Duplicated identifiers

[MortenHofft]

I'm trying to replicate https://arctos.database.museum/guid/DMNS:Mamm:11098

I notice that the identifiers for the parasite relationship appears 2 places

I can ask for the identifiers for the entity entityIdentifiersByEntityId But I can also ask for entityRelationshipsBySubjectEntityId and get the externalObjectEntityId value. Both will point me to e.g. http://arctos.database.museum/guid/DMNS:Para:64.

It looks to me like it shouldn't be in the identifiers table, but only in the relationsships

query {
  # the entity can have many IDs, so we need to ask for the entity through an entity identifiers table
  specimensIDs: allEntityIdentifiers(condition: {
    entityIdentifier: "https://arctos.database.museum/guid/DMNS:Mamm:11098"
  }) {
    # there should only be one entity with this ID
    nodes {
      entityId
      entityIdentifier
      entityIdentifierType
      specimen: entityByEntityId {
        entityId
        entityType

        # Identifiers section 
        # This is missing 2/5 columns: "relationsship" and "ID value" and "assignedBy" is missing. But might be inferred from the others?
        entityIdentifiersByEntityId {
          nodes {
            entityIdentifier
            entityIdentifierType
          }
        }
        # above identifiers include the parasites
        # I can also get to those via the related entities path like below
        entityRelationshipsBySubjectEntityId {
          nodes {
            externalObjectEntityId
          }
        }

      }
    }
  }
}

[tucotuco]

I'm not sure I understand the issue expressed here. The Identifiers table should only represent relationships to self, whereas the EntityRelationships would take care of relationships to other things.

On Wed, Jun 15, 2022 at 8:06 AM Morten Høfft @.***> wrote:

I notice that the identifiers for the parasite relationship appears 2 places

I can ask for the identifiers for the entity entityIdentifiersByEntityId But I can also ask for entityRelationshipsBySubjectEntityId and get the externalObjectEntityId value. Both will point me to e.g. http://arctos.database.museum/guid/DMNS:Para:64.

query {

the entity can have many IDs, so we need to ask for the entity through an entity identifiers table

specimensIDs: allEntityIdentifiers(condition: { entityIdentifier: "https://arctos.database.museum/guid/DMNS:Mamm:11098" }) {

there should only be one entity with this ID

nodes {
  entityId
  entityIdentifier
  entityIdentifierType
  specimen: entityByEntityId {
    entityId
    entityType

    # Identifiers section
    # This is missing 2/5 columns: "relationsship" and "ID value" and "assignedBy" is missing. But might be inferred from the others?
    entityIdentifiersByEntityId {
      nodes {
        entityIdentifier
        entityIdentifierType
      }
    }
    # above identifiers include the parasites
    # I can also get to those via the related entities path like below
    entityRelationshipsBySubjectEntityId {
      nodes {
        externalObjectEntityId
      }
    }

  }
}

} }

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[MortenHofft]

https://github.com/timrobertson100/model-tests/blob/c64965fc18b7c0df150133d44b97fbe4949d717e/arctos/files/entity_identifier.csv line	entityID	entityIdentifier	entityIdentifierType
4	21714980	https://arctos.database.museum/guid/DMNS:Mamm:11098	Arctos object
22	21714980	http://arctos.database.museum/guid/DMNS:Para:664	DMNS:Para

The Identifiers table should only represent relationships to self

I'm not sure I get that. entity 21714980 has 2 identifiers that seem to point to different organisms? The types are different though, making me think that the type was intended to indicate the type of relationship (that one was a parasite of the other). But since that also appears in the relationship table it was confused https://github.com/timrobertson100/model-tests/blob/4a6ef6f4c9fe3e76238ae51fde985d7097427463/arctos/files/entity_relationship.csv

[timrobertson100]

Isn't this just a data mistake in the CSV, where http://arctos.database.museum/guid/DMNS:Para:664 is being added to the wrong entity?

[MortenHofft]

That is the question I'm posing yes.

It looks to me like it shouldn't be in the identifiers table, but only in the relationsships

[tucotuco]

Those references to other entities are spurious here. The belong only in the EntityRelationship. Fixed with https://github.com/timrobertson100/model-tests/commit/37f212580606944a29b5c1da116eff4b88c5386e.