OMIM_phenotypic_series.yaml

pattern_name: OMIM_phenotypic_series

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

description: 'This pattern is meant to be used for OMIM phenotypic series (OMIMPS),
  which are represented as grouping classes in Mondo. Note:  - every instance of this
  metaclass should be equivalent to (via annotated xref) to something in OMIMPS namespace
  - it will never have an asserted causative gene as logical axiom (and no single
  causative gene in text def) - it must never be equivalent to an OMIM:nnnnnn (often
  redundant with the above rule) - it must have an acronym synonym, e.g. HPE - it
  must have two or more subclasses (direct or indirect) that are equivalent to OMIMs
  - the subclasses should (not must) have a logical def that uses the PS as a genus
  (see http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml)
  - 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
  - the first member in OMIM usually has documentation that is pertinent to the parent
  PS - the members may(?) generally share high semantic similarity
  - All OMIMPS disease should have a has characteristic some inherited restricted, see http://purl.obolibrary.org/obo/mondo/sparql/omimps-should-be-inherited-violation.sparql
  
  Examples: [holoprosencephaly](http://purl.obolibrary.org/obo/MONDO_0016296) [OMIMPS:236100](https://omim.org/phenotypicSeries/PS236100),
  ''3-M syndrome''(http://purl.obolibrary.org/obo/MONDO_0007477) [OMIMPS:236100](https://omim.org/phenotypicSeries/PS273750). '

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

classes:
  disease: MONDO:0700096
  inherited: MONDO:0021152

relations:
  has_modifier: RO:0000053

vars:
  disease: '''disease'''

name:
  text: '%s'
  vars:
  - disease

subClassOf:
  text: '%s and ''has_modifier'' some ''inherited'''
  vars:
  - disease