History of interactome_figeys
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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index a344fb8..83a26e5 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -29,7 +29,7 @@ The network has the following properties:
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'https://web.archive.org/web/20180916202441/http://research.mssm.edu/maayan/datasets/qualitative_networks.shtml'
citation = [('R. M. Ewing et al., "Large-scale mapping of human protein–protein interactions by mass spectrometry." Molecular Systems Biology 3, 89 (2007)', 'https://doi.org/10.1038/msb4100134')]
-icon_hash = '581760328cf714f319c3e779'
+date_added = '2020-08-11'
upstream_license = None
# The Ma'ayan Laboratory site is gone; the file is obtained from the Internet
# Archive.
[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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 1f9f2f4..a344fb8 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -25,7 +25,7 @@ Nodes are proteins, and a directed edge points from a bait protein to a protein
The network has the following properties:
-- Nodes: `name`, the gene symbol of the protein."""
+- (Node) `name`: the gene symbol of the protein."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'https://web.archive.org/web/20180916202441/http://research.mssm.edu/maayan/datasets/qualitative_networks.shtml'
citation = [('R. M. Ewing et al., "Large-scale mapping of human protein–protein interactions by mass spectrometry." Molecular Systems Biology 3, 89 (2007)', 'https://doi.org/10.1038/msb4100134')]
[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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 5ea6331..1f9f2f4 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -55,7 +55,6 @@ def read_sig(f):
@coerce_props()
@annotate()
def parse(alts=None):
- global files
name = __name__.split(".")[-1]
for fname, 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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index b72e733..5ea6331 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -18,32 +18,65 @@
from .. import *
-title = "Figeys human interactome (2007)"
-description = """A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+title = 'Figeys human interactome (2007)'
+description = """A network of interactions between human proteins, from the first large-scale study of protein–protein interactions in human cells using mass spectrometry, by Ewing et al. (2007). Flag-tagged versions of 338 bait proteins, selected for known or suspected disease and functional associations, were expressed in HEK293 cells and immunoprecipitated, and the co-purified proteins were identified by LC-ESI-MS/MS. Of the 24,540 potential interactions identified, false positives and redundant hits were removed using empirical criteria and a computed confidence score, giving 6,463 interactions between 2,235 proteins. The data were obtained from the network collection of the Ma'ayan Laboratory (Mount Sinai School of Medicine), which distributed them in its SIG flat file format, with proteins identified by gene symbols.
+
+Nodes are proteins, and a directed edge points from a bait protein to a protein co-purified with it (the 338 nodes with outgoing edges are the baits). Twenty pairs of proteins are connected in both directions.
+
+The network has the following properties:
+
+- Nodes: `name`, the gene symbol of the protein."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
-url = 'http://konect.cc/networks/maayan-figeys'
-citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'https://doi.org/10.1038/msb4100134')]
+url = 'https://web.archive.org/web/20180916202441/http://research.mssm.edu/maayan/datasets/qualitative_networks.shtml'
+citation = [('R. M. Ewing et al., "Large-scale mapping of human protein–protein interactions by mass spectrometry." Molecular Systems Biology 3, 89 (2007)', 'https://doi.org/10.1038/msb4100134')]
icon_hash = '581760328cf714f319c3e779'
-upstream_prefix = 'http://konect.cc/files'
-files = [('download.tsv.maayan-figeys.tar.bz2', None, 'konect')]
+upstream_license = None
+# The Ma'ayan Laboratory site is gone; the file is obtained from the Internet
+# Archive.
+upstream_prefix = 'https://web.archive.org/web/20150912005130id_/http://research.mssm.edu:80/maayan/datasets'
+files = [('figeys.sig', None, 'sig')]
def fetch_upstream(force=False):
return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
force)
+def read_sig(f):
+ """Read a SIG file of the Ma'ayan Laboratory: one interaction per line, with
+ 13 space-separated columns (source name, human and mouse accessions, type
+ and location; the same for the target; effect, interaction type, PubMed
+ IDs), "NA" denoting missing values."""
+ for line in f.read().decode("utf-8").splitlines():
+ line = line.split()
+ if len(line) == 0:
+ continue
+ yield [None if x == "NA" else x for x in line]
+
@cache_network()
@coerce_props()
@annotate()
def parse(alts=None):
global files
name = __name__.split(".")[-1]
- for fnames, alt, fmt in files:
+ for fname, 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)
+ g = Graph(directed=True)
+ vs = {}
+ acc = defaultdict(lambda: [None, None])
+ edges = []
+ with open_upstream_file(name, fname, "rb") as f:
+ for row in read_sig(f):
+ ends = []
+ for i in (0, 5):
+ v = vs.setdefault(row[i], len(vs))
+ ends.append(v)
+ for j in (0, 1):
+ if row[i + 1 + j] is not None:
+ acc[v][j] = row[i + 1 + j]
+ edges.append(ends)
+ g.add_vertex(len(vs))
+ g.vp.name = g.new_vp("string")
+ for k, v in vs.items():
+ g.vp.name[v] = k
+ g.add_edge_list(edges)
yield alt, g
Update copyright information 73a4f0d
diff --git a/entries/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 9c07a46..b72e733 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index ff7a1a5..9c07a46 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 1817a61..ff7a1a5 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 777fb0e..1817a61 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index b35ad38..777fb0e 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -26,7 +26,6 @@ url = 'http://konect.cc/networks/maayan-figeys'
citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'https://doi.org/10.1038/msb4100134')]
icon_hash = '581760328cf714f319c3e779'
upstream_prefix = 'http://konect.cc/files'
-orphan = True
files = [('download.tsv.maayan-figeys.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Update citations to use DOIs e878874
diff --git a/entries/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 423b15e..b35ad38 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -23,7 +23,7 @@ description = """A network of human proteins and their binding interactions. Nod
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://konect.cc/networks/maayan-figeys'
-citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'http://msb.embopress.org/content/3/1/89.abstract')]
+citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'https://doi.org/10.1038/msb4100134')]
icon_hash = '581760328cf714f319c3e779'
upstream_prefix = 'http://konect.cc/files'
orphan = True
Add support for 'orphan' datasets and tag konect entries e330b80
diff --git a/entries/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 89f645b..423b15e 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -26,6 +26,7 @@ url = 'http://konect.cc/networks/maayan-figeys'
citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'http://msb.embopress.org/content/3/1/89.abstract')]
icon_hash = '581760328cf714f319c3e779'
upstream_prefix = 'http://konect.cc/files'
+orphan = True
files = [('download.tsv.maayan-figeys.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 04e26c9..89f645b 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__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/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
index 443e29a..04e26c9 100644
--- a/entries/interactome_figeys/__init__.py
+++ b/entries/interactome_figeys/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Figeys human interactome (2007)"
-description = "A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach."
+description = """A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://konect.cc/networks/maayan-figeys'
citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'http://msb.embopress.org/content/3/1/89.abstract')]
Initial commit cc85872
diff --git a/entries/interactome_figeys/__init__.py b/entries/interactome_figeys/__init__.py
new file mode 100644
index 0000000..443e29a
--- /dev/null
+++ b/entries/interactome_figeys/__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 = "Figeys human interactome (2007)"
+description = "A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach."
+tags = ['Biological', 'Protein interactions', 'Unweighted']
+url = 'http://konect.cc/networks/maayan-figeys'
+citation = [('R. Ewing, et al. "Large‐scale mapping of human protein–protein interactions by mass spectrometry." Molecular systems biology 3.1 (2007).', 'http://msb.embopress.org/content/3/1/89.abstract')]
+icon_hash = '581760328cf714f319c3e779'
+upstream_prefix = 'http://konect.cc/files'
+files = [('download.tsv.maayan-figeys.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