Package pid

Class Summary
Abstraction A link to another pathway from a pathway.
ActivityStateLabel Label containing the info about the activity state
Agent  
AliasName Alternative name for a protein
ChemicalAbstractName Chemical Abstract reference, used for chemical compounds
Complex Type of molecule, composed of sub-unit (Complex Components)
ComplexComponent A Complex Component is of of the building block composing a complex molecule.
Compound Type of molecule, chemical compound, usually bio-active.
Condition A generic condition, influencing an interaction
EntrezGeneName Entrez Gene reference
FamilyMember A molecule member of a family (higher order).
FunctionLabel  
GeneOntologyName Gene Ontology reference
Inhibitor  
Input  
Interaction Interaction between two entities
InteractionComponent An entity interacting in an interaction.
Label Labels give information about the location, activity state, etc...
LabelType LabelTypes are top level categories for a small ontology present within PID
LabelValue A label Value is a category of a label type pseudoo-ontology
LocationLabel Information about the location of the molecule.
Model The main content of PID.
Molecule Generic type of molecule, this class represent a structured sequence of atoms.
MoleculePart If the molecule is part of a bigger molecule, in some occasion, it is described within that class.
Name Reference to a name for an entity.
NegativeCondition A negative condition influencing a pathway
Ontology Ontologies behind PID
Output  
Pathway A pathway from PID
PathwayComponent A step in a pathway, pointing to an interaction.
PID An Object mimicking the XML coming from PID
PositiveCondition A positive condition influencing an interaction
PreferredSymbolName Set of symbols corresponding to the most used by the community.
Protein Type of molecule, mostly used within PID
PTMExpression A Post-Translational Modification (http://en.wikipedia.org/wiki/Posttranslational_modification) expression: A set of PTMs for this molecule.
PTMTerm A PTM for the current molecule.
RNA Type of molecule, storing the information about protein structures among other things.
UniprotName Reference to a uniprot accession string