Visualize an RDFLIB Graph in Python

Question

I am new to RDFLIB in python. I found this example of creating a graph on here. What is the simplest way to visualize graph created by this code?

import rdflib
# Now we create a graph, a representaiton of the ontology
g = rdflib.Graph()

# Now define the key words that we will use (the edge weights of the graph)
has_border_with = rdflib.URIRef('http://www.example.org/has_border_with')
located_in = rdflib.URIRef('http://www.example.org/located_in')

# define the things - base level objects that will be the nodes
# In this case first we have countries
germany = rdflib.URIRef('http://www.example.org/country1')
france = rdflib.URIRef('http://www.example.org/country2')
china = rdflib.URIRef('http://www.example.org/country3')
mongolia = rdflib.URIRef('http://www.example.org/country4')

# then we have continents
europa = rdflib.URIRef('http://www.example.org/part1')
asia = rdflib.URIRef('http://www.example.org/part2')

# Having defined the things and the edge weights, now assemble the graph
g.add((germany,has_border_with,france))
g.add((china,has_border_with,mongolia))
g.add((germany,located_in,europa))
g.add((france,located_in,europa))
g.add((china,located_in,asia))
g.add((mongolia,located_in,asia))

I see that the rdflib package has a tools component that has a function called rdfs2dot. How can I use this function to display a plot with the RDF graph in it?

I gave it a look but could not find a complete solution. What I found is that rdfs2dot is a commandline tool: you must first export your graph `g.serialize("world.rdf")`, then convert it the dot syntax: `rdfs2dot world.rdf > world.dot`, then use whatever tools that allows to plot dot graphs. For instance xdot `xdot world.dot`. For some reason, rdfs2dot produces an empty graph. According to the doc of Graph.serialize, rdf is supposed to be the default format, thus either there is a bug here or in rdfs2dot. Maybe look open tickets on github, or post a new issue. — Emilien, Sep 01 '16 at 14:54
Thanks! This makes sense. So you need to first export the graph and then run a command in cmd to create the graph dot file. — MadProgrammer, Sep 01 '16 at 15:01

score 14 · Accepted Answer · edited Mar 11 '21 at 16:26

14

Using the hint in this question: https://www.researchgate.net/post/Is_there_any_open_source_RDF_graph_converter

I was able to plot the RDF Graph by converting to Networkx Graph and using the Networkx/Matplotlib plotting tools.

import rdflib
from rdflib.extras.external_graph_libs import rdflib_to_networkx_multidigraph
import networkx as nx
import matplotlib.pyplot as plt

url = 'https://www.w3.org/TeamSubmission/turtle/tests/test-30.ttl'

g = rdflib.Graph()
result = g.parse(url, format='turtle')

G = rdflib_to_networkx_multidigraph(result)

# Plot Networkx instance of RDF Graph
pos = nx.spring_layout(G, scale=2)
edge_labels = nx.get_edge_attributes(G, 'r')
nx.draw_networkx_edge_labels(G, pos, edge_labels=edge_labels)
nx.draw(G, with_labels=True)

#if not in interactive mode for 
plt.show()

To visualise large RDF Graphs the styling might need some finetuning ;-)

edited Mar 11 '21 at 16:26

Jonsey

1
5

answered Jan 08 '19 at 15:49

Tom Hemmes

2,000
2
17
23

Interesting, your answer is a couple years newer than the question. I wonder what has changed or improved in the mean time. – MadProgrammer Mar 09 '19 at 23:47
From the history in the RDFLib GitHub it seems as if this `rdflib.extras.external_graph_libs.rdflib_to_networkx_multidigraph` was already available at the time you asked the question. Do you mean that you think there should be a better solution in this day and age? – Tom Hemmes Mar 10 '19 at 16:40
2

The line `result = g.parse(url, 'ttl')` did not work for me. The format argument wasn't recognized and rdflib tried to parse it as rdf/xml. I had to write the "format" keyword, and also, use "turtle" rather than "ttl" to make it work. `result = g.parse(url, format='turtle')` – Asahiko Jan 21 '20 at 02:49
I put the edge labels from another dictionary and I needed `nx.draw(G, pos, with_labels=True)` to draw them in positions – Lostefra Jun 27 '21 at 08:05
@TomHemmes would you know about any interactive graph solutions, in case the graph size is large? – Karl 17302 Jan 29 '23 at 15:11

score 14 · Answer 2 · answered Apr 28 '20 at 15:28

14

I could make a picture of your RDF Graph with rdf2dot, as you suggested. Nevertheless I am not completely happy with that library since it makes no nodes for literals. This is my code:

!pip install pydotplus
!pip install graphviz

import io
import pydotplus
from IPython.display import display, Image
from rdflib.tools.rdf2dot import rdf2dot

def visualize(g):
    stream = io.StringIO()
    rdf2dot(g, stream, opts = {display})
    dg = pydotplus.graph_from_dot_data(stream.getvalue())
    png = dg.create_png()
    display(Image(png))

visualize(g)

Giving the following result:

answered Apr 28 '20 at 15:28

Christian Wartena

193
1
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that seems great! Would you mind sharing how to replicate this result using a standalone ttl or (if possible) a sparql endpoint? – K3it4r0 May 19 '20 at 08:40
1

I am not sure what yoe mean. You can load the graph in any way you want. A small example with an RDF-fragment from a standard intorduction to RDF. If you first load the ttl-data into a string, eg the variabe ttlstring, then you can get the graph in the following way: from rdflib import Graph, URIRef, Literal g = Graph() g.parse(data=ttlstring, format='turtle') and then proceed as above. Sorry, I can't get any code formatting or new lines here. – Christian Wartena May 20 '20 at 10:00
@ChristianWartena - this is a fabulous answer! - I've not come across such an elegant solution as this before today - works a treat! – Thomas Kimber Nov 10 '22 at 13:11
@ChristianWartena would you know about any interactive graph solutions, in case the graph size is large? – Karl 17302 Jan 29 '23 at 15:12

Visualize an RDFLIB Graph in Python

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