History of celegans_metabolic

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/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
index d13c331..6c08e5c 100644
--- a/entries/celegans_metabolic/__init__.py
+++ b/entries/celegans_metabolic/__init__.py
@@ -19,13 +19,17 @@
 from .. import *
 
 title = "Metabolic network (C. elegans)"
-description = """List of edges comprising the metabolic network of the nematode C. elegans.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """The metabolic network of the nematode *Caenorhabditis elegans*, as used by J. Duch and A. Arenas to test their community detection method based on extremal optimization. Nodes are metabolites (substrates), and an undirected edge connects two metabolites that participate in the same metabolic reaction. The data are derived from the metabolic network reconstructions of H. Jeong et al., *Nature* 407, 651 (2000), which are based on the WIT database. Nodes are identified only by anonymous labels (`v1` to `v453`), so the identities of the metabolites are not available. The network contains parallel edges (pairs of metabolites connected by more than one edge) and a few self-loops, as present in the source file.
+
+The network has the following properties:
+
+- Nodes: `name` and `id`, the node label (`v1` to `v453`); `x`, `y` and `z`, the node coordinates in the Pajek source file (without meaning).
+- Edges: `weight`, which is always 1."""
 tags = ['Biological', 'Metabolic', 'Unweighted']
 url = 'https://deim.urv.cat/~alexandre.arenas/data/welcome.htm'
 citation = [('J. Duch and A. Arenas, "Community identification using Extremal Optimization." Physical Review E 72, 027104 (2005).', 'https://doi.org/10.1103/physreve.72.027104')]
 icon_hash = '56a85c8e26855e083a2f78d6'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'http://deim.urv.cat/~alexandre.arenas/data/xarxes'
 files = [('celegans_metabolic.zip:celegans_metabolic.net', None, 'pajek')]

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

diff --git a/entries/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
index 4cd4cf2..d13c331 100644
--- a/entries/celegans_metabolic/__init__.py
+++ b/entries/celegans_metabolic/__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/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
index 693db67..4cd4cf2 100644
--- a/entries/celegans_metabolic/__init__.py
+++ b/entries/celegans_metabolic/__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/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
index 06501ae..693db67 100644
--- a/entries/celegans_metabolic/__init__.py
+++ b/entries/celegans_metabolic/__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/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
index 0e789d5..06501ae 100644
--- a/entries/celegans_metabolic/__init__.py
+++ b/entries/celegans_metabolic/__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/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
index d50c48d..0e789d5 100644
--- a/entries/celegans_metabolic/__init__.py
+++ b/entries/celegans_metabolic/__init__.py
@@ -23,7 +23,7 @@ description = """List of edges comprising the metabolic network of the nematode
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Metabolic', 'Unweighted']
 url = 'https://deim.urv.cat/~alexandre.arenas/data/welcome.htm'
-citation = [('J. Duch and A. Arenas, "Community identification using Extremal Optimization." Physical Review E 72, 027104 (2005).', 'http://arxiv.org/abs/cond-mat/0501368')]
+citation = [('J. Duch and A. Arenas, "Community identification using Extremal Optimization." Physical Review E 72, 027104 (2005).', 'https://doi.org/10.1103/physreve.72.027104')]
 icon_hash = '56a85c8e26855e083a2f78d6'
 ustream_license = None
 upstream_prefix = 'http://deim.urv.cat/~alexandre.arenas/data/xarxes'

2020-09-26 Add celegans_metabolic by Tiago de Paula Peixoto 6976ef4

diff --git a/entries/celegans_metabolic/__init__.py b/entries/celegans_metabolic/__init__.py
new file mode 100644
index 0000000..d50c48d
--- /dev/null
+++ b/entries/celegans_metabolic/__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 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 Affero General Public License for more
+# details.
+#
+# 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 *
+
+title = "Metabolic network (C. elegans)"
+description = """List of edges comprising the metabolic network of the nematode C. elegans.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+tags = ['Biological', 'Metabolic', 'Unweighted']
+url = 'https://deim.urv.cat/~alexandre.arenas/data/welcome.htm'
+citation = [('J. Duch and A. Arenas, "Community identification using Extremal Optimization." Physical Review E 72, 027104 (2005).', 'http://arxiv.org/abs/cond-mat/0501368')]
+icon_hash = '56a85c8e26855e083a2f78d6'
+ustream_license = None
+upstream_prefix = 'http://deim.urv.cat/~alexandre.arenas/data/xarxes'
+files = [('celegans_metabolic.zip:celegans_metabolic.net', None, 'pajek')]
+
+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