release commit

biocypher/_config/test_schema_config.yaml

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+Title: BioCypher graph schema configuration file
+
+# ---
+# "Named Things"
+# ---
+
+protein:
+  represented_as: node
+  preferred_id: uniprot
+  input_label: protein
+  db_collection_name: proteins
+  properties:
+    name: str
+    score: float
+    taxon: int
+    genes: str[]
+
+microRNA:
+  represented_as: node
+  preferred_id: mirbase.mature
+  input_label: mirna
+
+complex:
+  synonym_for: macromolecular complex
+  represented_as: node
+  preferred_id: complexportal
+  input_label: complex
+
+pathway:
+  represented_as: node
+  preferred_id: [reactome, wikipathways]
+  input_label: [reactome, wikipathways]
+
+gene:
+  represented_as: node
+  preferred_id: hgnc
+  input_label: [hgnc, ensg]
+  exclude_properties: accession
+
+disease:
+  represented_as: node
+  preferred_id: doid
+  input_label: Disease
+
+side effect:
+  is_a: phenotypic feature
+  represented_as: node
+  preferred_id: sider.effect
+  input_label: sider
+
+sequence variant:
+  represented_as: node
+  preferred_id: [clinically relevant, known, somatic]
+  input_label: [Clinically_relevant_variant, Known_variant, Somatic_mutation]
+  properties:
+    source: str
+    original_source: str
+    effect: str
+    biotype: str
+
+snRNA sequence:
+  is_a: nucleic acid entity
+  represented_as: node
+  preferred_id: [intact, rnacentral]
+  input_label: [intact_snrna, rnacentral_snrna]
+  properties:
+    ac: str
+    fullName: str
+    shortName: str
+    preferredName: str
+  exclude_properties: sequence
+
+DNA sequence:
+  is_a: nucleic acid entity
+  represented_as: node
+  preferred_id: ensembl
+  input_label: dna
+  properties:
+    ac: str
+    fullName: str
+    shortName: str
+    preferredName: str
+    sequence: str
+
+dsDNA sequence:
+  is_a: [DNA sequence, nucleic acid entity]
+  inherit_properties: True
+  represented_as: node
+  preferred_id: [intact, uniparc]
+  input_label: [intact_dsdna, uniprot_archive_dsdna]
+
+# ---
+# Associations
+# ---
+
+post translational interaction:
+  is_a: pairwise molecular interaction
+  represented_as: node
+  label_as_edge: INTERACTS_POST_TRANSLATIONAL
+  input_label: post_translational
+
+phosphorylation:
+  is_a: post translational interaction
+  represented_as: edge
+  input_label: phosphorylation
+
+gene to disease association:
+  represented_as: edge
+  label_as_edge: PERTURBED_IN_DISEASE
+  input_label: [protein_disease, gene_disease]
+  exclude_properties: accession
+
+mutation to tissue association:
+  is_a: [genotype to tissue association, entity to tissue association, association]
+  represented_as: edge
+  label_as_edge: Is_Mutated_In
+  input_label: Gene_Is_Mutated_In_Cell_Tissue
+
+variant to gene association: # -> Known.... and Somatic....
+  represented_as: edge
+  source: [known.sequence variant, somatic.sequence variant]
+  target: gene
+  input_label: [
+    VARIANT_FOUND_IN_GENE_Known_variant_Gene,
+    VARIANT_FOUND_IN_GENE_Somatic_mutation_Gene
+  ]
+
+gene to gene association:
+  represented_as: edge
+  input_label: gene_gene
+  properties:
+    directional: bool
+    curated: bool
+    score: float
+    id: str  # should be removed
+
+gene to variant association:  # should be removed
+  is_a: gene to variant association
+  represented_as: edge
+  input_label: gene_variant