History of netscience

The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.

2026-10-25 [entries] Fix parse bugs and improve the metadata of existing entries by Tiago de Paula Peixoto c996a0e

From a review of the dataset descriptions against the upstream sources
and papers, and from user reports:

- parse fixes (wrong edge direction or directedness, shifted or
  misnamed properties, merged node identities, duplicated or missing
  edges and nodes, wrong types), e.g. arxiv_citation (the HepTh dates
  were a copy of the HepPh ones; now from the KDD Cup 2003 data),
  eu_procurements, foursquare_global, hiv_transmission, genetic_multiplex,
  gnutella (adds the 05 snapshot), roadnet, macaque_neural, python_dependency
- descriptions rewritten from the upstream sources, documenting every
  property
- corrected titles, citations and DOIs, licences (ustream_license typo,
  the data's own terms), tags and ICON ids
- url lists for entries with several sources or dataset pages
- SocioPatterns entries moved to the site's new data location, with the
  daily networks of sp_infectious and sp_primary_school
- the Michael Fire entries marked as orphans (served from the mirror)
- redundant type forcings removed after the graph-tool coercion fixes

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index ef031a8..b9cef22 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -19,13 +19,19 @@
 from .. import *
 
 title = "Scientific collaborations in network science (2006)"
-description = """A coauthorship network among scientists working on network science, from 2006. This network is a one-mode projection from the bipartite graph of authors and their scientific publications.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """Coauthorship network of scientists working on network theory and experiment, compiled by M. E. J. Newman in May 2006 from the bibliographies of two review articles on networks, M. E. J. Newman, SIAM Review 45, 167-256 (2003), and S. Boccaletti et al., Physics Reports 424, 175-308 (2006), with a few additional references added by hand. Nodes are scientists and two scientists are connected if they coauthored at least one of the papers. This version contains all components of the network (1,589 scientists), not just the largest component of 379 scientists that was originally analyzed.
+
+The edges are weighted as described in M. E. J. Newman, Phys. Rev. E 64, 016132 (2001): each paper with $n$ authors contributes $1/(n-1)$ to the weight of the edge between every pair of its authors, so that the weight $w_{ij}$ is the sum of these contributions over all papers coauthored by $i$ and $j$.
+
+The network has the following properties:
+
+- `label`: the name of the scientist, as surname and initials (as in "ABRAMSON, G").
+- `value`: the edge weight $w_{ij}$."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'https://doi.org/10.1103/physreve.74.036104/'
 citation = [('M. E. J. Newman, "Finding community structure in networks using the eigenvectors of matrices." Phys. Rev. E 74, 036104 (2006). arxiv:physics/0605087', 'https://doi.org/10.1103/physreve.74.036104')]
 icon_hash = '56a85c8e26855e083a2f78a9'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
 files = [('netscience.zip:netscience.gml', None, 'gml')]

2026-10-24 Update copyright information by Tiago de Paula Peixoto 73a4f0d

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 40bbcc8..ef031a8 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2026 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2024-05-27 Update copyright information by Tiago de Paula Peixoto 3d288ea

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 0ff3b5b..40bbcc8 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2023-02-19 Update copyright information by Tiago de Paula Peixoto 8d005ae

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 5351ccf..0ff3b5b 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2021-06-22 Update copyright info by Tiago de Paula Peixoto db2efcc

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index cf69b0d..5351ccf 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2021-02-01 Fix entry 'netscience' by Tiago de Paula Peixoto 393b0f3

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 71fbaac..cf69b0d 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -26,7 +26,7 @@ url = 'https://doi.org/10.1103/physreve.74.036104/'
 citation = [('M. E. J. Newman, "Finding community structure in networks using the eigenvectors of matrices." Phys. Rev. E 74, 036104 (2006). arxiv:physics/0605087', 'https://doi.org/10.1103/physreve.74.036104')]
 icon_hash = '56a85c8e26855e083a2f78a9'
 ustream_license = None
-upstream_prefix = 'https://doi.org/10.1103/physreve.74.036104'
+upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
 files = [('netscience.zip:netscience.gml', None, 'gml')]
 
 def fetch_upstream(force=False):

2020-11-28 Update citations to use DOIs by Tiago de Paula Peixoto e878874

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 5312307..71fbaac 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -22,11 +22,11 @@ title = "Scientific collaborations in network science (2006)"
 description = """A coauthorship network among scientists working on network science, from 2006. This network is a one-mode projection from the bipartite graph of authors and their scientific publications.[^icon]
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
-url = 'http://www-personal.umich.edu/~mejn/netdata/'
-citation = [('M. E. J. Newman, "Finding community structure in networks using the eigenvectors of matrices." Phys. Rev. E 74, 036104 (2006). arxiv:physics/0605087', 'http://www-personal.umich.edu/~mejn/netdata')]
+url = 'https://doi.org/10.1103/physreve.74.036104/'
+citation = [('M. E. J. Newman, "Finding community structure in networks using the eigenvectors of matrices." Phys. Rev. E 74, 036104 (2006). arxiv:physics/0605087', 'https://doi.org/10.1103/physreve.74.036104')]
 icon_hash = '56a85c8e26855e083a2f78a9'
 ustream_license = None
-upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
+upstream_prefix = 'https://doi.org/10.1103/physreve.74.036104'
 files = [('netscience.zip:netscience.gml', None, 'gml')]
 
 def fetch_upstream(force=False):

2020-09-15 Change license from GPLv3 to AGPLv3 by Tiago de Paula Peixoto d754be5

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 48713c6..5312307 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -3,18 +3,18 @@
 #
 # Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
 #
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
 #
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more
+# details.
 #
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU Affero General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 from .. import *

2020-09-13 Add explicit attribution to descriptions obtained from ICON by Tiago de Paula Peixoto 1645314

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
index 5549ae2..48713c6 100644
--- a/entries/netscience/__init__.py
+++ b/entries/netscience/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Scientific collaborations in network science (2006)"
-description = "A coauthorship network among scientists working on network science, from 2006. This network is a one-mode projection from the bipartite graph of authors and their scientific publications."
+description = """A coauthorship network among scientists working on network science, from 2006. This network is a one-mode projection from the bipartite graph of authors and their scientific publications.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'http://www-personal.umich.edu/~mejn/netdata/'
 citation = [('M. E. J. Newman, "Finding community structure in networks using the eigenvectors of matrices." Phys. Rev. E 74, 036104 (2006). arxiv:physics/0605087', 'http://www-personal.umich.edu/~mejn/netdata')]

2020-08-11 Initial commit by Tiago de Paula Peixoto cc85872

diff --git a/entries/netscience/__init__.py b/entries/netscience/__init__.py
new file mode 100644
index 0000000..5549ae2
--- /dev/null
+++ b/entries/netscience/__init__.py
@@ -0,0 +1,49 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from .. import *
+
+title = "Scientific collaborations in network science (2006)"
+description = "A coauthorship network among scientists working on network science, from 2006. This network is a one-mode projection from the bipartite graph of authors and their scientific publications."
+tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
+url = 'http://www-personal.umich.edu/~mejn/netdata/'
+citation = [('M. E. J. Newman, "Finding community structure in networks using the eigenvectors of matrices." Phys. Rev. E 74, 036104 (2006). arxiv:physics/0605087', 'http://www-personal.umich.edu/~mejn/netdata')]
+icon_hash = '56a85c8e26855e083a2f78a9'
+ustream_license = None
+upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
+files = [('netscience.zip:netscience.gml', None, 'gml')]
+
+def fetch_upstream(force=False):
+    return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+                                force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+    global files
+    name = __name__.split(".")[-1]
+    for fnames, alt, fmt in files:
+        if alts is not None and alt not in alts:
+            continue
+        if isinstance(fnames, str):
+            fnames = [fnames]
+        with ExitStack() as stack:
+            fs = [stack.enter_context(open_upstream_file(name, fn, "rb")) for fn in fnames]
+            g = parse_graph(fs, fmt, directed=False)
+        yield alt, g