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Property graph

Property graph is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Property graph rather than just read about it. In short: A property graph, labeled property graph, or attributed graph is a data model of various graph-oriented databases, where pairs of entities are associated by directed relationships, and entities and relationships can have properties. In graph theory terms, a property graph is a directed multigraph, whose vertices represent entities and arcs represent relationships.

Property graph — main illustration
Property graph — illustration

Key takeaways

  • Property graph belongs to biology; place it in that map before memorising details.
  • Learn the definition first, then one example that makes the definition concrete.
  • Connect Property graph to a quantity you can measure, compute or draw — that is where exam questions come from.
  • Reproduce the core statement of Property graph from memory before moving on to harder problems.

Reference excerpt

A property graph, labeled property graph, or attributed graph is a data model of various graph-oriented databases, where pairs of entities are associated by directed relationships, and entities and relationships can have properties. In graph theory terms, a property graph is a directed multigraph, whose vertices represent entities and arcs represent relationships. Each arc has an identifier, a source node and a target node, and may have properties. Properties are key-value pairs where keys are character strings and values are numbers or character strings. They are analogous to attributes in entity-attribute-value and object-oriented modeling. By contrast, in RDF graphs, "properties" is the term for the arcs. This is why a clearer name is attributed graphs, or graphs with properties. This data model emerged in the early 2000s.

Formal definition Building upon widely adopted definitions, a property graph/attributed graph can be defined by a 7-tuple (N, A, K, V, α, κ {\displaystyle \kappa } , π), where

N is the set of nodes/vertices of the graph A is the set of arcs (directed edges) of the graph K is a set of keys, taken from a countable set, defining the nature of attributes/properties V is a set of values, to be associated with these keys in order to define full-fledged attributes

α : A → N × N {\displaystyle \alpha \colon A\to N\times N} is a total function, defining the multigraph proper. For a ∈ A, u∈ N, v ∈ N, α (a) = (u, v) means that a is an arc of the graph having node u for origin and node v for target

κ {\displaystyle \kappa } is a binary relation over (A∪N) and K (formally defined as a subset of the cartesian product (A∪N)×K ), associating zero, one or several keys to each arc and node of the graph

π : κ → V {\displaystyle \pi \colon \kappa \to V} is a partial function, providing values for the properties of the nodes and the arcs which include them. For u ∈ N, a ∈ A and k ∈ K, π (u, k) (respectively π (a, k)) is the value associated with the property key k for the node u, (respectively the arc a), if the corresponding attribute property is defined there. A complementary construct, used in several implementations of property graphs with commercial graph databases, is that of labels, which can be associated both with nodes and arcs of the graph. Labels have a practical rather than theoretical justification, as they were originally intended for users of Entity-Relationship models and relational databases, to facilitate the import of their legacy data sets into graph databases :. labels make it possible to associate the same identifier (that of the relational table, or of the ER entity) to all graph nodes which would correspond to the different rows of this relational table, or to instances of the same generic entity / class. With the proposed definition, these labels could in fact be viewed as attributes defined only by a key, without an associated value (this is why κ {\displaystyle \kappa } is defined separately as a binary relation, and π as a partial function). The basic definition thus becomes much clearer, simpler, and satisfies a principle of parsimony. Alternatively, and more consistently, labels can be defined through type graphs, as special types associated with nodes and arcs.

Relations with other models

Graph theory and classical graph algorithms Attributed graphs are especially useful and relevant in that they are an "umbrella" hypernymic concept ( i.e. a generalization) for several key graph-theoretic models, which have long been widely used in classical graph algorithms

Labeled graphs associate labels to each vertex and/or edge of a graph. Matched with attributed graphs, these labels correspond to attributes comprising only a key, taken from a countable set (typically a character string, or an integer) Colored graphs, as used in classical graph coloring problems, are special cases of labeled graphs, whose labels are defined on a finite set of keys, matched to colors. Weighted graphs associate a numerical value to arcs/edges, and, when relevant, to the vertices of a directed or undirected graph. These weights correspond to the values of a set of attributes with the same key. For example, for a model of a road network, where each segment has a length and a capacity (number of vehicles per unit time) can be represented by an edge with two weights. Flow networks are weighted graphs whose weights are interpreted as capacities. They are used in all kinds of very classical models of transport networks, used e.g. with maximum flow algorithms. Shortest path problems, as solved by very classical algorithms (like Dijkstra's algorithm), operate on weighted graphs for which the weights correspond to distances, real or virtual.

Standardization

NGSI-LD The NGSI-LD data model specified by ETSI has been the first attempt to standardize property graphs under a de jure standards body. Compared to the basic model defined here, the NGSI-LD meta-model adds a formal definition of basic categories (entity, relation, property) on the basis of semantic webstandards (OWL, RDFS, RDF), which makes it possible to convert all data represented in NGSI-LD into RDF datasets, through JSON-LD serialization. NGSI-LD entities, relations and properties are thus defined by reference to types which can themselves be defined by reference to ontologies, thesauri, taxonomies or microdata vocabularies, for the purpose of ensuring the semantic interoperability of the corresponding information.

GQL The ISO/IEC JTC1/SC32/WG3 group of ISO, which established the SQL standard, specified a new query language suitable for graph-oriented databases, called GQL (Graph Query Language). This standard includes the specification of a property graph data model, which should be along the lines of the basic model described here, possibly adding notions of labels, types, and schemas. The GQL standard drew on prior industry work, including contributions from graph database vendors such as Neo4j, whose graph database also helped popularize property graphs.

… excerpt ends here. Continue reading the full article.

Illustrations

Property graph: A labelled property graph.
A labelled property graph.

Worked examples

Example 1 — a first encounter with Property graph

Start with the simplest possible case. Write down what Property graph claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Property graph before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Property graph ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Property graph

In research
Property graph appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry
Engineering practice reuses Property graph in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom
Property graph is common in secondary-school and first-year university syllabi. It links to neighbouring topics Extensions and generalizations of graphs, Graph databases, so understanding it makes those chapters shorter.
In everyday life
Look for Property graph outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Property graph in 20 minutes

  1. Read the reference excerpt below once, without taking notes.
  2. Close the page and write down what Property graph means in your own words.
  3. Compare your version with the excerpt and mark what you missed.
  4. Work through the three examples above with pen and paper.
  5. Explain Property graph out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Property graph in simple terms?

A property graph, labeled property graph, or attributed graph is a data model of various graph-oriented databases, where pairs of entities are associated by directed relationships, and entities and relationships can have properties. In graph theory terms, a property graph is a directed multigraph…

Why does Property graph matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Property graph?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Property graph.

Tags

  • Extensions and generalizations of graphs
  • Graph databases

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