metalinks/cypher_query.txt at main · biocypher/metalinks · GitHub

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#Production degradation sets

MATCH (m)-[a]->(p:Protein)
WHERE type(a) in ['ReconProductionDegradation','HMDBProductionDegradation', 'HmrProductionDegradation']
AND ANY(value in m.cellular_locations WHERE value = 'Extracellular')
AND (ANY(value in m.tissue_locations WHERE value in ['Kidney', 'All Tissues']) OR ANY(value in m.biospecimen_locations WHERE value = 'Urine'))
AND NOT (a.transport_direction = 'out' AND a.direction = 'degradation')
RETURN m.id as HMDB,
       m.name as MetName,
       m.cellular_locations as CellLoc,
       m.tissue_locations as TissueLoc,
       m.biospecimen_locations as BiospecLoc,
       a.transport_direction as Transport_direction,
       a.mode as Mode,
       a.direction as Direction,
       a.status as Status,
       p.id as Uniprot,
       p.protein_names as ProtName


#Metabolite receptor links

MATCH (m)-[a]->(p:Protein)
WHERE (a.database > 500 OR a.experiment > 500 OR a.combined_score > 900)
AND type(a) = 'StitchMetaboliteReceptor'
AND ANY(value in m.cellular_locations WHERE value = 'Extracellular')
AND (ANY(value in m.tissue_locations WHERE value in ['Kidney', 'All Tissues']) OR ANY(value in m.biospecimen_locations WHERE value = 'Urine'))
AND NOT a.mode in ['reaction', 'catalysis', 'expression', 'pred_binding']
RETURN m.id as HMDB,
       m.name as MetName,
       m.cellular_locations as CellLoc,
       m.tissue_locations as TissueLoc,
       m.biospecimen_locations as BiospecLoc,
       a.mode as Mode,
       a.direction as Direction,
       a.status as Status,
       p.id as Uniprot,
       p.protein_names as ProtName


# DB F 0.4.1

MATCH (m)-[a]->(p:Protein)
WHERE
  (type(a) IN ['StitchMetaboliteReceptor', 'NeuronchatMetaboliteReceptor', 'CellphoneMetaboliteReceptor', 'CellinkerMetaboliteReceptor'] AND
  ((type(a) = 'StitchMetaboliteReceptor' AND (a.database > 200 OR a.experiment > 300 OR a.predicted > 700 OR a.combined_score > 900)) OR
  (type(a) <> 'StitchMetaboliteReceptor')))
AND ANY(value in m.cellular_locations WHERE value = 'Extracellular')
AND ((p.receptor_type in ['catalytic_receptor', 'gpcr', 'nhr']) OR ((p.receptor_type in ['lgic',  'other_ic', 'transporter', 'vgic'] AND a.mode in ['activation', 'binding'])))
AND NOT a.mode in ['reaction', 'catalysis', 'expression', 'pred_binding']
RETURN
  m.id as HMDB,
  m.name as metabolite,
  p.symbol as Symbol,
  p.id as Uniprot,
  p.protein_names as ProtName,
  m.pubchem_compound_id as pubchem,
  m.cellular_locations as CellLoc,
  m.tissue_locations as TissueLoc,
  m.biospecimen_locations as BSLoc,
  m.sub_class as metabolite_subclass,
  a.combined_score,
  a.experiment,
  a.database,
  a.prediction,
  a.textmining,
  m.diseases as disease,
  m.pathways as pathway

# PD_0.4.5

MATCH (m)-[a]->(p:Protein)
WHERE type(a) in ['ReconProductionDegradation','HmdbProductionDegradation', 'HmrProductionDegradation', 'RheaProductionDegradation']
AND NOT (a.transport_direction = 'out' AND a.direction = 'degradation')
RETURN
  m.id as HMDB,
       m.name as MetName,
       m.symbol as Symbol,
       m.cellular_locations as CellLoc,
       m.tissue_locations as TissueLoc,
       m.biospecimen_locations as BiospecLoc,
       a.transport_direction as Transport_direction,
       a.mode as Mode,
       a.direction as Direction,
       a.status as Status,
       p.id as Uniprot,
       p.protein_names as ProtName


# actual truth and webpage:

MATCH (m)-[a]->(p:Protein)
WHERE
type(a) IN ['CellinkerMetaboliteReceptor', 'ScconnectMetaboliteReceptor', 'StitchMetaboliteReceptor', 'NeuronchatMetaboliteReceptor', 'CellphoneMetaboliteReceptor']
AND ((a.database >= 200 OR a.experiment >= 300 OR a.predicted >= 700 OR a.combined_score >= 900) OR
  (type(a) <> 'StitchMetaboliteReceptor'))
AND ANY(value in m.cellular_locations WHERE value = 'Extracellular')
AND ((p.receptor_type in ['catalytic_receptor', 'gpcr', 'nhr']) OR ((p.receptor_type in ['lgic',  'other_ic', 'transporter', 'vgic'] AND a.mode in ['activation', 'inhibition'])))
AND NOT a.mode in ['reaction', 'catalysis', 'expression']
RETURN
  m.id as HMDB,
  a.mode,
  m.name as metabolite,
  p.symbol as Symbol,
  p.id as Uniprot,
  type(a),
  p.protein_names as ProtName,
  m.pubchem_compound_id as pubchem,
  m.cellular_locations as CellLoc,
  m.tissue_locations as TissueLoc,
  m.biospecimen_locations as BSLoc,
  m.sub_class as metabolite_subclass,
  a.combined_score,
  a.experiment,
  a.database,
  a.prediction,
  a.textmining