Created
August 11, 2021 18:30
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More complicated ARAX commands
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| add_qnode(key=n0,ids=NCBIGENE:1956,categories=biolink:Gene) | |
| add_qnode(key=n1,categories=biolink:ChemicalSubstance) | |
| add_qedge(key=e0,subject=n0,object=n1,predicates=[biolink:entity_negatively_regulates_entity,biolink:negatively_regulates_entity_to_entity, biolink:decreases_activity_of, biolink:decreases_expression_of,biolink:disrupts,biolink:increases_degradation_of,biolink:negatively_regulates]) | |
| # Cytotoxic node | |
| add_qnode(key=n2,ids=UMLS:C1511636,categories=biolink:InformationContentEntity) | |
| # Exclude drugs that are cytotoxic | |
| add_qedge(key=e1,subject=n1,object=n2,exclude=true) | |
| # FDA approved drug | |
| add_qnode(key=n3,ids=MI:2099,categories=biolink:InformationContentEntity) | |
| add_qedge(key=e2,subject=n1,object=n3) | |
| # Acanthosis nigricans node | |
| add_qnode(key=n4,ids=MONDO:0007035,categories=biolink:Disease,option_group_id=1) | |
| add_qedge(key=e3,subject=n1,object=n4,option_group_id=1) | |
| expand(kp=RTX-KG2) | |
| # overlay literature info | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N1,subject_qnode_key=n0,object_qnode_key=n1) | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N2,subject_qnode_key=n1,object_qnode_key=n4) | |
| # overlay EHR info | |
| overlay(action=overlay_clinical_info,COHD_method=paired_concept_frequency,virtual_relation_label=C1,subject_qnode_key=n1,object_qnode_key=n4) | |
| # ML model | |
| overlay(action=predict_drug_treats_disease,virtual_relation_label=P1,subject_qnode_key=n1,object_qnode_key=n4,threshold=0.6,slow_mode=true) | |
| resultify() | |
| ------------------------------------ | |
| add_qnode(key=n0,ids=NCBIGENE:1956,categories=biolink:Gene) | |
| add_qnode(key=n1,categories=biolink:ChemicalSubstance) | |
| add_qedge(key=e0,subject=n0,object=n1,predicates=[biolink:entity_negatively_regulates_entity,biolink:negatively_regulates_entity_to_entity, biolink:decreases_activity_of, biolink:decreases_expression_of,biolink:disrupts,biolink:increases_degradation_of,biolink:negatively_regulates]) | |
| # Cytotoxic node | |
| add_qnode(key=n2,ids=UMLS:C1511636,categories=biolink:InformationContentEntity) | |
| # Exclude drugs that are cytotoxic | |
| add_qedge(key=e1,subject=n1,object=n2,exclude=true) | |
| # FDA approved drug | |
| add_qnode(key=n3,ids=MI:2099,categories=biolink:InformationContentEntity) | |
| add_qedge(key=e2,subject=n1,object=n3) | |
| # Acanthosis nigricans node | |
| add_qnode(key=n4,ids=MONDO:0007035,categories=biolink:Disease,option_group_id=1) | |
| add_qedge(key=e3,subject=n1,object=n4,option_group_id=1) | |
| # Direct query | |
| expand(kp=RTX-KG2) | |
| # Look at EHR data | |
| expand(kp=COHD,edge_key=e3,COHD_method=paired_concept_freq,COHD_method_top_N=1000) | |
| # ML model for drug-treats-disease | |
| expand(kp=DTD,edge_key=e3,DTD_threshold=0.6,DTD_slow_mode=true) | |
| resultify() | |
| ------------------------------------ | |
| #WITHOUT DERMAL | |
| add_qnode(key=n0,ids=NCBIGENE:1956,categories=biolink:Gene) | |
| add_qnode(key=n1,categories=biolink:ChemicalSubstance) | |
| add_qedge(key=e0,subject=n0,object=n1,predicates=[biolink:entity_negatively_regulates_entity,biolink:negatively_regulates_entity_to_entity, biolink:decreases_activity_of, biolink:decreases_expression_of,biolink:disrupts,biolink:increases_degradation_of,biolink:negatively_regulates]) | |
| # Cytotoxic node | |
| add_qnode(key=n2,ids=UMLS:C1511636,categories=biolink:InformationContentEntity) | |
| # Exclude drugs that are cytotoxic | |
| add_qedge(key=e1,subject=n1,object=n2,exclude=true) | |
| # FDA approved drug | |
| add_qnode(key=n3,ids=MI:2099,categories=biolink:InformationContentEntity) | |
| add_qedge(key=e2,subject=n1,object=n3) | |
| # Acanthosis nigricans node | |
| add_qnode(key=n4,ids=MONDO:0007035,categories=biolink:Disease,option_group_id=1) | |
| add_qedge(key=e3,subject=n1,object=n4,option_group_id=1) | |
| # Direct query | |
| expand(kp=RTX-KG2) | |
| # Look at EHR data | |
| expand(kp=COHD,edge_key=e3,COHD_method=paired_concept_freq,COHD_method_top_N=1000) | |
| # ML model for drug-treats-disease | |
| expand(kp=DTD,edge_key=e3) | |
| # PubMed abstracts | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N1,subject_qnode_key=n0,object_qnode_key=n1) | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N2,subject_qnode_key=n1,object_qnode_key=n4) | |
| resultify() | |
| ---------------------------------- | |
| #WITH DERMAL REQUIREMENT | |
| add_qnode(key=n0,ids=NCBIGENE:1956,categories=biolink:Gene) | |
| add_qnode(key=n1,categories=biolink:ChemicalSubstance) | |
| add_qedge(key=e0,subject=n0,object=n1,predicates=[biolink:entity_negatively_regulates_entity,biolink:negatively_regulates_entity_to_entity, biolink:decreases_activity_of, biolink:decreases_expression_of,biolink:disrupts,biolink:increases_degradation_of,biolink:negatively_regulates]) | |
| # Cytotoxic node | |
| add_qnode(key=n2,ids=UMLS:C1511636,categories=biolink:InformationContentEntity) | |
| # Exclude drugs that are cytotoxic | |
| add_qedge(key=e1,subject=n1,object=n2,exclude=true) | |
| # FDA approved drug | |
| add_qnode(key=n3,ids=MI:2099,categories=biolink:InformationContentEntity) | |
| add_qedge(key=e2,subject=n1,object=n3) | |
| # Acanthosis nigricans node | |
| add_qnode(key=n4,ids=MONDO:0007035,categories=biolink:Disease,option_group_id=1) | |
| add_qedge(key=e3,subject=n1,object=n4,option_group_id=1) | |
| # Dermal chemical substance | |
| add_qnode(key=n5,ids=UMLS:C0221928,categories=biolink:InformationContentEntity) | |
| add_qedge(key=e4,subject=n1,object=n5) | |
| # Direct query | |
| expand(kp=RTX-KG2) | |
| # Look at EHR data | |
| expand(kp=COHD,edge_key=e3,COHD_method=paired_concept_freq,COHD_method_top_N=1000) | |
| # ML model for drug-treats-disease | |
| expand(kp=DTD,edge_key=e3,DTD_threshold=0.6,DTD_slow_mode=true) | |
| # PubMed abstracts | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N1,subject_qnode_key=n0,object_qnode_key=n1) | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N2,subject_qnode_key=n1,object_qnode_key=n4) | |
| resultify() | |
| ------------------------------------ | |
| # Hit all KPs | |
| add_qnode(key=n0,ids=NCBIGENE:1956,categories=biolink:Gene) | |
| add_qnode(key=n1,categories=biolink:ChemicalSubstance) | |
| add_qedge(key=e0,subject=n0,object=n1,predicates=[biolink:entity_negatively_regulates_entity,biolink:negatively_regulates_entity_to_entity, biolink:decreases_activity_of, biolink:decreases_expression_of,biolink:disrupts,biolink:increases_degradation_of,biolink:negatively_regulates]) | |
| # Cytotoxic node | |
| add_qnode(key=n2,ids=UMLS:C1511636,categories=biolink:InformationContentEntity) | |
| # Exclude drugs that are cytotoxic | |
| add_qedge(key=e1,subject=n1,object=n2,exclude=true) | |
| # FDA approved drug | |
| add_qnode(key=n3,ids=MI:2099,categories=biolink:InformationContentEntity) | |
| add_qedge(key=e2,subject=n1,object=n3) | |
| # Acanthosis nigricans node | |
| add_qnode(key=n4,ids=MONDO:0007035,categories=biolink:Disease,option_group_id=1) | |
| add_qedge(key=e3,subject=n1,object=n4,option_group_id=1) | |
| # Direct query | |
| expand() | |
| # Look at EHR data | |
| expand(kp=COHD,edge_key=e3,COHD_method=paired_concept_freq,COHD_method_top_N=1000) | |
| # ML model for drug-treats-disease | |
| expand(kp=DTD,edge_key=e3) | |
| # PubMed abstracts | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N1,subject_qnode_key=n0,object_qnode_key=n1) | |
| overlay(action=compute_ngd,default_value=inf,virtual_relation_label=N2,subject_qnode_key=n1,object_qnode_key=n4) | |
| resultify() |
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