cls.ReactomeBiopaxParser Namespace Reference

Parses a Biopax level 3 file to provide its content to an accessor class. More...

Classes
class	CReactomeBiopaxParser

Variables
string	ID_REACTOME = "Reactome"
string	ID_UNIPROT = "UniProt"
string	ID_ENSEMBL = "ENSEMBL"
string	ID_UNIPROT_ISO = "UniProt Isoform"
string	ID_CHEBI = "ChEBI"
string	ID_MIRBASE = "miRBase"
string	ID_EMBL = "EMBL"
list	SUPPORTED_IDS
dictionary	X_NS
dictionary	NS_MAP
string	X_RDF = "{http://www.w3.org/1999/02/22-rdf-syntax-ns#}"
string	X_ID = X_RDF + "ID"
string	X_ID2 = X_RDF + "about"
string	X_RES = X_RDF + "resource"
dictionary	ENTRIES
list	PARSE_CATEGORIES = [x for x in ENTRIES]
list	QUERY_CATEGORIES
list	ID_CATEGORIES = [x for x in ENTRIES if "followForXref" in ENTRIES[x] ]

Detailed Description

Parses a Biopax level 3 file to provide its content to an accessor class.

Authors

Hagen Blankenburg

Date

2014-06

Copyright

See LICENSE file.

Variable Documentation

ENTRIES

dictionary cls.ReactomeBiopaxParser.ENTRIES

ID_CATEGORIES

list cls.ReactomeBiopaxParser.ID_CATEGORIES = [x for x in ENTRIES if "followForXref" in ENTRIES[x] ]

ID_CHEBI

string cls.ReactomeBiopaxParser.ID_CHEBI = "ChEBI"

ID_EMBL

string cls.ReactomeBiopaxParser.ID_EMBL = "EMBL"

ID_ENSEMBL

string cls.ReactomeBiopaxParser.ID_ENSEMBL = "ENSEMBL"

ID_MIRBASE

string cls.ReactomeBiopaxParser.ID_MIRBASE = "miRBase"

ID_REACTOME

string cls.ReactomeBiopaxParser.ID_REACTOME = "Reactome"

ID_UNIPROT

string cls.ReactomeBiopaxParser.ID_UNIPROT = "UniProt"

ID_UNIPROT_ISO

string cls.ReactomeBiopaxParser.ID_UNIPROT_ISO = "UniProt Isoform"

NS_MAP

dictionary cls.ReactomeBiopaxParser.NS_MAP

Initial value:

=  {"http://www.w3.org/2001/XMLSchema#" :"xsd",
        "http://www.biopax.org/release/biopax-level3.owl#" : "bp",
        "http://www.w3.org/1999/02/asced22-rdf-syntax-ns#" : "rdf",
        "http://www.w3.org/2002/07/owl#" : "owl" }

PARSE_CATEGORIES

list cls.ReactomeBiopaxParser.PARSE_CATEGORIES = [x for x in ENTRIES]

QUERY_CATEGORIES

list cls.ReactomeBiopaxParser.QUERY_CATEGORIES

Initial value:

=  ["Dna", "Complex", "Pathway", "BioSource",
            "Modulation", "Rna", "Degradation", "PhysicalEntity",
            "Control", "SmallMolecule", "BiochemicalReaction",
            "Protein", "Catalysis"]

SUPPORTED_IDS

list cls.ReactomeBiopaxParser.SUPPORTED_IDS

Initial value:

=  [ID_REACTOME, ID_UNIPROT, ID_UNIPROT_ISO, ID_CHEBI, ID_ENSEMBL,
                ID_MIRBASE, ID_EMBL]

X_ID

string cls.ReactomeBiopaxParser.X_ID = X_RDF + "ID"

X_ID2

string cls.ReactomeBiopaxParser.X_ID2 = X_RDF + "about"

X_NS

dictionary cls.ReactomeBiopaxParser.X_NS

Initial value:

=  {"xsd:" : "{http://www.w3.org/2001/XMLSchema#}",
        "bp": "{http://www.biopax.org/release/biopax-level3.owl#}",
        "rdf" : "{http://www.w3.org/1999/02/22-rdf-syntax-ns#}",
        "owl" : "{http://www.w3.org/2002/07/owl#}" }

X_RDF

string cls.ReactomeBiopaxParser.X_RDF = "{http://www.w3.org/1999/02/22-rdf-syntax-ns#}"

X_RES

string cls.ReactomeBiopaxParser.X_RES = X_RDF + "resource"