Merge pull request #262 from nanglo123/extract_eiffel_ontology

Extract Climate Information from the EIFFEL Ontology to be added to the DKG

mira/dkg/construct.py

@@ -139,6 +139,8 @@ def __init__(self, use_case: str, config: Optional[DKGConfig] = None):
  prefixes.append(self.askemo_prefix)
  if self.use_case == "space":
  prefixes.append("uat")
+ if self.use_case == "climate":
+ prefixes.append("eiffel")
  self.EDGES_PATHS: Dict[str, Path] = {
  prefix: self.module.join("sources", name=f"edges_{prefix}.tsv")
  for prefix in prefixes
@@ -421,6 +423,31 @@ def construct(
  for term in get_cso_obo().iter_terms():
  node_sources[term.curie].add("cso")
  nodes[term.curie] = get_node_info(term)
+
+ from .resources.extract_eiffel_ontology import get_eiffel_ontology_terms
+
+ eiffel_edges = []
+ for term in tqdm(get_eiffel_ontology_terms(), unit="term", desc="Eiffel"):
+ node_sources[term.curie].add("eiffel")
+ nodes[term.curie] = get_node_info(term)
+ for typedef, object_references in term.relationships.items():
+ for object_reference in object_references:
+ eiffel_edges.append(
+ (
+ term.curie,
+ object_reference.curie,
+ typedef.name.replace(" ", "").lower(),
+ typedef.curie,
+ "eiffel",
+ "eiffel",
+ "",
+ )
+ )
+
+ with use_case_paths.EDGES_PATHS["eiffel"].open("w") as file:
+ writer = csv.writer(file, delimiter="\t", quoting=csv.QUOTE_MINIMAL)
+ writer.writerow(EDGE_HEADER)
+ writer.writerows(eiffel_edges)
  if use_case == "epi":
  from .resources.geonames import get_geonames_terms
  geonames_edges = []

mira/dkg/resources/cso.py

@@ -21,7 +21,7 @@ def get_cso_obo():
  description="An ontology for climate systems",
  )
  download(url=URL, path=PATH)
- return from_obo_path(PATH, ontology="cso", default_prefix="cso", strict=False)
+ return from_obo_path(PATH, prefix="cso", default_prefix="cso", strict=False)
 
 
 if __name__ == "__main__":