annotations link to ontologies

NCEAS / metadig-checks

MetaDIG suites and checks for data and metadata improvement and guidance.

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annotations link to ontologies #108

Open amilan17 opened 4 years ago

amilan17 commented 4 years ago

Description

Keywords or terms that are come from an ontology is referenced.

Priority

Choose a priority for the FAIR suite (Required or Optional)

FAIR: Optional

Issues

List of issues to be resolved

Procedure

Briefly describe the procedure or algorithm to implement the check.

kaiiam commented 4 years ago

From the Wilkinson FAIR paper

We have the following The FAIR Guiding Principles subchecks

To be Interoperable:
I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation. 
I2. (meta)data use vocabularies that follow FAIR principles
I3. (meta)data include qualified references to other (meta)data

@amilan17 was suggesting the prioritized use of ontology terms over weaker semantics such as those of controlled vocabularies. I agree but not that controlled vocabularies are still useful and shouldn't not be avoided just that ontologies should be preferred.

Spin45 commented 4 years ago

Test that IRI links to ontologies are resolvable.

kaiiam commented 4 years ago

@Spin45 makes a great point that if a web semantic such as an ontology term is employed, we do want it to be as persistent as possible. What we don't want is for people to annotate data with terms which become no longer resolvable, getting a 404 issue etc.

tedhabermann commented 4 years ago

There are a few ways to connect terms to ontologies: links to the vocabularies themselves as well as links/URIs to items themselves. There are also mechanisms for identifying ontologies and links to ontologies included in the ISO citations. These should also be used if appropriate... In DataCite there is a name (title?) for the vocabulary scheme and a separate URI.

mbjones commented 8 months ago

@jeanetteclark I was talking to @mobb about annotation checks, and she was suggesting this would be a good higher-priority item to check if annotations are being used and whether they are complete. I think A basic annotation check might check:

presence of annotation at least at 3 levels:
- dataset-level annotations
- entity-level annotations
- attribute-level annotations
whether each annotation term URI is:
- to a valid/resolvable ontology URI
- to a DataONE-indexed ontology

Let's discuss what it would take to add this... and I'll see if @mobb or @mpsaloha have further thoughts...