bp2.model-class: bp2.model class: S4 object model of BioPAX level 2
In microbiome/biopax2: BioPAX level 2 S4 object model

Description Objects from the class Slots Methods Author(s) See Also

"bp2.model" object contains the representaition of BioPAX level 2 databases as S4 objects. There is one S4 object for each BioPAX object. BioPAX objects are stored in codebp2.model@all.objects list.

The classes in the model are: bp2.biochemicalReaction bp2.biochemicalReaction, bp2.bioSource, bp2.catalysis, bp2.chemicalStructure, bp2.complex, bp2.complexAssembly, bp2.confidence, bp2.control, bp2.conversion, bp2.dataSource, bp2.dna, bp2.entity, bp2.evidence, bp2.experimentalForm, bp2.externalReferenceUtilityClass, bp2.interaction, bp2.modulation, bp2.openControlledVocabulary, bp2.pathway, bp2.pathwayStep, bp2.physicalEntity, bp2.physicalEntityParticipant, bp2.physicalInteraction, bp2.protein, bp2.publicationXref, bp2.relationshipXref, bp2.rna, bp2.sequenceFeature, bp2.sequenceInterval, bp2.sequenceLocation, bp2.sequenceParticipant, bp2.sequenceSite, bp2.smallMolecule, bp2.transport, bp2.transportWithBiochemicalReaction, bp2.unificationXref, bp2.utilityClass, and bp2.xref.

Each class contains all slots described in BioPAX level 2 specification in Java-style capiatalization, for example class "bp2.pathway" has slot "pathwayComponents". All slots that contains references to other objects also have corresponding slots for inverse relations on the receiving objects, for example "bp2.pathwayStep" objects contain slot "pathwayComponents.of" that contains references to all "bp2.pathways" that refer to this "bp2.pathwayStep".

The bp2 package uses its own reference system implemented similar to R factors: All fields of all objects in bp2.model are vectors of integers. These integers are indexes of @symbol.names list within the bp2.model object. The names of @all.objects list are located in the beginning of @symbol.names list. Thus, if there is integer value in any object that is less than length(my.bp2@all.objects) it is a reference to the object with that location in @all.objects list and the name of that object is found with the same index in @symbol.names list. If the integer is larger, then it is just a symbol name, not a reference to another object and the string value of the symbol is found in symbol.names list.

The show method for the objects automatically retrieves the names from the symbol name list so printing a objects gives human readable output.

Returned by bp2.create.model function.

all.objects: List of all BioPAX objects contained in the model. The root class of all model classes is virtual bp2.rdf.entity. There is concrete class for each class in BioPAX level 2 specification.
symbol.names: List of all symbol names that appear either as subjects or objects in RDF data. See Description
predicate.names: All predicate names that appreared in RDF data. These are converted to object slots.
all.slot.names: Character vector of all slot names in objects known to bp2.model..

show: signature(x = "bp2.model"): Prints the slot names of the object
show: signature(x = "bp2.rdf.entity"): Prints human readable presentation of model objects

Ossi Koivistoinen

bp2.create.model

microbiome/biopax2 documentation built on May 22, 2019, 9:56 p.m.