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#2707; add attribute_source for edge attributes from NGD ovelay #2709

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Merged
bazarkua merged 1 commit into from
Apr 2, 2026
+87 −16
Merged

#2707; add attribute_source for edge attributes from NGD ovelay #2709

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103 changes: 87 additions & 16 deletions code/ARAX/ARAXQuery/Overlay/compute_ngd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,8 @@ def compute_ngd(self):
The formula can be found here on [wikipedia.](https://en.wikipedia.org/wiki/Normalized_Google_distance)
Where in this case f(x,y) is the number of PubMed abstracts both concepts apear in, f(x)/f(y) are the number of abstracts individual concepts apear in, and N is the number of pubmed articles times the average number of search terms per article (35 million * 20).
"""

attribute_source = 'infores:arax'

# if you want to add virtual edges, identify the subject/objects, decorate the edges, add them to the KG, and then add one to the QG corresponding to them
# FW: changing this so if there is a virtual relation label but no subject and object then add edges for all subject object pairs in the quesry graph.
Expand Down Expand Up @@ -108,7 +110,12 @@ def compute_ngd(self):
edge_value = ngd_value
else:
edge_value = default_value
edge_attribute = EdgeAttribute(attribute_type_id=type, original_attribute_name=name, value=str(edge_value), value_url=url, description=ngd_description) # populate the NGD edge attribute
edge_attribute = EdgeAttribute(attribute_type_id=type,
original_attribute_name=name,
value=str(edge_value),
value_url=url,
description=ngd_description,
attribute_source=attribute_source) # populate the NGD edge attribute
if edge_attribute:
added_flag = True
# make the edge, add the attribute
Expand All @@ -131,15 +138,37 @@ def compute_ngd(self):
self.global_iter += 1
edge_attribute_list = [
edge_attribute,
EdgeAttribute(original_attribute_name="virtual_relation_label", value=relation, attribute_type_id="EDAM-OPERATION:0226"),
EdgeAttribute(original_attribute_name="virtual_relation_label",
value=relation,
attribute_type_id="EDAM-OPERATION:0226",
attribute_source=attribute_source),
#EdgeAttribute(original_attribute_name="is_defined_by", value=is_defined_by, attribute_type_id="biolink:Unknown"),
# EdgeAttribute(original_attribute_name=None, value="infores:rtx-kg2", attribute_type_id="biolink:knowledge_source", attribute_source="infores:rtx-kg2", value_type_id="biolink:InformationResource"),
# EdgeAttribute(original_attribute_name=None, value="infores:arax", attribute_type_id="primary_knowledge_source", attribute_source="infores:arax", value_type_id="biolink:InformationResource"),
EdgeAttribute(original_attribute_name="defined_datetime", value=defined_datetime, attribute_type_id="metatype:Datetime"),
EdgeAttribute(original_attribute_name="defined_datetime",
value=defined_datetime,
attribute_type_id="metatype:Datetime",
attribute_source=attribute_source),
# EdgeAttribute(original_attribute_name=None, value=provided_by, attribute_type_id="aggregator_knowledge_source", attribute_source=provided_by, value_type_id="biolink:InformationResource"),
EdgeAttribute(original_attribute_name=None, value=True, attribute_type_id="EDAM-DATA:1772", attribute_source="infores:arax", value_type_id="metatype:Boolean", value_url=None, description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
EdgeAttribute(original_attribute_name=None, value="statistical_association", attribute_type_id="biolink:knowledge_level", value_url=None, description=None),
EdgeAttribute(original_attribute_name=None, value="automated_agent", attribute_type_id="biolink:agent_type", value_url=None, description=None)
EdgeAttribute(original_attribute_name=None,
value=True,
attribute_type_id="EDAM-DATA:1772",
attribute_source=attribute_source,
value_type_id="metatype:Boolean",
value_url=None,
description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
EdgeAttribute(original_attribute_name=None,
value="statistical_association",
attribute_type_id="biolink:knowledge_level",
value_url=None,
description=None,
attribute_source=attribute_source),
EdgeAttribute(original_attribute_name=None,
value="automated_agent",
attribute_type_id="biolink:agent_type",
value_url=None,
description=None,
attribute_source=attribute_source)
#EdgeAttribute(original_attribute_name="confidence", value=confidence, attribute_type_id="biolink:ConfidenceLevel"),
#EdgeAttribute(original_attribute_name="weight", value=weight, attribute_type_id="metatype:Float"),
#EdgeAttribute(original_attribute_name="qedge_keys", value=qedge_keys)
Expand All @@ -153,7 +182,10 @@ def compute_ngd(self):
## fix #1980 issue
temp_list = [f"PMID:{pmid}" for pmid in pmid_set]
if len(temp_list) != 0:
pmid_attribute = EdgeAttribute(attribute_type_id="biolink:publications", original_attribute_name="publications", value=temp_list)
pmid_attribute = EdgeAttribute(attribute_type_id="biolink:publications",
original_attribute_name="publications",
value=temp_list,
attribute_source=attribute_source)
edge_attribute_list.append(pmid_attribute)

#### FIXME temporary hack by EWD
Expand Down Expand Up @@ -220,7 +252,12 @@ def compute_ngd(self):
edge_value = ngd_value
else:
edge_value = default_value
edge_attribute = EdgeAttribute(attribute_type_id=type, original_attribute_name=name, value=str(edge_value), value_url=url, description=ngd_description) # populate the NGD edge attribute
edge_attribute = EdgeAttribute(attribute_type_id=type,
original_attribute_name=name,
value=str(edge_value),
value_url=url,
description=ngd_description,
attribute_source=attribute_source) # populate the NGD edge attribute

if edge_attribute:
added_flag = True
Expand All @@ -243,15 +280,37 @@ def compute_ngd(self):
self.global_iter += 1
edge_attribute_list = [
edge_attribute,
EdgeAttribute(original_attribute_name="virtual_relation_label", value=relation, attribute_type_id="EDAM-OPERATION:0226"),
EdgeAttribute(original_attribute_name="virtual_relation_label",
value=relation,
attribute_type_id="EDAM-OPERATION:0226",
attribute_source=attribute_source),
#EdgeAttribute(original_attribute_name="is_defined_by", value=is_defined_by, attribute_type_id="biolink:Unknown"),
# EdgeAttribute(original_attribute_name=None, value="infores:arax", attribute_type_id="biolink:knowledge_source", attribute_source="infores:arax", value_type_id="biolink:InformationResource"),
# EdgeAttribute(original_attribute_name=None, value="infores:arax", attribute_type_id="primary_knowledge_source", attribute_source="infores:arax", value_type_id="biolink:InformationResource"),
EdgeAttribute(original_attribute_name="defined_datetime", value=defined_datetime, attribute_type_id="metatype:Datetime"),
EdgeAttribute(original_attribute_name="defined_datetime",
value=defined_datetime,
attribute_type_id="metatype:Datetime",
attribute_source=attribute_source),
# EdgeAttribute(original_attribute_name=None, value=provided_by, attribute_type_id="aggregator_knowledge_source", attribute_source=provided_by, value_type_id="biolink:InformationResource"),
EdgeAttribute(original_attribute_name=None, value=True, attribute_type_id="EDAM-DATA:1772", attribute_source="infores:arax", value_type_id="metatype:Boolean", value_url=None, description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
EdgeAttribute(original_attribute_name=None, value="statistical_association", attribute_type_id="biolink:knowledge_level", value_url=None, description=None),
EdgeAttribute(original_attribute_name=None, value="automated_agent", attribute_type_id="biolink:agent_type", value_url=None, description=None)
EdgeAttribute(original_attribute_name=None,
value=True,
attribute_type_id="EDAM-DATA:1772",
attribute_source=attribute_source,
value_type_id="metatype:Boolean",
value_url=None,
description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
EdgeAttribute(original_attribute_name=None,
value="statistical_association",
attribute_type_id="biolink:knowledge_level",
value_url=None,
description=None,
attribute_source=attribute_source),
EdgeAttribute(original_attribute_name=None,
value="automated_agent",
attribute_type_id="biolink:agent_type",
value_url=None,
description=None,
attribute_source=attribute_source)
#EdgeAttribute(original_attribute_name="confidence", value=confidence, attribute_type_id="biolink:ConfidenceLevel"),
#EdgeAttribute(original_attribute_name="weight", value=weight, attribute_type_id="metatype:Float"),
#EdgeAttribute(original_attribute_name="qedge_keys", value=qedge_keys)
Expand All @@ -265,7 +324,10 @@ def compute_ngd(self):
## fix #1980 issue
temp_list = [f"PMID:{pmid}" for pmid in pmid_set]
if len(temp_list) != 0:
pmid_attribute = EdgeAttribute(attribute_type_id="biolink:publications", original_attribute_name="publications", value=temp_list)
pmid_attribute = EdgeAttribute(attribute_type_id="biolink:publications",
original_attribute_name="publications",
value=temp_list,
attribute_source=attribute_source)
edge_attribute_list.append(pmid_attribute)

#### FIXME temporary hack by EWD
Expand Down Expand Up @@ -331,12 +393,21 @@ def compute_ngd(self):
edge_value = ngd_value
else:
edge_value = default_value
ngd_edge_attribute = EdgeAttribute(attribute_type_id=type, original_attribute_name=name, value=str(edge_value), value_url=url, description=ngd_description) # populate the NGD edge attribute
ngd_edge_attribute = EdgeAttribute(attribute_type_id=type,
original_attribute_name=name,
value=str(edge_value),
value_url=url,
description=ngd_description,
attribute_source=attribute_source) # populate the NGD edge attribute
edge.attributes.append(ngd_edge_attribute) # append it to the list of attributes
## fix #1980 issue
temp_list = [f"PMID:{pmid}" for pmid in pmid_set]
if len(temp_list) != 0:
pmid_edge_attribute = EdgeAttribute(attribute_type_id="biolink:publications", original_attribute_name="ngd_publications", value_type_id="EDAM-DATA:1187", value=temp_list)
pmid_edge_attribute = EdgeAttribute(attribute_type_id="biolink:publications",
original_attribute_name="ngd_publications",
value_type_id="EDAM-DATA:1187",
value=temp_list,
attribute_source=attribute_source)
edge.attributes.append(pmid_edge_attribute)
except Exception:
tb = traceback.format_exc()
Expand Down
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