Merge pull request #283 from gyorilab/sif

Process SIF models and export to regnets

docs/source/sources.rst

@@ -78,26 +78,32 @@ ACSets DecaExpr extraction (:py:mod:`mira.sources.acsets.decapodes.deca_expr`)
  :members:
  :show-inheritance:
 
-Utility Methods (:py:mod:`mira.sources.util`)
----------------------------------------------
-.. automodule:: mira.sources.util
- :members:
- :show-inheritance:
-
-Vensim (:py:mod:`mira.sources.system_dynamics.vensim`)
-------------------------------------------------------
+Vensim models (:py:mod:`mira.sources.system_dynamics.vensim`)
+-------------------------------------------------------------
 .. automodule:: mira.sources.system_dynamics.vensim
  :members:
  :show-inheritance:
 
-Stella (:py:mod:`mira.sources.system_dynamics.stella`)
-------------------------------------------------------
+Stella models (:py:mod:`mira.sources.system_dynamics.stella`)
+-------------------------------------------------------------
 .. automodule:: mira.sources.system_dynamics.stella
  :members:
  :show-inheritance:
 
-PYSD Model Parsing (:py:mod:`mira.sources.system_dynamics.pysd`)
-----------------------------------------------------------------
+PySD models (:py:mod:`mira.sources.system_dynamics.pysd`)
+---------------------------------------------------------
 .. automodule:: mira.sources.system_dynamics.pysd
  :members:
- :show-inheritance:
+ :show-inheritance:
+
+SIF networks (:py:mod:`mira.sources.sif`)
+-----------------------------------------
+.. automodule:: mira.sources.sif
+ :members:
+ :show-inheritance:
+
+Utility Methods (:py:mod:`mira.sources.util`)
+---------------------------------------------
+.. automodule:: mira.sources.util
+ :members:
+ :show-inheritance:

mira/modeling/amr/regnet.py

@@ -42,10 +42,13 @@ def __init__(self, model: Model):
  self.transitions = []
  self.parameters = []
  self.model_name = model.template_model.annotations.name if \
+ model.template_model.annotations and \
  model.template_model.annotations.name else "Model"
  self.model_description = model.template_model.annotations.description \
- if model.template_model.annotations.description else self.model_name
+ if model.template_model.annotations and \
+ model.template_model.annotations.description else self.model_name
  self.metadata = {}
+ self._states_by_id = {}
  vmap = {}
  for key, var in model.variables.items():
  # Use the variable's concept name if possible but fall back
@@ -67,6 +70,7 @@ def __init__(self, model: Model):
  initial = safe_parse_expr(str(initial))
  state_data['initial'] = str(initial)
  self.states.append(state_data)
+ self._states_by_id[name] = state_data
 
  for idx, transition in enumerate(model.transitions.values()):
  # Regnets cannot represent conversions (only
@@ -77,35 +81,34 @@ def __init__(self, model: Model):
  # sign on the state so we have special handling for it
  elif isinstance(transition.template, NaturalDegradation):
  var = vmap[transition.consumed[0].key]
+ state_for_var = self._states_by_id.get(var)
  if transition.template.rate_law:
  pnames = transition.template.get_parameter_names()
  if len(pnames) == 1:
  rate_const = list(pnames)[0]
  else:
  rate_const = float(list(pnames)[0])
- for state in self.states:
- if state['id'] == var:
- state['rate_constant'] = rate_const
- state['sign'] = False
- else:
- state['sign'] = False
+ if state_for_var:
+ state_for_var['rate_constant'] = rate_const
+ if state_for_var:
+ state_for_var['sign'] = False
  continue
  # Controlled production corresponds to an inherent positive
  # sign on the state so we have special handling for it
  elif isinstance(transition.template, ControlledProduction):
  var = vmap[transition.produced[0].key]
+ state_for_var = self._states_by_id.get(var)
  if transition.template.rate_law:
  pnames = transition.template.get_parameter_names()
  if len(pnames) == 1:
  rate_const = list(pnames)[0]
  else:
  rate_const = float(list(pnames)[0])
- for state in self.states:
- if state['id'] == var:
- state['rate_constant'] = rate_const
- state['sign'] = True
- else:
- state['sign'] = True
+ state_for_var = self._states_by_id.get(var)
+ if state_for_var:
+ state_for_var['rate_constant'] = rate_const
+ if state_for_var:
+ state_for_var['sign'] = True
  continue
  # Beyond these, we can assume that the transition is a
  # form of production or degradation corresponding to

mira/sources/sif.py

@@ -0,0 +1,96 @@
+"""This module provides functions to create a MIRA TemplateModel from a
+Simple Interaction Format (SIF) file. The SIF format is a simple
+space-delimited format where each line represents a relationship
+between two entities. The first column is the source node, the second
+column is the relation, and the third column is the target node. The
+relation is a string that represents the type of interaction between
+the source and target nodes. SIF files are useful as a minimal representation
+of regulatory networks with positive/negative regulation."""
+
+__all__ = ['template_model_from_sif_edges',
+ 'template_model_from_sif_file',
+ 'template_model_from_sif_url']
+
+import requests
+from mira.metamodel import *
+
+
+def template_model_from_sif_edges(edges):
+ """Return TemplateModel from a list of SIF edges.
+
+ Parameters
+ ----------
+ edges : list
+ A list of tuples of the form (source, rel, target) where source and
+ target are strings representing the source and target nodes and rel
+ is a string representing the relation between them.
+
+ Returns
+ -------
+ TemplateModel
+ A MIRA TemplateModel.
+ """
+ templates = []
+ for source, rel, target in edges:
+ source_concept = Concept(name=source)
+ target_concept = Concept(name=target)
+ if rel == 'POSITIVE':
+ if source == target:
+ t = ControlledProduction(
+ controller=source_concept,
+ outcome=target_concept)
+ else:
+ t = GroupedControlledProduction(
+ controllers=[source_concept, target_concept],
+ outcome=target_concept)
+ elif rel == 'NEGATIVE':
+ if source == target:
+ t = NaturalDegradation(subject=source_concept)
+ else:
+ t = ControlledDegradation(
+ controller=source_concept,
+ subject=target_concept)
+ templates.append(t)
+ tm = TemplateModel(templates=templates)
+ return tm
+
+
+def template_model_from_sif_file(fname):
+ """Return TemplateModel from a SIF file.
+
+ Parameters
+ ----------
+ fname : str
+ The path to the SIF file.
+
+ Returns
+ -------
+ TemplateModel
+ A MIRA TemplateModel.
+ """
+ with open(fname, 'r') as fh:
+ edges = [line.strip().split()
+ for line in fh.readlines()
+ if line and not line.startswith('#')]
+ return template_model_from_sif_edges(edges)
+
+
+def template_model_from_sif_url(url):
+ """Return TemplateModel from a SIF URL.
+
+ Parameters
+ ----------
+ url : str
+ The URL to the SIF file.
+
+ Returns
+ -------
+ TemplateModel
+ A MIRA TemplateModel.
+ """
+ res = requests.get(url)
+ res.raise_for_status()
+ edges = [line.strip().split()
+ for line in res.text.split('\n')
+ if line and not line.startswith('#')]
+ return template_model_from_sif_edges(edges)

scripts/covid19_diseasemaps/process_covid19_diseasemaps.py

@@ -0,0 +1,25 @@
+import json
+import tqdm
+from mira.modeling.amr.regnet import template_model_to_regnet_json
+from mira.sources.sif import template_model_from_sif_url
+
+
+models = ['Apoptosis', 'Coagulation-pathway', 'ER_Stress', 'ETC', 'E_protein',
+ 'HMOX1_Pathway', 'IFN-lambda', 'Interferon1', 'JNK_pathway',
+ 'Kynurenine_pathway', 'NLRP3_Activation', 'Nsp14', 'Nsp4_Nsp6',
+ 'Nsp9_protein', 'Orf10_Cul2_pathway', 'Orf3a', 'PAMP_signaling',
+ 'Pyrimidine_deprivation', 'RTC-and-transcription',
+ 'Renin_angiotensin', 'TGFB_pathway', 'Virus_replication_cycle']
+
+
+SIF_URL_BASE = ('https://git-r3lab.uni.lu/covid/models/-/raw/master/'
+ 'Executable%20Modules/SBML_qual_build/sif')
+
+
+if __name__ == "__main__":
+ for model in tqdm.tqdm(models):
+ url = f'{SIF_URL_BASE}/{model}_stable.sif'
+ tm = template_model_from_sif_url(url)
+ regnet = template_model_to_regnet_json(tm)
+ with open(f'{model}.json', 'w') as fh:
+ json.dump(regnet, fh, indent=1)

tests/test_sif.py

@@ -0,0 +1,16 @@
+from mira.sources.sif import template_model_from_sif_edges
+from mira.modeling.amr.regnet import template_model_to_regnet_json
+
+
+def test_sif_processing():
+ # Lotka volterra example
+ edges = [
+ ('prey', 'POSITIVE', 'predator'),
+ ('predator', 'NEGATIVE', 'prey'),
+ ('prey', 'POSITIVE', 'prey'),
+ ('predator', 'NEGATIVE', 'predator')
+ ]
+ tm = template_model_from_sif_edges(edges)
+ assert len(tm.templates) == 4
+ regnet = template_model_to_regnet_json(tm)
+ assert len(regnet['model']['edges']) == 2