DC vs oboInOwl annotation properties?

[turbomam]

@pbuttigieg recently suggested switching to Dublin Core annotation properties, as opposed to of oboInOwl.

The NMDC team has been using oboInOwl in our templates, like NMDC-03_EnvO_template_robot_sheet

• oboInOwl:created_by
• oboInOwl:creation_date^^xsd:dateTime
• oboInOwl:hasBroadSynonym@en
• oboInOwl:hasDbXref
• oboInOwl:hasExactSynonym@en
• oboInOwl:hasNarrowSynonym@en
• oboInOwl:hasRelatedSynonym@en
• oboInOwl:inSubset

That's based on @kaiiam's nice EnvO/robot documentation

I have checked for predicate usage in EnvO via http://sparql.hegroup.org/sparql/

Remember there are two different Dublin Core prefixes.

     xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:terms="http://purl.org/dc/terms/"

---

SELECT  ?p (COUNT(?s) AS ?count)
WHERE
  { GRAPH <http://purl.obolibrary.org/obo/merged/ENVO>
      { ?s  ?p  ?o }
  }
GROUP BY ?p

DC and oboInOwl usage

?p	?count
http://purl.org/dc/elements/1.1/contributor	186
http://purl.org/dc/elements/1.1/creator	451
http://purl.org/dc/elements/1.1/date	352
http://purl.org/dc/elements/1.1/description	1
http://purl.org/dc/elements/1.1/source	3
http://purl.org/dc/elements/1.1/title	1
http://purl.org/dc/terms/creator	3
http://purl.org/dc/terms/date	1
http://purl.org/dc/terms/license	2
http://purl.org/dc/terms/rightsHolder	1
http://www.geneontology.org/formats/oboInOwl#consider	101
http://www.geneontology.org/formats/oboInOwl#created_by	810
http://www.geneontology.org/formats/oboInOwl#creation_date	591
http://www.geneontology.org/formats/oboInOwl#default-namespace	1
http://www.geneontology.org/formats/oboInOwl#hasAlternativeId	86
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym	468
http://www.geneontology.org/formats/oboInOwl#hasDbXref	7676
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym	3131
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym	465
http://www.geneontology.org/formats/oboInOwl#hasOBONamespace	1130
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym	1999
http://www.geneontology.org/formats/oboInOwl#hasSynonym	36
http://www.geneontology.org/formats/oboInOwl#hasSynonymType	106
http://www.geneontology.org/formats/oboInOwl#id	1115
http://www.geneontology.org/formats/oboInOwl#inSubset	1253
http://www.geneontology.org/formats/oboInOwl#is_class_level	1
http://www.geneontology.org/formats/oboInOwl#is_inferred	4
http://www.geneontology.org/formats/oboInOwl#is_metadata_tag	1
http://www.geneontology.org/formats/oboInOwl#shorthand	2
http://www.geneontology.org/formats/oboInOwl#source	1

Searching for owl:onPropertys associated with owl:Restrictions doesn't show any DC or oboInOwl usage that might need remediation.

There is also heterogeneity in the objects of the various APs for mentioning creators and contributors:

SELECT  ?o (COUNT(?s) AS ?count)
WHERE
  { GRAPH <http://purl.obolibrary.org/obo/merged/ENVO>
      { ?s  <http://purl.org/dc/elements/1.1/contributor>  ?o }
  }
GROUP BY ?o

• dc:contributor all IRIs, except for nine "https://orcid.org/0000-0002-7556-2097" strings
• dc:creator? mixture of ORCID IRIs, ORCID strings and some non-ORCID strings. Some http and some https
• terms:creator? All names or initials
• http://www.geneontology.org/formats/oboInOwl#created_by most heterogeneous!

[cmungall]

Thanks for this analysis

The very first thing that should be done is replace elements with terms. This should not be controversial. See OBOFoundry/OBOFoundry.github.io#540

I am not sure that the question should be "dc vs oio". There are no synonyms in dc for example.

I would strongly advocate for ENVO continuing to use

oboInOwl:hasBroadSynonym@en
oboInOwl:hasExactSynonym@en
oboInOwl:hasNarrowSynonym@en
oboInOwl:hasRelatedSynonym@en

for synonyms (there is no equivalent for this in dc. there is also no direct equivalent in skos, as skos predicates map between concept URIs, and should not be used for literals)

I would also recommend keeping on using

oboInOwl:inSubset

for subsets

and

oboInOwl:hasDbXref

on axiom annotations for provenenance

This will all be made clearer with the next OMO release

I think your analysis is showing a lot of terms from other ontologies. I am not sure it's the best use of your time to redo on envo-base as this will all be folded into OMO-based validation tools soon.

[turbomam]

recently discussed wrt

• added freshwater stream and biome #1477
• added stream water #1479