Other Deliverable - associatedSequences review

[Jegelewicz]

Task Group will make a recommendation [...] as to which class in the Darwin Core standard these properties belong which may also include recommendations for terms being revised, added, disambiguated, or deprecated. Depends upon definitions provided [in primary deliverable].

Current Darwin Core Placement/Definition

http://rs.tdwg.org/dwc/terms/associatedSequences

this term is a property of Occurrence

Defintion

A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.

Examples

http://www.ncbi.nlm.nih.gov/nuccore/U34853.1, http://www.ncbi.nlm.nih.gov/nuccore/GU328060 | http://www.ncbi.nlm.nih.gov/nuccore/AF326093

Comments

See also

Change term - associatedSequences: tdwg/dwc#332

[smrgeoinfo]

the ability to link to relatedResources should be a property of any entity; I'm not familiar enough with all of Darwin Core to know if that's already there. Clearly there are many materialEntities that do not have associated 'genetic sequence information'. A subclass of materialEntity could be defined to include entities that have genetic sequences (?biologicalEntity?)

[Jegelewicz]

ability to link to relatedResources should be a property of any entity

I think the problem might be what class does 'genetic sequence information' belong to?

ResourceRelationship is A relationship of one rdfs:Resource (http://www.w3.org/2000/01/rdf-schema#Resource) to another.

and

Resources can be thought of as identifiable records or instances of classes and may include, but need not be limited to dwc:Occurrence, dwc:Organism, dwc:MaterialSample, dwc:Event, dwc:Location, dwc:GeologicalContext, dwc:Identification, or dwc:Taxon.

I just don't see a class that sequence information belongs in and am feeling @albenson-usgs pain.

Or is a sequence a MeasurementOrFact?

It feels like dwc:associatesSequences was created simply because we don't have an "Identifier" or an "InformationArtefact" class?

A subclass of materialEntity could be defined to include entities that have genetic sequences (?biologicalEntity?)

This would make me very sad - we already have at least four of those: Organism, MaterialSample, LivingSpecimen, PreservedSpecimen and perhaps even a fifth as FossilSpecimens can sometimes yield DNA.

[albenson-usgs]

I'm coming to this without the benefit of the last few task group meetings but I am puzzled by this statement "Clearly there are many materialEntities that do not have associated 'genetic sequence information'." I would put this term in the MaterialEntity class because I don't think it's necessary for every term organized into that class to apply to every record or observation that might be documented in that class. As it stands now if I have an Occurrence that has an associatedSequences then I populated that term with the corresponding information. If I have an Occurrence that does not have an associatedSequences then I don't populate that term with any information. I'm confused why this wouldn't be possible if it was put in the MaterialEntity class?

[deepreef]

I am also lacking the benefit of recent meetings, and am slowly getting caught up on the GitHub commentary, but I just wanted to say that I completely agree with what @albenson-usgs says above.

[dagendresen]

Agree, however, I also do see the worry of @smrgeoinfo. If classes are sort of seen as defined by the terms organized under or grouped by the class. I know Darwin Core is only a bag of terms, but I think it is a valid thought for many to make even so. Would spicing the MaterialEntity class with the task or "organizing" (too many) terms that too clearly belong to biological things sort of alienate things that are more geological by nature?

Would it harm to move associatedSequences (etc) to be organized under the Record-level terms? Or simply keep associatedSequences organized under Occurrence?

Would be nice if we could also describe geology with Darwin Core...???

A bigger question could be if we actually want a new class for DNA Sequences in Darwin Core...???

[dagendresen]

The definition for associatedSequences states

A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.

We could propose to get rid of "associated with the Occurrence" or propose a change to "associated with the subject" or to something along "associated with the Organism, Occurrence, MaterialEntity, Event, Location, or other subjects or interest" :-)

[Jegelewicz]

more geological by nature

DNA sequences can be taken from water and soil....

[Jegelewicz]

A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the MaterialEntity.

[Jegelewicz]

added changes to review package https://github.com/tdwg/material-sample/blob/main/review%20package/associatedSequences.md

[Jegelewicz]

submitted to dwc repo - tdwg/dwc#454

[Jegelewicz]

change complete - tdwg/dwc#454