History of cora
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.
[entries] Add the date when each entry was added, and remove icon_hash beff7c9
The dates are those of the commits that first added the entries' files (2020-08-11 for the entries of the initial commit); renamed entries keep the date of their first name. Changed: none
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index b8d8d07..1c68a7a 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -29,7 +29,7 @@ tags = ['Informational', 'Citation', 'Unweighted', 'Metadata']
url = 'http://wwwlovre.appspot.com/support.jsp'
citation = [('A. McCallum, K. Nigam, J. Rennie, K. Seymore, "Automating the Construction of Internet Portals with Machine Learning." Information Retrieval 3(2), 127-163 (2000)', 'https://doi.org/10.1023/A:1009953814988'),
('L. Šubelj, M. Bajec, "Model of complex networks based on citation dynamics." Proceedings of the 22nd International Conference on World Wide Web (LSNA \'13), 527-530 (2013)', 'https://doi.org/10.1145/2487788.2487987')]
-icon_hash = '57574483bd3e93b53c695552'
+date_added = '2020-08-11'
upstream_license = None
upstream_prefix = 'http://wwwlovre.appspot.com/resources/research/networks'
files = [(('cpm/cora', 'cpm/cora.map'), None, None)]
[entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) bc3dbbd
The lists of properties at the end of the descriptions marked edge properties with "Edge" but left node properties unmarked, or grouped them in "Nodes: `a`, ...; `b`, ..." items, so the kind of a property was often unclear. Every item now starts with (Node), (Edge) or (Graph), followed by the property names, a colon and the explanation, one item per property or group of properties; qualifications (kinds of nodes, networks) follow the names in parentheses. Properties that were only named got a short explanation, and a few items that named the wrong kind of property were corrected.
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 4654e70..b8d8d07 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -23,8 +23,8 @@ description = """Citations among computer science research papers from the Cora
The network has the following properties:
-- `cora_id`: the paper ID in the original Cora data set.
-- `topic`: the topic of the paper in the Cora topic hierarchy, given as a path, e.g. `/Artificial_Intelligence/Machine_Learning/Neural_Networks/` (70 topics in total)."""
+- (Node) `cora_id`: the paper ID in the original Cora data set.
+- (Node) `topic`: the topic of the paper in the Cora topic hierarchy, given as a path, e.g. `/Artificial_Intelligence/Machine_Learning/Neural_Networks/` (70 topics in total)."""
tags = ['Informational', 'Citation', 'Unweighted', 'Metadata']
url = 'http://wwwlovre.appspot.com/support.jsp'
citation = [('A. McCallum, K. Nigam, J. Rennie, K. Seymore, "Automating the Construction of Internet Portals with Machine Learning." Information Retrieval 3(2), 127-163 (2000)', 'https://doi.org/10.1023/A:1009953814988'),
[entries] Remove unneeded code from the entries 2c69f19
Unneeded "global files" statements, unused imports and variables, f-strings without placeholders, duplicate keys in foodweb_little_rock (keeping the order and the values used), and the second definition of get_lines() in twitter_higgs. Nothing changes in the networks or descriptions. Changed: none
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index c1011ed..4654e70 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -42,7 +42,6 @@ def fetch_upstream(force=False):
@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:
[entries] Move KONECT-derived entries to their original sources 45943ea
The entries now download the data from where KONECT obtained them (live or via the Wayback Machine), gaining the metadata KONECT dropped (names, identifiers, timestamps, attributes), with descriptions and citations rewritten from the original sources: - Ma'ayan lab collection: faa_routes, foodweb_little_rock (taxon names were assigned to the wrong nodes), interactome_pdz, interactome_figeys, interactome_stelzl, interactome_vidal - Pajek collection and primary sources: word_assoc (from the Edinburgh Associative Thesaurus; KONECT dropped all counts >= 10), foldoc, new_guinea_tribes - bitriad: elite, ceo_club (adds the CEO KONECT's copy lacked) - Lovro Subelj: cora, euroroad (adds isolated cities and parallel roads) - SNAP: elec (all votes, with elections and nominators) - Zenodo: wiki_talk (user ids and roles) - MPI-SWS: flickr_growth, facebook_wall (edges now point from poster to wall owner, as documented), wikipedia_growth (full timestamps) - Other sources: prosper, jester, reactome (the 2014 release KONECT used), unicodelang (CLDR 27), wordnet (WordNet 3.1), chicago_road (TNTP ChicagoRegional)
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 4503ae1..c1011ed 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -19,14 +19,20 @@
from .. import *
title = "CORA citations (1998)"
-description = """Citations among papers indexed by CORA, from 1998, an early computer science research paper search engine. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) Self-loops may be present. The dates of these snapshots are uncertain.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
-tags = ['Informational', 'Citation', 'Unweighted']
-url = 'http://konect.cc/networks/subelj_cora'
-citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'https://doi.org/10.1023/A:1009953814988')]
+description = """Citations among computer science research papers from the Cora collection, assembled by A. McCallum and collaborators in the late 1990s for the Cora research paper search engine. Cora gathered research papers from the web, automatically extracted their references, and classified the papers into a hierarchy of computer science topics. The network was extracted from the Cora data by L. Šubelj and M. Bajec, and contains only papers that were assigned a topic. Nodes are papers and a directed edge $(i,j)$ indicates that paper $i$ cites paper $j$. Citations to papers outside the data set are excluded. The dates of the papers are not included.
+
+The network has the following properties:
+
+- `cora_id`: the paper ID in the original Cora data set.
+- `topic`: the topic of the paper in the Cora topic hierarchy, given as a path, e.g. `/Artificial_Intelligence/Machine_Learning/Neural_Networks/` (70 topics in total)."""
+tags = ['Informational', 'Citation', 'Unweighted', 'Metadata']
+url = 'http://wwwlovre.appspot.com/support.jsp'
+citation = [('A. McCallum, K. Nigam, J. Rennie, K. Seymore, "Automating the Construction of Internet Portals with Machine Learning." Information Retrieval 3(2), 127-163 (2000)', 'https://doi.org/10.1023/A:1009953814988'),
+ ('L. Šubelj, M. Bajec, "Model of complex networks based on citation dynamics." Proceedings of the 22nd International Conference on World Wide Web (LSNA \'13), 527-530 (2013)', 'https://doi.org/10.1145/2487788.2487987')]
icon_hash = '57574483bd3e93b53c695552'
-upstream_prefix = 'http://konect.cc/files'
-files = [('download.tsv.subelj_cora.tar.bz2', None, 'konect')]
+upstream_license = None
+upstream_prefix = 'http://wwwlovre.appspot.com/resources/research/networks'
+files = [(('cpm/cora', 'cpm/cora.map'), None, None)]
def fetch_upstream(force=False):
return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
@@ -41,9 +47,34 @@ def parse(alts=None):
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=True)
+ # Pajek-like file: '*vertices N', then 'index "cora_id" topic 0',
+ # then '*edges M' and one 'citing cited' pair per line
+ with open_upstream_file(name, fnames[1], "r") as f:
+ topics = {}
+ for line in f:
+ if line.strip():
+ i, t = line.strip().split("\t")
+ topics[int(i)] = t
+ g = Graph(directed=True)
+ g.vp.cora_id = g.new_vp("int64_t")
+ g.vp.topic = g.new_vp("string")
+ edges = []
+ with open_upstream_file(name, fnames[0], "r") as f:
+ mode = None
+ for line in f:
+ s = line.split()
+ if not s:
+ continue
+ if s[0].startswith("*"):
+ mode = s[0].lower()
+ if mode == "*vertices":
+ g.add_vertex(int(s[1]))
+ continue
+ if mode == "*vertices":
+ v = g.vertex(int(s[0]) - 1)
+ g.vp.cora_id[v] = int(s[1].strip('"'))
+ g.vp.topic[v] = topics[int(s[2])]
+ elif mode == "*edges":
+ edges.append((int(s[0]) - 1, int(s[1]) - 1))
+ g.add_edge_list(edges)
yield alt, g
Update copyright information 73a4f0d
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 08847b6..4503ae1 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__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
Update copyright information 3d288ea
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index deeb25c..08847b6 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__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
Update copyright information 8d005ae
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 84cc59c..deeb25c 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__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
Update copyright info db2efcc
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 519453d..84cc59c 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__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
Un-orphan KONECT datasets 894eba5
KONECT has been brought back from the dead for the time being.
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index d60f348..519453d 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -26,7 +26,6 @@ url = 'http://konect.cc/networks/subelj_cora'
citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'https://doi.org/10.1023/A:1009953814988')]
icon_hash = '57574483bd3e93b53c695552'
upstream_prefix = 'http://konect.cc/files'
-orphan = True
files = [('download.tsv.subelj_cora.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Update citations to use DOIs e878874
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index b21bf39..d60f348 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -23,7 +23,7 @@ description = """Citations among papers indexed by CORA, from 1998, an early com
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Informational', 'Citation', 'Unweighted']
url = 'http://konect.cc/networks/subelj_cora'
-citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'http://www.kamalnigam.com/papers/cora-jnl.pdf')]
+citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'https://doi.org/10.1023/A:1009953814988')]
icon_hash = '57574483bd3e93b53c695552'
upstream_prefix = 'http://konect.cc/files'
orphan = True
Add support for 'orphan' datasets and tag konect entries e330b80
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index a3f5d9d..b21bf39 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -26,6 +26,7 @@ url = 'http://konect.cc/networks/subelj_cora'
citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'http://www.kamalnigam.com/papers/cora-jnl.pdf')]
icon_hash = '57574483bd3e93b53c695552'
upstream_prefix = 'http://konect.cc/files'
+orphan = True
files = [('download.tsv.subelj_cora.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 4ea107f..a3f5d9d 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__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 *
Add explicit attribution to descriptions obtained from ICON 1645314
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index be09137..4ea107f 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "CORA citations (1998)"
-description = "Citations among papers indexed by CORA, from 1998, an early computer science research paper search engine. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) Self-loops may be present. The dates of these snapshots are uncertain."
+description = """Citations among papers indexed by CORA, from 1998, an early computer science research paper search engine. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) Self-loops may be present. The dates of these snapshots are uncertain.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Informational', 'Citation', 'Unweighted']
url = 'http://konect.cc/networks/subelj_cora'
citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'http://www.kamalnigam.com/papers/cora-jnl.pdf')]
cora: fix typo 8f69c54
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
index 6d867b5..be09137 100644
--- a/entries/cora/__init__.py
+++ b/entries/cora/__init__.py
@@ -18,7 +18,7 @@
from .. import *
-title = "CoRA citations (1998)"
+title = "CORA citations (1998)"
description = "Citations among papers indexed by CORA, from 1998, an early computer science research paper search engine. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) Self-loops may be present. The dates of these snapshots are uncertain."
tags = ['Informational', 'Citation', 'Unweighted']
url = 'http://konect.cc/networks/subelj_cora'
Initial commit cc85872
diff --git a/entries/cora/__init__.py b/entries/cora/__init__.py
new file mode 100644
index 0000000..6d867b5
--- /dev/null
+++ b/entries/cora/__init__.py
@@ -0,0 +1,48 @@
+#! /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 = "CoRA citations (1998)"
+description = "Citations among papers indexed by CORA, from 1998, an early computer science research paper search engine. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) Self-loops may be present. The dates of these snapshots are uncertain."
+tags = ['Informational', 'Citation', 'Unweighted']
+url = 'http://konect.cc/networks/subelj_cora'
+citation = [('A. McCallum et al., "Automating the Construction of Internet Portals with Machine Learning." J. Information Retrieval 3(2), 127-163 (2000)', 'http://www.kamalnigam.com/papers/cora-jnl.pdf')]
+icon_hash = '57574483bd3e93b53c695552'
+upstream_prefix = 'http://konect.cc/files'
+files = [('download.tsv.subelj_cora.tar.bz2', None, 'konect')]
+
+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=True)
+ yield alt, g