A dataset containing Porphyrin metabolism pathway in Biopax Level 3 and parsed with
readBiopax.
data(ex_biopax)
ex_biopax
#> 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-level3.owl#"
#> owl
#> "http://www.w3.org/2002/07/owl#"
#> rdfs
#> "http://www.w3.org/2000/01/rdf-schema#"
#> 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] "porph.bio3.owl"
#>
#> $biopaxlevel
#> [1] 3
#>
#> $dt
#> Key: <id, class, property>
#> class id property property_attr
#> <char> <char> <char> <char>
#> 1: BioSource BioSource1 name rdf:datatype
#> 2: BioSource BioSource1 xref rdf:resource
#> 3: BiochemicalReaction BiochemicalReaction1 comment rdf:datatype
#> 4: BiochemicalReaction BiochemicalReaction1 comment rdf:datatype
#> 5: BiochemicalReaction BiochemicalReaction1 comment rdf:datatype
#> ---
#> 3005: UnificationXref UnificationXref98 id rdf:datatype
#> 3006: UnificationXref UnificationXref98 idVersion rdf:datatype
#> 3007: UnificationXref UnificationXref99 comment rdf:datatype
#> 3008: UnificationXref UnificationXref99 db rdf:datatype
#> 3009: UnificationXref UnificationXref99 id rdf:datatype
#> property_attr_value
#> <char>
#> 1: http://www.w3.org/2001/XMLSchema#string
#> 2: #UnificationXref17
#> 3: http://www.w3.org/2001/XMLSchema#string
#> 4: http://www.w3.org/2001/XMLSchema#string
#> 5: http://www.w3.org/2001/XMLSchema#string
#> ---
#> 3005: http://www.w3.org/2001/XMLSchema#string
#> 3006: http://www.w3.org/2001/XMLSchema#string
#> 3007: http://www.w3.org/2001/XMLSchema#string
#> 3008: http://www.w3.org/2001/XMLSchema#string
#> 3009: http://www.w3.org/2001/XMLSchema#string
#> property_value
#> <char>
#> 1: Homo sapiens
#> 2:
#> 3: The committed step for porphyrin synthesis is the formation of 5-aminolevulinate (ALA) by condensation of glycine (from the general amino acid pool) and succinyl-CoA (from the TCA cycle), in the mitochondrial matrix. The reaction is catalyzed by two different ALA synthases, one expressed ubiquitously (ALAS1) and the other only expressed in erythroid precursors (ALAS2). Both enzymes are expressed as homodimers and require pyridoxal 5-phosphate as a cofactor.<br>No disease-causing mutations of ALAS1 have been recognised in humans. Mutations in ALAS2 cause X-linked sideroblastic anaemia (XLSA), characterised by a microcytic hypochromic anaemia.
#> 4: Authored: Jassal, B, D'Eustachio, P, 2007-01-24 10:19:49
#> 5: Reviewed: Sassa, S, 2007-01-24 10:18:36
#> ---
#> 3005: REACT_9699
#> 3006: 3
#> 3007: Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113528
#> 3008: Reactome Database ID Release 46
#> 3009: 113528
#>
#> Dimension of internal data.table: 3009,6
#>
#> Summary of parsed internal data.table
#> class id property property_attr
#> Length:3009 Length:3009 Length:3009 Length:3009
#> Class :character Class :character Class :character Class :character
#> Mode :character Mode :character Mode :character Mode :character
#> property_attr_value property_value
#> Length:3009 Length:3009
#> Class :character Class :character
#> Mode :character Mode :character