graph

Documentation

Overview

Package graph provides primitives for building and accessing OBO Graphs(graph oriented ontology). The OBO Graphs can be traversed through a standard graph oriented API using familiar OBO term and relationship concepts.

Index

• type NodeID
• type OboGraph
  • func BuildGraph(r io.Reader) (OboGraph, error)
• type Relationship
  • func NewRelationship(obj, subj, pred NodeID) Relationship
  • func NewRelationshipWithMeta(obj, subj, pred NodeID, m *model.Meta) Relationship
• type Term
  • func NewTerm(id NodeID, rdfType, lbl, iri string) Term
  • func NewTermWithMeta(id NodeID, m *model.Meta, rdfType, lbl, iri string) Term

Types

type NodeID

type NodeID string

NodeID is a custom type for holding a node id.

type OboGraph

type OboGraph interface {
	// IRI represents a stable URL for locating the source OWL formatted file
	IRI() string
	// ID is a short and unique name of the graph
	ID() string
	// Label is a short human readable description of the graph
	Label() string
	// Meta returns the associated Meta container
	Meta() *model.Meta
	// ExistsTerm checks for existence of a term
	ExistsTerm(NodeID) bool
	// GetTerm fetches an existing term
	GetTerm(NodeID) Term
	// GetRelationship fetches relationship(edge) between parent(object) and
	// children(subject)
	GetRelationship(NodeID, NodeID) Relationship
	// Relationships returns all relationships(edges) in the graph
	Relationships() []Relationship
	// Terms returns all terms(node/vertex) in the graph
	Terms() []Term
	// TermsByType provides a filtered list of specific terms
	TermsByType(string) []Term
	// Children returns all children terms(depth one)
	Children(NodeID) []Term
	// Parents returns all parent terms(depth one)
	Parents(NodeID) []Term
	// Ancestors returns all reachable(direct or indirect) parent terms. It uses
	// BFS algorithm
	Ancestors(NodeID) []Term
	// Descendents returns all reachable(direct or indirect) children terms. It uses
	// BFS algorithm
	Descendents(NodeID) []Term
	// DescendentsDFS returns all reachable(direct or indirect) children terms
	// using DFS algorithm.
	DescendentsDFS(NodeID) []Term
	// AddRelationship creates relationship between terms, it overrides the
	// existing terms and relationship
	AddRelationship(Term, Term, Term) error
	// AddRelationshipWithID creates relationship between existing terms
	AddRelationshipWithID(NodeID, NodeID, NodeID) error
	// AddTerm add a new Term to the graph overwriting any existing one
	AddTerm(Term)
}

OboGraph is an interface for accessing OBO Graphs.

func BuildGraph

func BuildGraph(r io.Reader) (OboGraph, error)

BuildGraph builds an in memory graph from JSON-encoded obograph reader.

type Relationship

type Relationship interface {
	// Object is the unique identifier for parent term
	Object() NodeID
	// Subject is the unique identifier for child term
	Subject() NodeID
	// Predicate is the unique identifier for term that describes the relationship
	Predicate() NodeID
	// Meta returns the relationship's Meta object
	Meta() *model.Meta
}

Relationship is an interface for representing relationship between terms.

func NewRelationship

func NewRelationship(obj, subj, pred NodeID) Relationship

NewRelationship is a constructor for Relationship.

func NewRelationshipWithMeta

func NewRelationshipWithMeta(obj, subj, pred NodeID, m *model.Meta) Relationship

NewRelationshipWithMeta is a constructor for Relationship that receives an additional Meta object.

type Term

type Term interface {
	// ID is the term's unique identifier
	ID() NodeID
	// HasMeta check for presence of any metadata
	HasMeta() bool
	// Meta returns the term's Meta object
	Meta() *model.Meta
	// RdfType is one defined rdf type, either of CLASS,
	// INDIVIDUAL OR PROPERTY
	RdfType() string
	// Label is a short human readable description of the term
	Label() string
	// IRI represents a stable URL for term's information
	IRI() string
	// IsDeprecated provides the current status of the term
	IsDeprecated() bool
}

Term is an interface for obo term(node).

func NewTerm

func NewTerm(id NodeID, rdfType, lbl, iri string) Term

NewTerm is the constructor for Term without metadata.

func NewTermWithMeta

func NewTermWithMeta(id NodeID, m *model.Meta, rdfType, lbl, iri string) Term

NewTermWithMeta is the constructor for Term with metadata.