History of wiki_science

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/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index d89bf3e..5dcc592 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__init__.py
@@ -19,13 +19,19 @@
 from .. import *
 
 title = "Wikipedia Map of Science (2020)"
-description = """A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See <http://www.sinnefa.com/wikipediasciencemap/> for an interactive version.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """Network of similarities among branches of science, built by A. Calderone in January 2020 from the English Wikipedia. Nodes are the Wikipedia pages listed in the outlines of the natural, formal, social and applied sciences (pages titled "Outline of ..." excluded). The main text of each page was preprocessed (stop-word removal and lemmatization), and the pages were compared by the cosine similarity of their contents. Two pages are connected if their similarity is significantly high, i.e. has a z-score larger than 1.96. Isolated nodes were removed.
+
+The network has the following properties:
+
+- `name`: the title of the Wikipedia page.
+- `Class`: the branch of science of the page, according to the outline it was taken from: `Natural`, `Formal`, `Social` or `Applied`.
+- `WikipediaUrl`: the URL of the page.
+- `CosineSimilarity`: the cosine similarity of the contents of the two pages."""
 tags = ['Informational', 'Relatedness', 'Unweighted']
 url = 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932'
 citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare (2020)', 'https://doi.org/10.6084/m9.figshare.11638932.v5')]
 icon_hash = '5e23d5e078691ca4060b62b1'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'https://ndownloader.figshare.com/files'
 files = [('21191232', None, 'gml')]

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

diff --git a/entries/wiki_science/#__init__.py# b/entries/wiki_science/#__init__.py#
index 816cf6b..c0d2153 100644
--- a/entries/wiki_science/#__init__.py#
+++ b/entries/wiki_science/#__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 General Public License as published by
diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 982cda6..d89bf3e 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__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/wiki_science/#__init__.py# b/entries/wiki_science/#__init__.py#
index cb94425..816cf6b 100644
--- a/entries/wiki_science/#__init__.py#
+++ b/entries/wiki_science/#__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 General Public License as published by
diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 1607d81..982cda6 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__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/wiki_science/#__init__.py# b/entries/wiki_science/#__init__.py#
index 31960ae..cb94425 100644
--- a/entries/wiki_science/#__init__.py#
+++ b/entries/wiki_science/#__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 General Public License as published by
diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 5a64ca8..1607d81 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__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/wiki_science/#__init__.py# b/entries/wiki_science/#__init__.py#
index 91369b8..31960ae 100644
--- a/entries/wiki_science/#__init__.py#
+++ b/entries/wiki_science/#__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 General Public License as published by
diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index b5b789e..5a64ca8 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__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

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

diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 9761139..b5b789e 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__init__.py
@@ -23,7 +23,7 @@ description = """A network of scientific fields, extracted from the English Wiki
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Informational', 'Relatedness', 'Unweighted']
 url = 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932'
-citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare (2020)', 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932')]
+citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare (2020)', 'https://doi.org/10.6084/m9.figshare.11638932.v5')]
 icon_hash = '5e23d5e078691ca4060b62b1'
 ustream_license = None
 upstream_prefix = 'https://ndownloader.figshare.com/files'

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

diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 65186db..9761139 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__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 wiki_science: fix url format in description by Tiago de Paula Peixoto f77920c

diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 075d957..65186db 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__init__.py
@@ -19,11 +19,11 @@
 from .. import *
 
 title = "Wikipedia Map of Science (2020)"
-description = """A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See http://www.sinnefa.com/wikipediasciencemap/ for an interactive version.[^icon]
+description = """A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See <http://www.sinnefa.com/wikipediasciencemap/> for an interactive version.[^icon]
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Informational', 'Relatedness', 'Unweighted']
 url = 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932'
-citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare, https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932 (2020)', 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932')]
+citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare (2020)', 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932')]
 icon_hash = '5e23d5e078691ca4060b62b1'
 ustream_license = None
 upstream_prefix = 'https://ndownloader.figshare.com/files'

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

diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
index 67cded9..075d957 100644
--- a/entries/wiki_science/__init__.py
+++ b/entries/wiki_science/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Wikipedia Map of Science (2020)"
-description = "A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See http://www.sinnefa.com/wikipediasciencemap/ for an interactive version."
+description = """A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See http://www.sinnefa.com/wikipediasciencemap/ for an interactive version.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Informational', 'Relatedness', 'Unweighted']
 url = 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932'
 citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare, https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932 (2020)', 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932')]

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

diff --git a/entries/wiki_science/#__init__.py# b/entries/wiki_science/#__init__.py#
new file mode 100644
index 0000000..91369b8
--- /dev/null
+++ b/entries/wiki_science/#__init__.py#
@@ -0,0 +1,53 @@
+#! /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 = "Wikipedia Map of Science (2020)"
+description = "A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See http://www.sinnefa.com/wikipediasciencemap/ for an interactive version."
+tags = ['Informational', 'Relatedness', 'Unweighted']
+url = 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932'
+citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare, https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932 (2020)', 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932')]
+icon_hash = '5e23d5e078691ca4060b62b1'
+ustream_license = None
+upstream_prefix = 'https://ndownloader.figshare.com/files'
+files = [('21191232', 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, "r")) for fn in fnames]
+            # this is an *invalid* gml file, since it includes unicode characters
+            for i in range(3):
+                next(fs[0])
+            print(fs[0].read())
+            #g = load_graph(fs[0], fmt="gml")
+        yield alt, g
diff --git a/entries/wiki_science/__init__.py b/entries/wiki_science/__init__.py
new file mode 100644
index 0000000..67cded9
--- /dev/null
+++ b/entries/wiki_science/__init__.py
@@ -0,0 +1,50 @@
+#! /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 = "Wikipedia Map of Science (2020)"
+description = "A network of scientific fields, extracted from the English Wikipedia in early 2020. Nodes are wikipedia pages representing natural, formal, social and applied sciences, and two nodes are linked if the cosine similarity of the page content is above a threshold. See http://www.sinnefa.com/wikipediasciencemap/ for an interactive version."
+tags = ['Informational', 'Relatedness', 'Unweighted']
+url = 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932'
+citation = [('A. Calderone, "A Wikipedia Based Map of Science." Figshare, https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932 (2020)', 'https://figshare.com/articles/A_Wikipedia_Based_Map_of_Science/11638932')]
+icon_hash = '5e23d5e078691ca4060b62b1'
+ustream_license = None
+upstream_prefix = 'https://ndownloader.figshare.com/files'
+files = [('21191232', 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)
+            remove_parallel_edges(g)
+        yield alt, g