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.konect_data

Dictionary containing Graph objects, indexed by the name of the graph, fetched from the Koblenz Network Collection. See the website for a list of available data. The key of the dictionary must correspond to the name of the file minus the .tar.bz2 part. This is a “lazy” dictionary, i.e. it only downloads the graphs from the web when the items are accessed for the first time.

Examples

>>> g = gt.collection.data["karate"]
>>> print(g)
<Graph object, undirected, with 34 vertices and 78 edges 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).
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.