graph_tool.collection - Dataset collection

This module contains an assortment of useful networks.

graph_tool.collection.data

Dictionary containing Graph objects, indexed by the name of the graph. This is a “lazy” dictionary, i.e. it only loads the graphs from disk when the items are accessed for the first time. The description for each graph is given in the descriptions dictionary, or alternatively in the "description" graph property which accompanies each graph object.

graph_tool.collection.ns

Dictionary containing Graph objects, indexed by the name of the dataset, fetched from the Netzschleuder repository. For dataset entries with more than one network, they are accessed either via a string "<entry>/<network>" or a tuple ("<entry>", "<network>"). This is a “lazy” dictionary, i.e. it only downloads the graphs when the items are accessed for the first time. The description and summary information for each graph are given in the ns_info dictionary, or alternatively in the graph properties which accompanies each graph object.

Examples

>>> g = gt.collection.data["karate"]
>>> print(g)
<Graph object, undirected, with 34 vertices and 78 edges, 1 internal vertex property, 2 internal graph properties, at 0x...>
>>> print(g.gp.readme)
The file karate.gml contains the network of friendships between the 34
members of a karate club at a US university, as described by Wayne Zachary
in 1977.  If you use these data in your work, please cite W. W. Zachary, An
information flow model for conflict and fission in small groups, Journal of
Anthropological Research 33, 452-473 (1977).
>>> g = gt.collection.ns["advogato"]
>>> print(g.gp.description)
A network of trust relationships among users on Advogato, an online community of open source software developers. Edge direction indicates that node i trusts node j, and edge weight denotes one of four increasing levels of declared trust from i to j: observer (0.4), apprentice (0.6), journeyer (0.8), and master (1.0).
graph_tool.collection.ns_info

Dictionary containing descriptions and other summary information for datasets available in the Netzschleuder repository. For dataset entries with more than one network, they are accessed either via a string "<entry>/<network>" or a tuple ("<entry>", "<network>"). The information is downloaded on-the-fly via the available JSON API.

graph_tool.collection.descriptions

Dictionary with a short description and source information on each graph.

A summary, with some extra information, is available in the following table.

Name

N

E

Directed

Description

adjnoun

112

425

False

Word adjacencies: adjacency network of common adjectives and nouns in the novel David Copperfield by Charles Dickens. Please cite M. E. J. Newman, Phys. Rev. E 74, 036104 (2006). Retrieved from Mark Newman’s website.

as-22july06

22963

48436

False

Internet: a symmetrized snapshot of the structure of the Internet at the level of autonomous systems, reconstructed from BGP tables posted by the University of Oregon Route Views Project. This snapshot was created by Mark Newman from data for July 22, 2006 and is not previously published. Retrieved from Mark Newman’s website.

astro-ph

16706

121251

False

Astrophysics collaborations: weighted network of coauthorships between scientists posting preprints on the Astrophysics E-Print Archive between Jan 1, 1995 and December 31, 1999. Please cite M. E. J. Newman, Proc. Natl. Acad. Sci. USA 98, 404-409 (2001). Retrieved from Mark Newman’s website.

celegansneural

297

2359

True

Neural network: A directed, weighted network representing the neural network of C. Elegans. Data compiled by D. Watts and S. Strogatz and made available on the web here. Please cite D. J. Watts and S. H. Strogatz, Nature 393, 440-442 (1998). Original experimental data taken from J. G. White, E. Southgate, J. N. Thompson, and S. Brenner, Phil. Trans. R. Soc. London 314, 1-340 (1986). Retrieved from Mark Newman’s website.

cond-mat

16726

47594

False

Condensed matter collaborations 1999: weighted network of coauthorships between scientists posting preprints on the Condensed Matter E-Print Archive between Jan 1, 1995 and December 31, 1999. Please cite M. E. J. Newman, The structure of scientific collaboration networks, Proc. Natl. Acad. Sci. USA 98, 404-409 (2001). Retrieved from Mark Newman’s website.

cond-mat-2003

31163

120029

False

Condensed matter collaborations 2003: updated network of coauthorships between scientists posting preprints on the Condensed Matter E-Print Archive. This version includes all preprints posted between Jan 1, 1995 and June 30, 2003. The largest component of this network, which contains 27519 scientists, has been used by several authors as a test-bed for community-finding algorithms for large networks; see for example J. Duch and A. Arenas, Phys. Rev. E 72, 027104 (2005). These data can be cited as M. E. J. Newman, Proc. Natl. Acad. Sci. USA 98, 404-409 (2001). Retrieved from Mark Newman’s website.

cond-mat-2005

40421

175693

False

Condensed matter collaborations 2005: updated network of coauthorships between scientists posting preprints on the Condensed Matter E-Print Archive. This version includes all preprints posted between Jan 1, 1995 and March 31, 2005. Please cite M. E. J. Newman, Proc. Natl. Acad. Sci. USA 98, 404-409 (2001). Retrieved from Mark Newman’s website.

dolphins

62

159

False

Dolphin social network: an undirected social network of frequent associations between 62 dolphins in a community living off Doubtful Sound, New Zealand. Please cite D. Lusseau, K. Schneider, O. J. Boisseau, P. Haase, E. Slooten, and S. M. Dawson, Behavioral Ecology and Sociobiology 54, 396-405 (2003). Retrieved from Mark Newman’s website.

email-Enron

36692

367662

False

Enron email communication network covers all the email communication within a dataset of around half million emails. This data was originally made public, and posted to the web, by the Federal Energy Regulatory Commission during its investigation. Nodes of the network are email addresses and if an address i sent at least one email to address j, the graph contains an undirected edge from i to j. Note that non-Enron email addresses act as sinks and sources in the network as we only observe their communication with the Enron email addresses. The Enron email data was originally released by William Cohen at CMU. This version was retrieved from the SNAP database at http://snap.stanford.edu/data/email-Enron.html. Please cite: J. Leskovec, K. Lang, A. Dasgupta, M. Mahoney. Community Structure in Large Networks: Natural Cluster Sizes and the Absence of Large Well-Defined Clusters. Internet Mathematics 6(1) 29–123, 2009, B. Klimmt, Y. Yang. Introducing the Enron corpus. CEAS conference, 2004.

football

115

615

False

American College football: network of American football games between Division IA colleges during regular season Fall 2000. Please cite M. Girvan and M. E. J. Newman, Proc. Natl. Acad. Sci. USA 99, 7821-7826 (2002), and T.S. Evans, “Clique Graphs and Overlapping Communities”, J.Stat.Mech. (2010) P12037 [arXiv:1009.0638]. Retrieved from Mark Newman’s website, with corrections by T. S. Evans, available here.

hep-th

8361

15751

False

High-energy theory collaborations: weighted network of coauthorships between scientists posting preprints on the High-Energy Theory E-Print Archive between Jan 1, 1995 and December 31, 1999. Please cite M. E. J. Newman, Proc. Natl. Acad. Sci. USA 98, 404-409 (2001). Retrieved from Mark Newman’s website.

karate

34

78

False

Zachary’s karate club: social network of friendships between 34 members of a karate club at a US university in the 1970s. Please cite W. W. Zachary, An information flow model for conflict and fission in small groups, Journal of Anthropological Research 33, 452-473 (1977). Retrieved from Mark Newman’s website.

lesmis

77

254

False

Les Miserables: coappearance network of characters in the novel Les Miserables. Please cite D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley, Reading, MA (1993). Retrieved from Mark Newman’s website.

netscience

1589

2742

False

Coauthorships in network science: coauthorship network of scientists working on network theory and experiment, as compiled by M. Newman in May 2006. A figure depicting the largest component of this network can be found here. These data can be cited as M. E. J. Newman, Phys. Rev. E 74, 036104 (2006). Retrieved from Mark Newman’s website.

pgp-strong-2009

39796

301498

True

Strongly connected component of the PGP web of trust circa November 2009. The full data is available at http://key-server.de/dump/. Please cite: Richters O, Peixoto TP (2011) Trust Transitivity in Social Networks. PLoS ONE 6(4): e18384. DOI: 10.1371/journal.pone.0018384 [sci-hub, @tor].

polblogs

1490

19090

True

Political blogs: A directed network of hyperlinks between weblogs on US politics, recorded in 2005 by Adamic and Glance. Please cite L. A. Adamic and N. Glance, “The political blogosphere and the 2004 US Election”, in Proceedings of the WWW-2005 Workshop on the Weblogging Ecosystem (2005). Retrieved from Mark Newman’s website.

polbooks

105

441

False

Books about US politics: A network of books about US politics published around the time of the 2004 presidential election and sold by the online bookseller Amazon.com. Edges between books represent frequent copurchasing of books by the same buyers. The network was compiled by V. Krebs and is unpublished, but can found on Krebs’ web site. Retrieved from Mark Newman’s website.

power

4941

6594

False

Power grid: An undirected, unweighted network representing the topology of the Western States Power Grid of the United States. Data compiled by D. Watts and S. Strogatz and made available on the web here. Please cite D. J. Watts and S. H. Strogatz, Nature 393, 440-442 (1998). Retrieved from Mark Newman’s website.

serengeti-foodweb

161

592

True

Plant and mammal food web from the Serengeti savanna ecosystem in Tanzania. Please cite: Baskerville EB, Dobson AP, Bedford T, Allesina S, Anderson TM, et al. (2011) Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model. PLoS Comput Biol 7(12): e1002321. DOI: 10.1371/journal.pcbi.1002321 [sci-hub, @tor]

Contents

graph_tool.collection.get_data_path(name)[source]

Return the full path of the corresponding dataset.