Protein:
  pathway:
    name: 'pathway annotation'
    description: 'Pathways annotated to a list of proteins'
    involved_nodes:
      - Protein
      - Pathway
    involved_rels:
      - ANNOTATED_IN_PATHWAY
    query: >
      MATCH (p:Protein)-[r:ANNOTATED_IN_PATHWAY]->(ph:Pathway)
      WHERE p.ATTRIBUTE IN {query_list} AND toLOWER(r.source)="reactome"
      RETURN DISTINCT p.ATTRIBUTE AS source, LABELS(p) as source_type, ph.name AS target, LABELS(ph) as target_type, r.score AS weight, r.source, type(r) AS rel_type;
  biological_process:
    name: 'GO biological processes annotation'
    description: 'Gene Ontology Biological processes annotated to a list of proteins'
    involved_nodes:
      - Protein
      - Biological_process
    involved_rels:
      - ASSOCIATED_WITH
    query: >
      MATCH (p:Protein)-[r:ASSOCIATED_WITH]->(ph:Biological_process) 
      WHERE p.ATTRIBUTE IN {query_list}
      WITH p, ph, r, SIZE((ph)<-[:ASSOCIATED_WITH]-(:Protein)) AS bp_degree WHERE bp_degree < 200
      RETURN DISTINCT p.ATTRIBUTE AS source, LABELS(p) as source_type, ph.name AS target, LABELS(ph) as target_type, r.score AS weight, r.source, type(r) AS rel_type;
  complex:
    name: 'Protein complexes within the list of proteins'
    description: 'Protein complexes represented in the provided list of proteins'
    involved_nodes:
      - Protein
      - Complex
    involved_rels:
      - IS_SUBUNIT_OF
    query: >
      MATCH (p:Protein)-[r:IS_SUBUNIT_OF]->(ph:Complex) 
      WHERE p.ATTRIBUTE IN {query_list}
      RETURN DISTINCT p.ATTRIBUTE AS source, LABELS(p) as source_type, ph.name AS target, LABELS(ph) as target_type, r.score AS weight, r.source, type(r) AS rel_type;
  drug:
    name: 'Drugs targetting the list of proteins'
    description: 'Drugs targetting at least one of the proteins in the provided list of proteins and their interactions'
    involved_nodes:
      - Protein
      - Drug
    involved_rels:
      - ACTS_ON
      - INTERACTS_WITH
    query: >
      MATCH (p:Protein)<-[r:ACTS_ON]-(d:Drug) 
      WHERE p.ATTRIBUTE IN {query_list} AND r.score>0.7
      WITH p, d, r, SIZE((:Protein)<-[:ACTS_ON]-(d)) AS drug_degree WHERE drug_degree < 20
      RETURN DISTINCT p.ATTRIBUTE AS source, LABELS(p) as source_type, d.name AS target, LABELS(d) as target_type, r.score AS weight, r.source, type(r) AS rel_type;
  drug_interactions:
    name: 'Drugs interactions'
    description: 'Drugs that interact'
    involved_nodes:
      - Drug
    involved_rels:
      - INTERACTS_WITH
    query: >
      MATCH (d1:Drug)-[r:INTERACTS_WITH]-(d2:Drug)
      WHERE d1.name IN DRUGS AND d2.name IN DRUGS
      RETURN d1.name AS source, LABELS(d1) as source_type, d2.name AS target, LABELS(d2) as target_type, r.score AS weight, r.source, type(r) AS rel_type;
  disease:
    name: 'Diseases associated with the list of proteins'
    description: 'Diseases associated to the list of proteins'
    involved_nodes:
      - Protein
      - Disease
      - Drug
    involved_rels:
      - ASSOCIATED_WITH
      - IS_INDICATED_FOR
      - MAPS_TO
    query: >
      MATCH (p:Protein)-[r:ASSOCIATED_WITH]->(d:Disease)-[:HAS_PARENT]->(:Disease)
      WHERE p.ATTRIBUTE IN {query_list}  AND r.score > 3 DISEASE_COND
      WITH d, COLLECT(p) AS proteins, SIZE((:Protein)-[:ASSOCIATED_WITH]->(d)) AS disease_degree WHERE disease_degree < 4500
      WITH DISTINCT d, SIZE(proteins) AS c WHERE c>2
      MATCH (p:Protein)-[r:ASSOCIATED_WITH]->(d)
      WHERE p.ATTRIBUTE IN {query_list} AND (r.score > 3 DISEASE_COND)
      RETURN p.ATTRIBUTE AS source, LABELS(p) AS source_type, d.name AS target, LABELS(d) AS target_type, toFLOAT(r.score)/5 AS weight, r.source, type(r) AS rel_type;
  disease_ontology:
    name: 'Disease ontology relationships'
    description: 'Diseases associated to the same parent term in the ontology'
    involved_nodes:
      - Disease
    involved_rels:
      - HAS_PARENT
    query: >
      MATCH (d1:Disease)-[r:HAS_PARENT]->(d2:Disease)<-[:HAS_PARENT]-(d3:Disease)
      WHERE d1.name IN DISEASES AND d3.name IN DISEASES
      RETURN d1.name AS source, LABELS(d1) AS source_type, d3.name AS target, LABELS(d3) AS target_type, r.score AS weight, r.source, "SAME_PARENT" AS rel_type;
  indications:
    name: 'Drug-diseases indications'
    description: 'If any of the drugs is indicated for any of the diseases'
    involved_nodes:
      - Disease
      - Drug
    involved_rels:
      - IS_INDICATED_FOR
      - MAPS_TO
    query: >
      MATCH (p:Protein)<-[r]-(drug:Drug)
      WHERE p.ATTRIBUTE IN {query_list}
      WITH COLLECT(DISTINCT drug.id) AS drugs
      MATCH (drug:Drug)-[r:IS_INDICATED_FOR]->(p:Phenotype)-[:MAPS_TO]->(ef)<-[:MAPS_TO]-(d:Disease)
      WHERE drug.id IN drugs AND d.name IN DISEASES
      RETURN drug.name AS source, LABELS(drug) AS source_type, d.name AS target, LABELS(d) AS target_type, r.score AS weight, r.source, type(r) AS rel_type;
  protein:
    name: 'Protein-protein interactions'
    description: 'Protein-protein interactions within the provided list of proteins'
    involved_nodes:
      - Protein
    involved_rels:
      - CURATED_INTERACTS_WITH
      - COMPILED_INTERACTS_WITH
      - ACTS_ON
    query: >
      MATCH (p1:Protein)-[r:CURATED_INTERACTS_WITH|COMPILED_INTERACTS_WITH|ACTS_ON]-(p2:Protein)
      WHERE p1.ATTRIBUTE IN {query_list} AND p2.ATTRIBUTE IN {query_list} AND r.score>0.7
      RETURN p1.ATTRIBUTE AS source, LABELS(p1) AS source_type, p2.ATTRIBUTE AS target, LABELS(p2) AS target_type, r.score AS weight, r.source, type(r) AS rel_type;
  publication:
    name: 'Publications'
    description: 'Publications where the provided list of proteins are mentioned'
    involved_nodes:
      - Protein
      - Disease
      - Publication
    involved_rels:
      - MENTIONED_IN_PUBLICATION
    query: >
      MATCH (d:Disease)-[:MENTIONED_IN_PUBLICATION]->(pub:Publication)<-[r:MENTIONED_IN_PUBLICATION]-(p:Protein)
      WHERE d.name IN DISEASES AND p.ATTRIBUTE IN {query_list}
      RETURN DISTINCT p.ATTRIBUTE AS source, LABELS(p) AS source_type, "PMID:"+pub.id AS target, LABELS(pub) AS target_type, r.score AS weight, r.source, type(r) AS rel_type;
Drug:
  drug:
    name: 'Drug-drug interactions'
    description: 'Interaction among the drugs in the list'
    involved_nodes:
      - Drug
    involved_rels:
      - INTERACTS_WITH
    query: >
        MATCH (d1:Drug)-[r:INTERACTS_WITH]-(d2:Drug)
        WHERE d1.ATTRIBUTE IN {query_list} AND d2.ATTRIBUTE IN {query_list}
        RETURN DISTINCT d1.ATTRIBUTE AS source, LABELS(d1) AS source_type, d2.ATTRIBUTE AS target, LABELS(d2) AS target_type, r.score AS weight, type(r) AS rel_type;
  disease:
    name: 'disease indications'
    description: 'Diseases the list of drug are indicated for'
    involved_nodes:
      - Drug
      - Experimental_factor
      - Disease
    involved_rels:
      - INDICATED_FOR
      - MAPS_TO
    query: >
        MATCH (d:Drug)-[r:IS_INDICATED_FOR]-(ph:Phenotype)-[:MAPS_TO]-(ef:Experimental_factor)-[:MAPS_TO]-(doid:Disease)
        WHERE d.ATTRIBUTE IN {query_list}
        RETURN DISTINCT d.ATTRIBUTE AS source, LABELS(d) AS source_type, doid.name AS target, LABELS(doid) AS target_type, r.score AS weight, r.source, type(r) AS rel_type;
  target:
    name: 'protein targets'
    description: 'Proteins targeted by the drugs in the list'
    involved_nodes:
      - Drug
      - Protein
    involved_rels:
      - ACTS_ON
    query: >
        MATCH (d:Drug)-[r:ACTS_ON]-(p:Protein) 
        WHERE d.ATTRIBUTE IN {query_list} AND r.score>0.7
        RETURN DISTINCT d.ATTRIBUTE AS source, LABELS(d) AS source_type, p.name AS target, LABELS(p) AS target_type, r.score AS weight, r.source, r.action AS rel_type;
  target_disease:
    name: 'protein-disease associations'
    description: 'Associations between targeted proteins and the disases the list of drugs are indicated for'
    involved_nodes:
      - Protein
      - Disease
    involved_rels:
      - ASSOCIATED_WITH
    query: >
        MATCH (p:Protein)-[r:ASSOCIATED_WITH]-(d:Disease)
        WHERE p.name IN TARGETS AND d.name IN DISEASES AND r.score > 3.0
        RETURN DISTINCT p.name AS source, LABELS(p) AS source_type, d.name AS target, LABELS(d) AS target_type, r.score AS weight, type(r) AS rel_type;
  complexes:
    name: 'protein complexes'
    description: 'Protein complexes among the targets'
    involved_nodes:
      - Protein
      - Complex
    involved_rels:
      - BELONGS_TO
    query: >
        MATCH (p:Protein)-[r:IS_SUBUNIT_OF]-(c:Complex)
        WHERE p.name IN TARGETS
        RETURN DISTINCT p.name AS source, LABELS(p) AS source_type, c.name AS target, LABELS(c) AS target_type, r.score AS weight, type(r) AS rel_type;
  pathway:
    name: 'drug pathways'
    description: 'Pathways annotated for the list of drugs'
    involved_nodes:
      - Drug
      - Pathway
    involved_rels:
      - BELONGS_TO
    query: >
        MATCH (d:Drug)-[r]-(p:Pathway)
        WHERE d.name IN {query_list}
        RETURN DISTINCT d.name AS source, LABELS(d) AS source_type, p.name AS target, LABELS(p) AS target_type, r.score AS weight, type(r) AS rel_type;
  target_pathway:
    name: 'target pathways'
    description: 'Pathways annotated for the list of targets'
    involved_nodes:
      - Protein
      - Pathway
    involved_rels:
      - ANNOTATED_IN_PATHWAY
    query: >
        MATCH (p:Protein)-[r]-(c:Pathway)
        WHERE p.name IN TARGETS AND r.source="SMPDB"
        RETURN DISTINCT p.name AS source, LABELS(p) AS source_type, c.name AS target, LABELS(c) AS target_type, r.score AS weight, type(r) AS rel_type;
  side_effects:
    name: 'Drug side effects'
    description: 'Side effects associated to the list of drugs'
    involved_nodes:
      - Drug
      - Phenotype
    involved_rels:
      - HAS_SIDE_EFFECT
    query: >
        MATCH (d:Drug)-[r:HAS_SIDE_EFFECT]->(p:Phenotype)
        WHERE d.ATTRIBUTE IN {query_list}
        RETURN DISTINCT d.ATTRIBUTE AS source, LABELS(d) AS source_type, p.name AS target, LABELS(p) AS target_type, r.score AS weight, type(r) AS rel_type;
  publication:
    name: 'Publications'
    description: 'Publications where the provided list of drugs are mentioned'
    involved_nodes:
      - Drug
      - Disease
      - Publication
    involved_rels:
      - MENTIONED_IN_PUBLICATION
    query: >
      MATCH (di:Disease)-[:MENTIONED_IN_PUBLICATION]->(pub:Publication)<-[r:MENTIONED_IN_PUBLICATION]-(d:Drug)
      WHERE di.name IN DISEASES AND d.ATTRIBUTE IN {query_list}
      WITH di, d, pub
      MATCH (pub)-[r:MENTIONED_IN_PUBLICATION]-(p:Protein)
      WHERE p.name IN TARGETS
      RETURN DISTINCT d.ATTRIBUTE AS source, LABELS(d) AS source_type, "PMID:"+pub.id AS target, LABELS(pub) AS target_type, r.score AS weight, r.source, type(r) AS rel_type;