Webinar 2: Related specimens in distinct collections (Wouter Addink)

Data Publishing Diversifying the GBIF data model
1

The following question(s) were asked in the Collection Management Systems Webinar and will be answered here.

Wouter Addink: How would the following use case appear in the model?: A mammal in the collection and flea preserved as a separate specimen, but don’t know if the flea is linked to the same collection event - the flea may have jumped onto the mammal within the collection.

I’m not sure how realistic this scenario is, but no problem, it will certainly illustrate the capacity to be explicit about relationships. The chipmunk is a dwc:Organism Entity:
entityID: Chipmunk1
entityType: dwc:Organism

It was collected during “Event1” in the wild at “Location1”, but it wasn’t checked for fleas:
eventID: Event1
eventType: collection
eventDate: 2019-07-17
locationID: Location1

to connect the Organism with the collecting Event, we need an EntityEvent record:
entityID: Chipmunk1
eventID: Event1

The chipmunk has various parts in “Collection1”, one of which is the skin the flea was found on. This is a MaterialEntity:
materialEntityID: materialEntityID2
materialEntityType: skin

and therefore also an Entity:
entityID: materialEntityID2
entityType: MaterialEntity
collectionID: Collection1

The skin was part of the chipmunk, which can be expressed in an EntityRelationship:
entityRelationshipID: er_id11
subjectEntityID: materialEntityID2
entityRelationshipType: part of
objectEntityID: Chipmunk1

with the complementary EntityRelationship:
entityRelationshipID: er_id12
subjectEntityID: Chipmunk1
entityRelationshipType: has part
objectEntityID: materialEntityID2

The flea is a dwc:Organism Entity:
entityID: Flea1
entityType: dwc:Organism

It was collected during “Event2” in the collection from the chipmunk skin. It isn’t certain that the flea was a parasite of the chipmunk, only that is was found on the skin:
eventID: Event2
eventType: collection
eventDate: 2020-10-31
locationID: Location2
eventRemarks: flea found on skin in mammal collection

to connect the Organism with the collecting Event, we need an EntityEvent record:
entityID: Flea1
eventID: Event2

The remains of the flea in “Collection2” consist of the whole animal. This is a MaterialEntity:
materialEntityID: materialEntityID3
materialEntityType: complete individual

and therefore also an Entity:
entityID: materialEntityID3
entityType: MaterialEntity
collectionID: Collection2

The flea specimen was the corporeal embodiment of the flea as a dwc:Organism, which can be expressed in an EntityRelationship:
entityRelationshipID: er_id13
subjectEntityID: materialEntityID3
entityRelationshipType: physical remains of
objectEntityID: Flea1

entityRelationshipID: er_id14
subjectEntityID: Flea1
entityRelationshipType: has remains
objectEntityID: materialEntityID3

And the physical remains of the flea (the MaterialEntity) were found on the skin (MaterialEntity) of the chipmunk, which we capture in an EntityRelationship:
entityRelationshipID: er_id15
subjectEntityID: Flea1
entityRelationshipType: found on
objectEntityID: materialEntityID2

with the complementary EntityRelationship:
subjectEntityID: materialEntityID2
entityRelationshipType: held
objectEntityID: Flea1

2

@waddink we have something like this in Arctos. A jar of shrews from which fleas were removed, but it is not known which shrew any particular flea came from (the fleas were “found in the jar”). See https://arctos.database.museum/guid/Arctos:Entity:38

I think we would handle your situation in a similar manner, but the relationship between the flea and the mammal would need to be something uncertain. We might first assume the mammal was the “host of” the flea, but state in the assertion how we concluded this: “flea found on skin in collection - may have arrived after preparation”. In time, we might end up with some “uncertain” relationship in our relationship code table. In fact we have been discussing this for some time, but have been unable to agree on good terminology.