OMIM_disease_series_by_gene.yaml

pattern_name: OMIM_disease_series_by_gene

pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml

description: '

  This pattern is meant to be used for (1) OMIM Mendelian diseases (ie unitary genetic diseases, as described in
  [PMID:33417889](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820621/)), including children of OMIM phenotypic
  series (OMIMPS), which are represented as grouping classes in Mondo, and (2) OMIA Mendelian diseases (https://omia.org/) which are defined by a variation in a gene.
  Notes about the OMIMPS (see also OMIM_phenotypic_series.yaml):  - every instance of the OMIMPS
  metaclass should be equivalent to (via annotated xref) to something in OMIMPS namespace
  - the OMIMPS will never have an asserted causative gene as logical axiom (and no
  single causative gene in text def) - the OMIMPS must never be equivalent to an OMIM:nnnnnn
  (often redundant with the above rule) - the OMIMPS must have an acronym synonym,
  e.g. HPE - the OMIMPS must have two or more subclasses (direct or indirect) that
  are equivalent to OMIMs and conform to this pattern - the subclasses should (not
  must) have a logical def that uses the PS as a genus  - the OMIM subclasses must
  have acronym synonyms that are the parent syn + number, e.g. HPE1, HPE2 - the primary
  label for the children should also be parent + {"type"} + number - the first member
  will usually have the same number local ID as the PS Examples: [holoprosencephaly
  1](http://purl.obolibrary.org/obo/MONDO_0009349), [3M syndrome 1](http://purl.obolibrary.org/obo/MONDO_0010117)'

contributors:
- https://orcid.org/0000-0002-6601-2165
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-4142-7153

classes:
  disease: MONDO:0700096
  gene: SO:0000704

relations:
  has material basis in germline mutation in: RO:0004003

annotationProperties:
  exact_synonym: oio:hasExactSynonym
  related_synonym: oio:hasRelatedSynonym

vars:
  disease: '''disease'''
  gene: '''gene'''

name:
  text: '%s caused by variation in %s'
  vars:
  - disease
  - gene

annotations:
- annotationProperty: exact_synonym
  text: '%s %s'
  vars:
  - gene
  - disease

def:
  text: Any %s in which the cause of the disease is a variation in the %s gene.
  vars:
  - disease
  - gene

equivalentTo:
  text: '%s and ''has material basis in germline mutation in'' some %s'
  vars:
  - disease
  - gene