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