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#1593 update scripts of generating slim databases for kg2.7.1
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@chunyuma
chunyuma committed Aug 11, 2021
1 parent 4d898c3 commit 8b97a09
Showing 1 changed file with 21 additions and 21 deletions.
42 changes: 21 additions & 21 deletions code/ARAX/ARAXQuery/Overlay/GraphSage_train/py_scripts/generate_slim_databases.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,29 +59,29 @@
cohd_DSL_queries = [
{"operations": {"actions": [
"add_qnode(ids=DOID:1588, key=n00)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n01)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=COHD, COHD_method=paired_concept_freq, COHD_method_top_N=500)",
"return(message=true, store=false)"
]}},
{"operations": {"actions": [
"add_qnode(ids=DOID:1588, key=n00)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n01)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=COHD, COHD_method=observed_expected_ratio, COHD_method_top_N=500)",
"return(message=true, store=false)"
]}},
{"operations": {"actions": [
"add_qnode(ids=DOID:1588, key=n00)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n01)",
"add_qnode(categories=biolink:ChemicalEntity, key=n01)",
"add_qedge(subject=n00, object=n01, key=e00)",
"expand(edge_key=e00, kp=COHD, COHD_method=chi_square, COHD_method_top_N=500)",
"return(message=true, store=false)"
]}},
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, COHD_method=paired_concept_frequency)",
Expand All @@ -91,7 +91,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, COHD_method=observed_expected_ratio)",
Expand All @@ -101,7 +101,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, COHD_method=chi_square)",
Expand All @@ -122,7 +122,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, paired_concept_frequency=true, subject_qnode_key=n0, object_qnode_key=n1, virtual_relation_label=CP1)",
Expand All @@ -132,7 +132,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info,observed_expected_ratio=true, subject_qnode_key=n0, object_qnode_key=n1, virtual_relation_label=CP1)",
Expand All @@ -142,7 +142,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, chi_square=true, subject_qnode_key=n0, object_qnode_key=n1, virtual_relation_label=CP1)",
Expand All @@ -152,7 +152,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, paired_concept_frequency=true, subject_qnode_key=n1, object_qnode_key=n0, virtual_relation_label=V1)",
Expand All @@ -162,7 +162,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=DOID:1588, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, paired_concept_frequency=true)",
Expand All @@ -172,7 +172,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=UniProtKB:P62328, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, paired_concept_frequency=true, subject_qnode_key=n1, object_qnode_key=n0, virtual_relation_label=V1)",
Expand All @@ -182,7 +182,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(name=UniProtKB:P62328, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=overlay_clinical_info, paired_concept_frequency=true)",
Expand All @@ -193,7 +193,7 @@
"create_message",
"add_qnode(name=DOID:11830, key=n00)",
"add_qnode(categories=biolink:Protein, is_set=true, key=n01)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n02)",
"add_qnode(categories=biolink:ChemicalEntity, key=n02)",
"add_qedge(subject=n00, object=n01, key=e00)",
"add_qedge(subject=n01, object=n02, key=e01, predicates=biolink:molecularly_interacts_with)",
"expand(edge_key=[e00,e01], kp=RTX-KG2)",
Expand All @@ -211,7 +211,7 @@
]}},
{"operations": {"actions": [
"add_qnode(name=DOID:9406, key=n00)",
"add_qnode(categories=biolink:ChemicalSubstance, is_set=true, key=n01)",
"add_qnode(categories=biolink:ChemicalEntity, is_set=true, key=n01)",
"add_qnode(categories=biolink:Protein, key=n02)",
"add_qedge(subject=n00, object=n01, key=e00)",
"add_qedge(subject=n01, object=n02, key=e01)",
Expand Down Expand Up @@ -245,7 +245,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(ids=MONDO:0004992, key=n0, categories=biolink:Disease)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=predict_drug_treats_disease, subject_qnode_key=n1, object_qnode_key=n0, virtual_relation_label=P1)",
Expand All @@ -255,7 +255,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(ids=MONDO:0004992, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=predict_drug_treats_disease)",
Expand All @@ -265,7 +265,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(ids=MONDO:0004992, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=predict_drug_treats_disease, subject_qnode_key=n1, object_qnode_key=n0, virtual_relation_label=P1)",
Expand All @@ -275,7 +275,7 @@
{"operations": {"actions": [
"create_message",
"add_qnode(ids=UniProtKB:P62328, key=n0)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n1)",
"add_qnode(categories=biolink:ChemicalEntity, key=n1)",
"add_qedge(subject=n0, object=n1, key=e0)",
"expand(edge_key=e0, kp=RTX-KG2)",
"overlay(action=predict_drug_treats_disease, subject_qnode_key=n1, object_qnode_key=n0, virtual_relation_label=P1)",
Expand All @@ -285,7 +285,7 @@
{"operations": {"actions": [
"add_qnode(ids=DOID:11830, categories=biolink:Disease, key=n00)",
"add_qnode(categories=biolink:Gene, ids=[UniProtKB:P39060, UniProtKB:O43829, UniProtKB:P20849], is_set=true, key=n01)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n02)",
"add_qnode(categories=biolink:ChemicalEntity, key=n02)",
"add_qedge(subject=n00, object=n01, key=e00)",
"add_qedge(subject=n01, object=n02, key=e01)",
"expand(kp=BTE)",
Expand All @@ -297,7 +297,7 @@
"create_message",
"add_qnode(name=DOID:7551, key=n00)",
"add_qnode(categories=biolink:Protein, is_set=true, key=n01)",
"add_qnode(categories=biolink:ChemicalSubstance, key=n02)",
"add_qnode(categories=biolink:ChemicalEntity, key=n02)",
"add_qedge(subject=n00, object=n01, key=e00)",
"add_qedge(subject=n01, object=n02, key=e01, predicates=biolink:physically_interacts_with)",
"expand(edge_key=[e00,e01], kp=RTX-KG2)",
Expand Down

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