
920:  rdf:resource                            #ex_m_101860                     
921:  rdf:resource                              #cytoplasm                     
922:  rdf:resource                            #ex_m_101441                     
923:  rdf:resource                                #nucleus                     

Dimension of internal data.table:  923,6 

Summary of parsed internal data.table 
    class                id              property         property_attr     
 Length:923         Length:923         Length:923         Length:923        
 Class :character   Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character   Mode  :character  
 property_attr_value property_value    
 Length:923          Length:923        
 Class :character    Class :character  
 Mode  :character    Mode  :character  

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.