Merge pull request #284 from gyorilab/sif_dm

Add Regnet AMR export of COVID-19 Disease Map

mira/modeling/amr/regnet.py

@@ -147,6 +147,8 @@ def __init__(self, model: Model):
  self.transitions.append(transition_dict)
 
  for key, param in model.parameters.items():
+ if param.placeholder:
+ continue
  param_dict = {'id': str(key)}
  if param.value:
  param_dict['value'] = param.value

scripts/covid19_diseasemaps/process_covid19_diseasemaps.py

@@ -1,5 +1,6 @@
 import json
 import tqdm
+from mira.metamodel import Annotations
 from mira.modeling.amr.regnet import template_model_to_regnet_json
 from mira.sources.sif import template_model_from_sif_url
 
@@ -20,6 +21,15 @@
  for model in tqdm.tqdm(models):
  url = f'{SIF_URL_BASE}/{model}_stable.sif'
  tm = template_model_from_sif_url(url)
+ tm.annotations = Annotations(
+ name=model,
+ description=("A submodel of the COVID-10 Disease Map "
+ f"focusing on {model}"),
+ pathogens=["ncbitaxon:2697049"],
+ diseases=["doid:0080600"],
+ hosts=["ncbitaxon:9606"],
+ references=["pubmed:34664389"]
+ )
  regnet = template_model_to_regnet_json(tm)
- with open(f'{model}.json', 'w') as fh:
+ with open(f'regnet_amr/{model}.json', 'w') as fh:
  json.dump(regnet, fh, indent=1)