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Merge pull request #35 from linkml/environmental-health-edoh-valuesets
Add environmental health, oncology, and EDoH value sets
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‎src/valuesets/schema/chemistry/roles.yaml‎

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name: roles
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title: Chemical and Biological Roles
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description: >-
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Value sets for chemical and biological roles that molecular entities can play,
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based on the ChEBI ontology role hierarchy.
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id: https://w3id.org/linkml/valuesets/chemistry/roles
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imports:
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- linkml:types
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prefixes:
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linkml: https://w3id.org/linkml/
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valuesets: https://w3id.org/valuesets/
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CHEBI: http://purl.obolibrary.org/obo/CHEBI_
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rdfs: http://www.w3.org/2000/01/rdf-schema#
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orcid: https://orcid.org/
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valuesets_meta: https://w3id.org/valuesets/meta/
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default_prefix: valuesets
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slots:
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chemical_role:
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description: A role played by a molecular entity within a chemical context
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range: ChemicalRole
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biological_role:
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description: A role played by a molecular entity within a biological context
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range: BiologicalRole
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enums:
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ChemicalRole:
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title: Chemical Role
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description: >-
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Roles played by molecular entities within a chemical context, dynamically
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populated from ChEBI. Includes roles such as catalyst, reagent, solvent,
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indicator, buffer, and other chemical functions.
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status: STANDARD
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contributors:
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- orcid:0000-0002-6601-2165
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- https://github.com/anthropics/claude-code
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instantiates:
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- valuesets_meta:ValueSetEnumDefinition
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annotations:
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stewards: https://www.ebi.ac.uk/chebi
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publishers: https://www.ebi.ac.uk/chebi
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reachable_from:
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source_nodes:
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- CHEBI:51086
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is_direct: false
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relationship_types:
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- rdfs:subClassOf
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BiologicalRole:
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title: Biological Role
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description: >-
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Roles played by molecular entities within a biological context, dynamically
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populated from ChEBI. Includes biochemical roles, pharmacological roles,
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physiological roles, and other biological functions.
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status: STANDARD
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contributors:
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- orcid:0000-0002-6601-2165
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- https://github.com/anthropics/claude-code
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instantiates:
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- valuesets_meta:ValueSetEnumDefinition
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annotations:
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stewards: https://www.ebi.ac.uk/chebi
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publishers: https://www.ebi.ac.uk/chebi
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reachable_from:
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source_nodes:
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- CHEBI:24432
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is_direct: false
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relationship_types:
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- rdfs:subClassOf

‎src/valuesets/schema/clinical/genetics.yaml‎

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name: genetics
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title: Clinical Genetics Value Sets
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description: Value sets for clinical genetics including modes of inheritance
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id: https://w3id.org/linkml/valuesets/clinical/genetics
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imports:
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- linkml:types
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prefixes:
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linkml: https://w3id.org/linkml/
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valuesets: https://w3id.org/valuesets/
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HP: http://purl.obolibrary.org/obo/HP_
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orcid: https://orcid.org/
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valuesets_meta: https://w3id.org/valuesets/meta/
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default_prefix: valuesets
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slots:
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mode_of_inheritance:
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description: The mode of inheritance for a genetic condition
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range: ModeOfInheritance
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enums:
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ModeOfInheritance:
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title: Mode of Inheritance
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description: >-
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Patterns of genetic inheritance describing how traits or disorders are passed
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between generations. Based on HP:0000005 (Mode of inheritance).
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status: STANDARD
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contributors:
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- orcid:0000-0002-6601-2165
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- https://github.com/anthropics/claude-code
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instantiates:
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- valuesets_meta:ValueSetEnumDefinition
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annotations:
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stewards: https://hpo.jax.org
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publishers: https://hpo.jax.org
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permissible_values:
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AUTOSOMAL_DOMINANT:
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title: Autosomal dominant inheritance
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description: >-
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A mode of inheritance that is observed for traits related to a gene
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encoded on one of the autosomes in which a trait manifests in heterozygotes.
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meaning: HP:0000006
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AUTOSOMAL_RECESSIVE:
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title: Autosomal recessive inheritance
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description: >-
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A mode of inheritance that is observed for traits related to a gene
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encoded on one of the autosomes in which a trait manifests in individuals
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with two pathogenic alleles.
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meaning: HP:0000007
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X_LINKED:
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title: X-linked inheritance
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description: >-
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A mode of inheritance that is observed for traits related to a gene
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encoded on the X chromosome.
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meaning: HP:0001417
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X_LINKED_DOMINANT:
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title: X-linked dominant inheritance
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description: >-
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A mode of inheritance that is observed for dominant traits related to
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a gene encoded on the X chromosome.
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meaning: HP:0001423
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is_a: X_LINKED
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X_LINKED_RECESSIVE:
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title: X-linked recessive inheritance
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description: >-
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A mode of inheritance that is observed for recessive traits related to
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a gene encoded on the X chromosome.
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meaning: HP:0001419
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is_a: X_LINKED
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Y_LINKED:
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title: Y-linked inheritance
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description: >-
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A mode of inheritance that is observed for traits related to a gene
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encoded on the Y chromosome.
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meaning: HP:0001450
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MITOCHONDRIAL:
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title: Mitochondrial inheritance
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description: >-
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A mode of inheritance that is observed for traits related to a gene
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encoded on the mitochondrial genome. Maternally inherited.
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meaning: HP:0001427
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MENDELIAN:
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title: Mendelian inheritance
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description: >-
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A mode of inheritance of diseases whose pathophysiology can be traced
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back to deleterious variants in a single gene.
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meaning: HP:0034345
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NON_MENDELIAN:
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title: Non-Mendelian inheritance
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description: >-
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A mode of inheritance that depends on genetic determinants in more than one gene.
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meaning: HP:0001426
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DIGENIC:
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title: Digenic inheritance
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description: >-
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A type of multifactorial inheritance governed by the simultaneous action
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of two gene loci.
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meaning: HP:0010984
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is_a: NON_MENDELIAN
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OLIGOGENIC:
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title: Oligogenic inheritance
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description: >-
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A type of multifactorial inheritance governed by the simultaneous action
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of a few gene loci (typically three).
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meaning: HP:0010983
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is_a: NON_MENDELIAN
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POLYGENIC:
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title: Polygenic inheritance
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description: >-
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A mode of inheritance that depends on a mixture of major and minor genetic
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determinants possibly together with environmental factors.
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meaning: HP:0010982
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is_a: NON_MENDELIAN
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SEMIDOMINANT:
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title: Semidominant inheritance
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description: >-
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A mode of inheritance for traits that can manifest in both monoallelic
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and biallelic states, with similar or differing phenotype severity.
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meaning: HP:0032113
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PSEUDOAUTOSOMAL:
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title: Pseudoautosomal inheritance
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description: >-
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A pattern of inheritance observed for alleles in the X-Y identical regions,
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resembling autosomal inheritance.
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meaning: HP:0034339
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PSEUDOAUTOSOMAL_DOMINANT:
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title: Pseudoautosomal dominant inheritance
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description: >-
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A type of pseudoautosomal inheritance that is dominant.
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meaning: HP:0034340
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is_a: PSEUDOAUTOSOMAL
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PSEUDOAUTOSOMAL_RECESSIVE:
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title: Pseudoautosomal recessive inheritance
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description: >-
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A type of pseudoautosomal inheritance that is recessive.
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meaning: HP:0034341
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is_a: PSEUDOAUTOSOMAL

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