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linkML's slot concept will allow to share slot names between classes as IMHO is typical for the ontological approach to modeling. In most of my SiDIF based models i am using object oriented approaches where there are separate properties/attributes/slots per class. Therefore there needs to be a fully qualifying name for each slot that is globaly unique and locally unique per class

In my first attempt to assign slots to classes i didn't use fully qualifying names and ended up with the error message:

ValueError: No such slot {'name': 'name', 'description': 'Name of the context'} as an attribute of Context ancestors or as a slot definition in the schema

which does not explain how to solve the problem. I am assuming a fully qualified slot name would solve this problem.

What would solve the problem? If my assumption fully qualifying slot name solve the problem - what are allowed / recommended ways to assign fully qualified names - how are namespaces syntactically separated or is there no such official linkML way ot doing this.

Should i e.g. specify context.name or context::name or the like?

my current code is:

'''
Created on 2023-02-20

@author: wf
'''
from meta.metamodel import Context
from linkml_runtime.utils.schemaview import SchemaView
from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition
from linkml.generators.linkmlgen import LinkmlGenerator

class SiDIF2LinkML:
    """
    converter between SiDIF and LINKML
    """
    
    def __init__(self,context:Context):
        self.context=context
        
    def asYaml(self)->str:
        """
        convert my context
        """
        # https://linkml.io/linkml-model/docs/SchemaDefinition/
        sd=SchemaDefinition(id=self.context.name,name=self.context.name)
        sv=SchemaView(sd)
        for topic in self.context.topics.values():
            cd=ClassDefinition(name=topic.name)
            cd.description=topic.documentation
            sv.add_class(cd)
            for prop in topic.properties.values():
                slot=SlotDefinition(name=prop.name)
                if hasattr(prop,"documentation"):
                    slot.description=prop.documentation
                sv.add_slot(slot)
                cd.slots.append(slot)
                pass
            
            pass
      
        lml_gen=LinkmlGenerator(schema=sd,format='yaml')
        yaml_text=lml_gen.serialize()
        return yaml_text

see also How do i add a class to a SchemaDefinition in LinkML?

Wolfgang Fahl
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1 Answers1

0

Currently my workaround is to combine the descriptions and try to use the slots in the "ontological way" which means each slot might have different meanings in different classes /contexts and the qualified name problem would be consider a "followup-issue"

'''
Created on 2023-02-20

@author: wf
'''
from meta.metamodel import Context
from linkml_runtime.utils.schemaview import SchemaView
from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition
from linkml.generators.linkmlgen import LinkmlGenerator

class SiDIF2LinkML:
    """
    converter between SiDIF and LINKML
    """
    
    def __init__(self,context:Context):
        self.context=context
        
    def asYaml(self,common_property_slots:bool=True)->str:
        """
        convert my context
        
        Args:
            common_property_slots(bool): if True reuse slots 
            
        Returns:
            str: the yaml markup
        
        """
        # https://linkml.io/linkml-model/docs/SchemaDefinition/
        sd=SchemaDefinition(id=self.context.name,name=self.context.name)
        sv=SchemaView(sd)
        for topic in self.context.topics.values():
            cd=ClassDefinition(name=topic.name)
            cd.description=topic.documentation
            sv.add_class(cd)
            for prop in topic.properties.values():
                if prop.name in sd.slots:
                    slot=sd.slots[prop.name]
                    slot.description+=","+prop.documentation
                else:
                    slot=SlotDefinition(name=prop.name)
                    if hasattr(prop,"documentation"):
                        slot.description=prop.documentation         
                    sv.add_slot(slot)
                cd.attributes[prop.name]=slot
                pass
            
            pass
      
        lml_gen=LinkmlGenerator(schema=sd,format='yaml')
        yaml_text=lml_gen.serialize()
        return yaml_text

Tried with the Family Context of the Royal Family Example Wiki

see e.g.

LinkML yaml

name: FamilyContext
id: FamilyContext
default_prefix: FamilyContext/
slots:
  name:
    name: name
    description: the name of the family,The full name of the person
    from_schema: FamilyContext
  weddingDate:
    name: weddingDate
    description: The date of the wedding
    from_schema: FamilyContext
  weddingPlace:
    name: weddingPlace
    from_schema: FamilyContext
  yearMarried:
    name: yearMarried
    from_schema: FamilyContext
  monthMarried:
    name: monthMarried
    from_schema: FamilyContext
  divorced:
    name: divorced
    from_schema: FamilyContext
  husbandOf:
    name: husbandOf
    description: the male head of family/ father
    from_schema: FamilyContext
  wifeOf:
    name: wifeOf
    description: the female head of family / mother
    from_schema: FamilyContext
  qid:
    name: qid
    description: the id of a Person in WikiData
    from_schema: FamilyContext
  royal92id:
    name: royal92id
    description: the royal92id of a Person in the GEDCOM standard
    from_schema: FamilyContext
  nobleTitle:
    name: nobleTitle
    description: The noble title of the person
    from_schema: FamilyContext
  picture:
    name: picture
    description: The URL of a picture of the person
    from_schema: FamilyContext
  sex:
    name: sex
    description: the gender of a person - female or male
    from_schema: FamilyContext
  born:
    name: born
    description: The date the person was born
    from_schema: FamilyContext
  yearBorn:
    name: yearBorn
    description: The year the person was born
    from_schema: FamilyContext
  monthBorn:
    name: monthBorn
    description: The month the person was born
    from_schema: FamilyContext
  birthPlace:
    name: birthPlace
    description: The location where the person was born
    from_schema: FamilyContext
  died:
    name: died
    description: the date the person died
    from_schema: FamilyContext
  diedAt:
    name: diedAt
    description: The location where the person died
    from_schema: FamilyContext
  yearDied:
    name: yearDied
    description: The year the person died
    from_schema: FamilyContext
  monthDied:
    name: monthDied
    description: The month the person died
    from_schema: FamilyContext
  noInLine:
    name: noInLine
    description: the number in Line to the Throne of this person
    from_schema: FamilyContext
  wikiPedia:
    name: wikiPedia
    description: the wikiPedia link of the Person
    from_schema: FamilyContext
classes:
  Family:
    name: Family
    description: In most societies, the family is the principal institution for the
      socialization of children.
    from_schema: FamilyContext
    attributes:
      name:
        name: name
        description: the name of the family,The full name of the person
        from_schema: FamilyContext
      weddingDate:
        name: weddingDate
        description: The date of the wedding
        from_schema: FamilyContext
      weddingPlace:
        name: weddingPlace
        from_schema: FamilyContext
      yearMarried:
        name: yearMarried
        from_schema: FamilyContext
      monthMarried:
        name: monthMarried
        from_schema: FamilyContext
      divorced:
        name: divorced
        from_schema: FamilyContext
      husbandOf:
        name: husbandOf
        description: the male head of family/ father
        from_schema: FamilyContext
      wifeOf:
        name: wifeOf
        description: the female head of family / mother
        from_schema: FamilyContext
  Person:
    name: Person
    description: A Person is a human being
    from_schema: FamilyContext
    attributes:
      qid:
        name: qid
        description: the id of a Person in WikiData
        from_schema: FamilyContext
      royal92id:
        name: royal92id
        description: the royal92id of a Person in the GEDCOM standard
        from_schema: FamilyContext
      name:
        name: name
        description: the name of the family,The full name of the person
        from_schema: FamilyContext
      nobleTitle:
        name: nobleTitle
        description: The noble title of the person
        from_schema: FamilyContext
      picture:
        name: picture
        description: The URL of a picture of the person
        from_schema: FamilyContext
      sex:
        name: sex
        description: the gender of a person - female or male
        from_schema: FamilyContext
      born:
        name: born
        description: The date the person was born
        from_schema: FamilyContext
      yearBorn:
        name: yearBorn
        description: The year the person was born
        from_schema: FamilyContext
      monthBorn:
        name: monthBorn
        description: The month the person was born
        from_schema: FamilyContext
      birthPlace:
        name: birthPlace
        description: The location where the person was born
        from_schema: FamilyContext
      died:
        name: died
        description: the date the person died
        from_schema: FamilyContext
      diedAt:
        name: diedAt
        description: The location where the person died
        from_schema: FamilyContext
      yearDied:
        name: yearDied
        description: The year the person died
        from_schema: FamilyContext
      monthDied:
        name: monthDied
        description: The month the person died
        from_schema: FamilyContext
      noInLine:
        name: noInLine
        description: the number in Line to the Throne of this person
        from_schema: FamilyContext
      wikiPedia:
        name: wikiPedia
        description: the wikiPedia link of the Person
        from_schema: FamilyContext

ER Diagram

erDiagram
Family {
    string name  
    string weddingDate  
    string weddingPlace  
    string yearMarried  
    string monthMarried  
    string divorced  
    string husbandOf  
    string wifeOf  
}
Person {
    string qid  
    string royal92id  
    string name  
    string nobleTitle  
    string picture  
    string sex  
    string born  
    string yearBorn  
    string monthBorn  
    string birthPlace  
    string died  
    string diedAt  
    string yearDied  
    string monthDied  
    string noInLine  
    string wikiPedia  
}

Which would be automatically rendered in github see https://github.com/WolfgangFahl/pyMetaModel/issues/15

Family Context ER Diagram

Wolfgang Fahl
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