History of kegg_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.

2026-11-03 [entries] Add the date when each entry was added, and remove icon_hash by Tiago de Paula Peixoto 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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index bcdc4fd..c164dd9 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_metabolic/__init__.py
@@ -23,7 +23,7 @@ description = r"""Metabolic networks of 109 organisms (bacteria, archaea and euk
 tags = ['Biological', 'Metabolic', 'Unweighted']
 url = 'http://santafe.edu/~aaronc/data/kegg2006_metabolic.zip'
 citation = [('M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007)', 'https://doi.org/10.1049/iet-syb:20060077')]
-icon_hash = '56e99103a6d70217090cde5c'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'http://santafe.edu/~aaronc/data'
 files = [(f"kegg2006_metabolic.zip:kegg2006_metabolic/links_{d}", d, "loadtxt") for d in

2026-11-02 [entries] Remove unneeded code from the entries by Tiago de Paula Peixoto 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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index b2d41fe..bcdc4fd 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_metabolic/__init__.py
@@ -47,7 +47,6 @@ 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:

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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index 45733a2..b2d41fe 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_metabolic/__init__.py
@@ -19,13 +19,12 @@
 from .. import *
 
 title = "Metabolic networks from KEGG (2006)"
-description = """109 metabolic networks of various species, as extracted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006. Nodes are substances involved in enzymatic reactions present in the organism, and edges represent reactant-product pairs as extracted from the KEGG ligand database and matched against the present enzymes.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""Metabolic networks of 109 organisms (bacteria, archaea and eukaryotes), extracted by M. Huss and P. Holme from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006, and distributed by A. Clauset. Nodes are metabolites (substances) that take part in the enzymatic reactions annotated for the organism, and an undirected edge connects a reactant and a product of the same reaction, according to the reactant-product pairs listed in KEGG. The networks include a few self-loops. Each network is named after the KEGG organism code (e.g. `eco` for *Escherichia coli* K-12, `hsa` for *Homo sapiens*, `sce` for *Saccharomyces cerevisiae*). The metabolite names or KEGG compound identifiers are not included in the data."""
 tags = ['Biological', 'Metabolic', 'Unweighted']
 url = 'http://santafe.edu/~aaronc/data/kegg2006_metabolic.zip'
 citation = [('M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007)', 'https://doi.org/10.1049/iet-syb:20060077')]
 icon_hash = '56e99103a6d70217090cde5c'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'http://santafe.edu/~aaronc/data'
 files = [(f"kegg2006_metabolic.zip:kegg2006_metabolic/links_{d}", d, "loadtxt") for d in
          ['aae', 'afu', 'ana', 'ape', 'atc','ath', 'atu', 'bas', 'bbu', 'bha',

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

diff --git a/entries/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index b3e2c1b..45733a2 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index b07c9c5..b3e2c1b 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index 2dce771..b07c9c5 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index c7c4ffb..2dce771 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index ba630a3..c7c4ffb 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_metabolic/__init__.py
@@ -23,7 +23,7 @@ description = """109 metabolic networks of various species, as extracted from th
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Metabolic', 'Unweighted']
 url = 'http://santafe.edu/~aaronc/data/kegg2006_metabolic.zip'
-citation = [('M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007)', 'http://arxiv.org/abs/q-bio/0603038')]
+citation = [('M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007)', 'https://doi.org/10.1049/iet-syb:20060077')]
 icon_hash = '56e99103a6d70217090cde5c'
 ustream_license = None
 upstream_prefix = 'http://santafe.edu/~aaronc/data'

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

diff --git a/entries/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index 457cb2b..ba630a3 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_metabolic/__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/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
index 72736b0..457cb2b 100644
--- a/entries/kegg_metabolic/__init__.py
+++ b/entries/kegg_metabolic/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Metabolic networks from KEGG (2006)"
-description = "109 metabolic networks of various species, as extracted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006. Nodes are substances involved in enzymatic reactions present in the organism, and edges represent reactant-product pairs as extracted from the KEGG ligand database and matched against the present enzymes."
+description = """109 metabolic networks of various species, as extracted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006. Nodes are substances involved in enzymatic reactions present in the organism, and edges represent reactant-product pairs as extracted from the KEGG ligand database and matched against the present enzymes.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Metabolic', 'Unweighted']
 url = 'http://santafe.edu/~aaronc/data/kegg2006_metabolic.zip'
 citation = [('M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007)', 'http://arxiv.org/abs/q-bio/0603038')]

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

diff --git a/entries/kegg_metabolic/__init__.py b/entries/kegg_metabolic/__init__.py
new file mode 100644
index 0000000..72736b0
--- /dev/null
+++ b/entries/kegg_metabolic/__init__.py
@@ -0,0 +1,60 @@
+#! /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 = "Metabolic networks from KEGG (2006)"
+description = "109 metabolic networks of various species, as extracted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006. Nodes are substances involved in enzymatic reactions present in the organism, and edges represent reactant-product pairs as extracted from the KEGG ligand database and matched against the present enzymes."
+tags = ['Biological', 'Metabolic', 'Unweighted']
+url = 'http://santafe.edu/~aaronc/data/kegg2006_metabolic.zip'
+citation = [('M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007)', 'http://arxiv.org/abs/q-bio/0603038')]
+icon_hash = '56e99103a6d70217090cde5c'
+ustream_license = None
+upstream_prefix = 'http://santafe.edu/~aaronc/data'
+files = [(f"kegg2006_metabolic.zip:kegg2006_metabolic/links_{d}", d, "loadtxt") for d in
+         ['aae', 'afu', 'ana', 'ape', 'atc','ath', 'atu', 'bas', 'bbu', 'bha',
+          'bja', 'blo', 'bme', 'bms', 'bsu', 'buc', 'cac', 'ccr', 'cef', 'cel',
+          'cgl', 'cje', 'cmu', 'cpa', 'cpe', 'cpj', 'cpn', 'cte', 'ctr', 'dme',
+          'dra', 'ecc', 'ece', 'ecj', 'eco', 'ecs', 'fnu', 'hal', 'hin', 'hpj',
+          'hpy', 'hsa', 'lil', 'lin', 'lla', 'lmo', 'mac', 'mge', 'mja', 'mka',
+          'mle', 'mlo', 'mma', 'mmu', 'mpe', 'mpn', 'mpu', 'mtc', 'mth', 'mtu',
+          'nma', 'nme', 'oih', 'pab', 'pae', 'pai', 'pfu', 'pho', 'pmu', 'rco',
+          'rno', 'rpr', 'rso', 'sag', 'sam', 'san', 'sau', 'sav', 'sce', 'sco',
+          'sfl', 'sme', 'smu', 'son', 'spg', 'spm', 'spn', 'spo', 'spr', 'spy',
+          'sso', 'stm', 'sto', 'sty', 'syn', 'tac', 'tel', 'tma', 'tpa', 'tte',
+          'tvo', 'uur', 'vch', 'wbr', 'xac', 'xcc', 'xfa', 'ype', 'ypk']]
+
+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