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History of mist

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] Fix parse bugs and improve descriptions and metadata by Tiago de Paula Peixoto 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/mist/__init__.py b/entries/mist/__init__.py
index 9c29092..9a35d69 100644
--- a/entries/mist/__init__.py
+++ b/entries/mist/__init__.py
@@ -19,7 +19,7 @@
 from .. import *
 
 title = "MIST protein interaction database (2020)"
-description = """The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:
+description = """The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from several primary sources. This dataset contains the networks of the following species:
 
    1. Homo sapiens (Human)
    2. Drosophila melanogaster (Fly)
@@ -29,8 +29,7 @@ description = """The Molecular Interaction Search Tool (MIST) is a comprehensive
    6. Saccharomyces cerevisiae (Baker's yeast)
    7. Schizosaccharomyces pombe (Fission yeast)
    8. Danio rerio (Zebrafish)
-   9. Xenopus laevis (African clawed frog)
-   10. Xenopus tropicalis (Western clawed frog)
+   9. Xenopus tropicalis (Western clawed frog)
 
 The database contains four kinds of interactions:
 
@@ -38,6 +37,8 @@ The database contains four kinds of interactions:
    2. Interologs (PPI): Interactions predicted based on PPI data obtained for orthologous proteins.
    3. Genetic Interactions: Indicate that the effects of mutations in one gene can be modified by mutation of another gene.
    4. Genetic Interologs: Interactions predicted based on genetic interaction data obtained for orthologous proteins
+
+There is one network for each species and kind of interaction, named as `<kind>_<species>` (e.g. `ppi_human` or `genetic_interolog_fly`), with the kinds `ppi`, `ppi_interolog`, `genetic` and `genetic_interolog` (there is no genetic network for the western clawed frog, and no genetic interolog network for the fission yeast). Nodes are genes (or the proteins they encode), identified by their NCBI Entrez Gene IDs, and an undirected edge connects two genes for which MIST lists an interaction of the given kind; when the same pair is listed in several records, only one of them is kept. The files of a species also contain some interactions with genes of other species (e.g. about 8% of the records of the human PPI file), which are included. The interolog files of a species contain both the interactions predicted for its genes and those predicted for the genes of other species (including Xenopus laevis) from its data, and all of them are included. The species of each gene is given by the vertex property `tax_id` (NCBI Taxonomy ID).
 """
 tags = ['Biological', 'Protein interactions', 'Unweighted']
 url = 'https://fgrtools.hms.harvard.edu/MIST/index.jsp'
@@ -86,13 +87,13 @@ def parse(alts=None):
         g.vp.tax_id = g.new_vp("string")
 
         vertices = {}
-        def get_vertex(name, tid):
-            v = vertices.get(tid, None)
+        def get_vertex(tid, name):
+            v = vertices.get(name, None)
             if v is None:
                 v = g.add_vertex()
                 g.vp.gene[v] = name
                 g.vp.tax_id[v] = tid
-                vertices[tid] = v
+                vertices[name] = v
             return v
 
         props = None
Update copyright information by Tiago de Paula Peixoto 73a4f0d
diff --git a/entries/mist/__init__.py b/entries/mist/__init__.py
index 2aad45c..9c29092 100644
--- a/entries/mist/__init__.py
+++ b/entries/mist/__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 by Tiago de Paula Peixoto 3d288ea
diff --git a/entries/mist/__init__.py b/entries/mist/__init__.py
index ceb69f8..2aad45c 100644
--- a/entries/mist/__init__.py
+++ b/entries/mist/__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
mist: fix parallel edges by Tiago de Paula Peixoto 809f17d
diff --git a/entries/mist/__init__.py b/entries/mist/__init__.py
index 854fa3f..ceb69f8 100644
--- a/entries/mist/__init__.py
+++ b/entries/mist/__init__.py
@@ -60,6 +60,10 @@ files = []
 
 for kind in ["ppi", "ppi_interolog", "genetic", "genetic_interolog"]:
     for s in species.keys():
+        if s == "western_clawed_frog" and kind == "genetic":
+            continue
+        if s == "fission_yeast" and kind == "genetic_interolog":
+            continue
         files += [(f'MIST_interaction_{kind}_vs5_0-{species[s]}.txt.zip:' + \
                    f'MIST_interaction_{kind}_vs5_0-{species[s]}.txt', f"{kind}_{s}", None)]
 
@@ -115,4 +119,7 @@ def parse(alts=None):
                     if val in ignore:
                         continue
                     g.ep[val][e] = vals[j]
+
+        remove_parallel_edges(g)
+
         yield alt, g
Add 'mist' entry by Tiago de Paula Peixoto b684521
diff --git a/entries/mist/__init__.py b/entries/mist/__init__.py
new file mode 100644
index 0000000..854fa3f
--- /dev/null
+++ b/entries/mist/__init__.py
@@ -0,0 +1,118 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# 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
+# 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 = "MIST protein interaction database (2020)"
+description = """The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:
+
+   1. Homo sapiens (Human)
+   2. Drosophila melanogaster (Fly)
+   3. Mus musculus (Mouse)
+   4. Caenorhabditis elegans (Worm)
+   5. Rattus norvegicus (Rat)
+   6. Saccharomyces cerevisiae (Baker's yeast)
+   7. Schizosaccharomyces pombe (Fission yeast)
+   8. Danio rerio (Zebrafish)
+   9. Xenopus laevis (African clawed frog)
+   10. Xenopus tropicalis (Western clawed frog)
+
+The database contains four kinds of interactions:
+
+   1. Protein-protein interaction (PPI): “PPI” refers to physical interactions between two or more proteins.
+   2. Interologs (PPI): Interactions predicted based on PPI data obtained for orthologous proteins.
+   3. Genetic Interactions: Indicate that the effects of mutations in one gene can be modified by mutation of another gene.
+   4. Genetic Interologs: Interactions predicted based on genetic interaction data obtained for orthologous proteins
+"""
+tags = ['Biological', 'Protein interactions', 'Unweighted']
+url = 'https://fgrtools.hms.harvard.edu/MIST/index.jsp'
+citation = [('Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E Mohr, and Norbert Perrimon, “Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data.” Nucleic Acids Res, 46, D1, Pp. D567-D574 (2017)', 'http://dx.doi.org/10.1093/nar/gkx1116')]
+icon_hash = None
+upstream_license = None
+upstream_prefix = "http://fgrtools.hms.harvard.edu/downloads/MIST5_0/"
+
+species = {"fission_yeast" : 4896,
+           "yeast" : 4932,
+           "worm" : 6239,
+           "fly" : 7227,
+           "zebrafish" : 7955,
+           "western_clawed_frog" : 8364,
+           "human" : 9606,
+           "mouse" : 10090,
+           "rat" : 10116}
+
+files = []
+
+for kind in ["ppi", "ppi_interolog", "genetic", "genetic_interolog"]:
+    for s in species.keys():
+        files += [(f'MIST_interaction_{kind}_vs5_0-{species[s]}.txt.zip:' + \
+                   f'MIST_interaction_{kind}_vs5_0-{species[s]}.txt', f"{kind}_{s}", None)]
+
+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 fname, alt, fmt in files:
+        if alts is not None and alt not in alts:
+            continue
+
+        g = Graph(directed=False)
+        g.vp.gene = g.new_vp("string")
+        g.vp.tax_id = g.new_vp("string")
+
+        vertices = {}
+        def get_vertex(name, tid):
+            v = vertices.get(tid, None)
+            if v is None:
+                v = g.add_vertex()
+                g.vp.gene[v] = name
+                g.vp.tax_id[v] = tid
+                vertices[tid] = v
+            return v
+
+        props = None
+        ignore = ["GeneA", "GeneB", "TaxID_A", "TaxID_B"]
+        with open_upstream_file(name, fname, "r") as f:
+
+            for i, line in enumerate(f):
+                vals = line.strip().split()
+                vals = [x.strip('"') for x in vals]
+
+                if i == 0:
+                    props = vals
+                    for j, val in enumerate(props):
+                        if val in ignore:
+                            continue
+                        g.ep[val] = g.new_ep("string")
+                    continue
+
+                u = get_vertex(vals[1], vals[2])
+                v = get_vertex(vals[3], vals[4])
+                e = g.add_edge(u, v)
+
+                for j, val in enumerate(props):
+                    if val in ignore:
+                        continue
+                    g.ep[val][e] = vals[j]
+        yield alt, g