History of collins_yeast
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] Merge duplicate entries and add cross-references between related ones 9bc6033
- Removed duplicates, merged into the entries holding the same data: dblp_coauthor_snap (soc_net_comms), cattle and bison (dom; bison's breeding data move there, as do the wolves' age and sex), football_tsevans (football, with both conference assignments), eu_procurements_alt (eu_procurements), foursquare_friendships (foursquare_global). - software_dependencies: colt and scolt are one network; ambassador: the duplicate 2001 network is dropped and the three same-edge networks combined; dom: the dataset count corrected (436). - macaque_neural: Young's 71-area network added (young71; the 47-area one is now cocomac47), both from archived copies. - collins_yeast, celegans_interactomes: from archived copies of the dead CCSB site (byte-identical files). - Cross-references between entries holding versions of the same data (food webs, Wikipedia, Slashdot, physicians, SNAP/Mislove, CCSB). - ICON ids of duplicate records added; macaque_neural's corrected. - prosper, dbpedia_all: string properties given in edge-index order (needs graph-tool with the fixed vals ordering).
diff --git a/entries/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 1621fb2..e3834c4 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__init__.py
@@ -19,17 +19,22 @@
from .. import *
title = "Collins yeast interactome (2007)"
-description = """A network of physical protein–protein interactions in the budding yeast *Saccharomyces cerevisiae*, from the study of S. R. Collins and collaborators. The authors re-analyzed the two large-scale data sets of protein complexes identified by tandem affinity purification followed by mass spectrometry (AP/MS) of Gavin et al. (2006) and Krogan et al. (2006), and combined them with a purification enrichment (PE) scoring system calibrated against a reference set of known protein complexes. Nodes are proteins, and an undirected edge connects two proteins that were found to be co-complex associated (i.e. members of the same complex) in the high-confidence set of interactions. The node property `name` holds the systematic (ORF) name of the protein (e.g. `YAL001C`); the network has no edge properties."""
+description = """A network of physical protein–protein interactions in the budding yeast *Saccharomyces cerevisiae*, from the study of S. R. Collins and collaborators. The authors re-analyzed the two large-scale data sets of protein complexes identified by tandem affinity purification followed by mass spectrometry (AP/MS) of Gavin et al. (2006) and Krogan et al. (2006), and combined them with a purification enrichment (PE) scoring system calibrated against a reference set of known protein complexes. Nodes are proteins, and an undirected edge connects two proteins that were found to be co-complex associated (i.e. members of the same complex) in the high-confidence set of interactions. The node property `name` holds the systematic (ORF) name of the protein (e.g. `YAL001C`); the network has no edge properties.
+
+This network comes from the yeast download page of the CCSB Interactome Database (Center for Cancer Systems Biology, Dana-Farber Cancer Institute), whose other data sets are in the entries `yeast_interactome_ccsb` (the yeast binary Y2H maps CCSB-YI1, Ito core and Uetz screen, and literature-curated and gold-standard reference sets), `interactome_vidal` (the first human binary map CCSB-HI1/HI-I-05), `human_interactome_2014` (the human maps HI-II-14 and Lit-BM-13) and `celegans_interactomes` (the *C. elegans* interactome networks)."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
-url = 'http://interactome.dfci.harvard.edu/S_cerevisiae/index.php?page=download'
+url = 'https://web.archive.org/web/20200205030615/http://interactome.dfci.harvard.edu/S_cerevisiae/index.php?page=download'
citation = [('S.R. Collins et al., "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell. Proteomics 6(3), 439-450 (2007)', 'https://doi.org/10.1074/mcp.m600381-mcp200')]
icon_hash = '56a85c8e26855e083a2f7946'
-upstream_prefix = 'http://interactome.dfci.harvard.edu/S_cerevisiae/download'
+# The CCSB site is offline; the file is obtained from the Internet Archive.
+upstream_prefix = 'https://web.archive.org/web/20200804052058id_/http://interactome.dfci.harvard.edu/S_cerevisiae/download'
files = [('Collins.txt', None, 'loadtxt')]
+archived_urls = {
+ 'Collins.txt': 'https://web.archive.org/web/20200804052058id_/http://interactome.dfci.harvard.edu/S_cerevisiae/download/Collins.txt'}
def fetch_upstream(force=False):
- return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
- force)
+ return fetch_archived_files(__name__.split(".")[-1], archived_urls, force,
+ tries=5, timeout=600)
@cache_network()
@coerce_props()
[entries] Fix parse bugs and improve descriptions and metadata 6bb6851
- parse fixes from the review of the descriptions, e.g. us_patents (directed), celegans_2019 (synapse direction), ecoli_transcription and yeast_transcription (regulator to target), bitcoin (direction, phantom node), ego_social (Google+ features and circles), scotus_majority, arxiv_authors and social_location (as in SNAP), caida_as, dnc, dom, mist, reuters and bibsonomy (names on the right nodes), uci_zoo - every description now states explicitly what the nodes and edges represent; corrected titles, years, tags, citations and licences - the "Hypergraph" tag is removed; very large entries are marked `huge = True` (see --skip-huge) - ICON ids of partial duplicates added (hiv_transmission, congress_bills, openflights, dutch_school)
diff --git a/entries/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 291ea8c..1621fb2 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__init__.py
@@ -19,8 +19,7 @@
from .. import *
title = "Collins yeast interactome (2007)"
-description = """Network of protein-protein interactions in Saccharomyces cerevisiae (budding yeast), measured by co-complex associations identified by high-throughput affinity purification and mass spectrometry (AP/MS)[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """A network of physical protein–protein interactions in the budding yeast *Saccharomyces cerevisiae*, from the study of S. R. Collins and collaborators. The authors re-analyzed the two large-scale data sets of protein complexes identified by tandem affinity purification followed by mass spectrometry (AP/MS) of Gavin et al. (2006) and Krogan et al. (2006), and combined them with a purification enrichment (PE) scoring system calibrated against a reference set of known protein complexes. Nodes are proteins, and an undirected edge connects two proteins that were found to be co-complex associated (i.e. members of the same complex) in the high-confidence set of interactions. The node property `name` holds the systematic (ORF) name of the protein (e.g. `YAL001C`); the network has no edge properties."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://interactome.dfci.harvard.edu/S_cerevisiae/index.php?page=download'
citation = [('S.R. Collins et al., "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell. Proteomics 6(3), 439-450 (2007)', 'https://doi.org/10.1074/mcp.m600381-mcp200')]
Update copyright information 73a4f0d
diff --git a/entries/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 1e3ab3f..291ea8c 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__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/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 09dcc88..1e3ab3f 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__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/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 89c0e6a..09dcc88 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__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/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 5b0bfa5..89c0e6a 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__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
Update citations to use DOIs e878874
diff --git a/entries/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 84f10e1..5b0bfa5 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__init__.py
@@ -23,7 +23,7 @@ description = """Network of protein-protein interactions in Saccharomyces cerevi
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://interactome.dfci.harvard.edu/S_cerevisiae/index.php?page=download'
-citation = [('S.R. Collins et al., "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell. Proteomics 6(3), 439-450 (2007)', 'http://www.ncbi.nlm.nih.gov/pubmed/17200106')]
+citation = [('S.R. Collins et al., "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell. Proteomics 6(3), 439-450 (2007)', 'https://doi.org/10.1074/mcp.m600381-mcp200')]
icon_hash = '56a85c8e26855e083a2f7946'
upstream_prefix = 'http://interactome.dfci.harvard.edu/S_cerevisiae/download'
files = [('Collins.txt', None, 'loadtxt')]
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 619b1df..84f10e1 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__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/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
index 355ac52..619b1df 100644
--- a/entries/collins_yeast/__init__.py
+++ b/entries/collins_yeast/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Collins yeast interactome (2007)"
-description = "Network of protein-protein interactions in Saccharomyces cerevisiae (budding yeast), measured by co-complex associations identified by high-throughput affinity purification and mass spectrometry (AP/MS)"
+description = """Network of protein-protein interactions in Saccharomyces cerevisiae (budding yeast), measured by co-complex associations identified by high-throughput affinity purification and mass spectrometry (AP/MS)[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://interactome.dfci.harvard.edu/S_cerevisiae/index.php?page=download'
citation = [('S.R. Collins et al., "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell. Proteomics 6(3), 439-450 (2007)', 'http://www.ncbi.nlm.nih.gov/pubmed/17200106')]
Initial commit cc85872
diff --git a/entries/collins_yeast/__init__.py b/entries/collins_yeast/__init__.py
new file mode 100644
index 0000000..355ac52
--- /dev/null
+++ b/entries/collins_yeast/__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 = "Collins yeast interactome (2007)"
+description = "Network of protein-protein interactions in Saccharomyces cerevisiae (budding yeast), measured by co-complex associations identified by high-throughput affinity purification and mass spectrometry (AP/MS)"
+tags = ['Biological', 'Protein interactions', 'Unweighted']
+url = 'http://interactome.dfci.harvard.edu/S_cerevisiae/index.php?page=download'
+citation = [('S.R. Collins et al., "Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae." Mol. Cell. Proteomics 6(3), 439-450 (2007)', 'http://www.ncbi.nlm.nih.gov/pubmed/17200106')]
+icon_hash = '56a85c8e26855e083a2f7946'
+upstream_prefix = 'http://interactome.dfci.harvard.edu/S_cerevisiae/download'
+files = [('Collins.txt', None, 'loadtxt')]
+
+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