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Specify the mapped/equivalent terms #31

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zhengj2007 opened this issue Mar 6, 2018 · 5 comments

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@zhengj2007
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commented Mar 6, 2018

Most commonly used approach is using annotationProperty: database_cross_reference (example: http://purl.obolibrary.org/obo/DOID_9351). When multiple mapped terms need to be listed, what is the correct format we should use to separate these mapped terms? Is this approach applied to both OBO Foundry ontologies and other ontologies/terminologies, like SNOMED, ICD-9?

Some used class equivalent, like GO:cell = CL:cell, when should we take this approach? Does it only apply to OBO Foundry ontologies?

Some used rdfs:seeAlso annotationProperty, see example: http://purl.obolibrary.org/obo/VO_0000609, (Note: it may not the correct annotationProperty to use.)

Some used self-defined annotationProperty, see example: http://purl.obolibrary.org/obo/DRON_00016163

Related issue: #24

Comments from Chris M:
Loosely I think we should encourage in order:

  • OWL Logical Axioms when these can be stated confidently. Always preferred
  • oio:hasDbXref, with CURIEs using standard prefixes
  • rdfs:seeAlso or more descriptive AP with URIs

We should discourage db-specific prefixes

@cmungall

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commented Mar 6, 2018

xref has no semantics. It's not that it isn't useful, it's just weaker than equivalence. If you know it's equivalent, use an equivalence axiom. If you don't know then don't. In some cases we shadow an equivalence axiom with an xref, for applications that want xrefs. See notes for obo version of obofoundry.org/ontology/mondo.html. Also I believe OxO expects xrefs, cc @simonjupp

I would say seeAlso is even weaker. It is also typically used with a URL not a CURIE. E.g. it may link a class to a page about that class.

@zhengj2007

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commented Mar 27, 2018

Ramona: In BCO, we use OWL same as, and use an imported ontology to specify those axioms so they can be included or not as needed.

@zhengj2007

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commented Mar 27, 2018

Discussed on Mar 27, 2018 call. @cmungall will make some examples and how they deal with them now.

@jonquet

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commented May 7, 2018

Glad to see the discussion here.
Within the AgroPortal project with @elcioabrahao we ware currently working on building a mapping repository and therefore extracting mappings from the ontology source files. Honestly working with XREFS is a bit of a nightmare ;)

  • Ambiguous target prefixes (some time one word, sometime a URL, ... most of the times not defined in the OBO Foundry name spaces of courses...
  • Complete mixes of targets that are "ontologies" and "databases" or just web page
  • Non standard (e.g., ncbitaxonref) while a prefix exist in the Foundry (ncbitaxon)
  • Multiples: unitprot, uniprotkb, uniprotkb_var
  • Spelling mistakes
  • etc..

We will share a document soon that groups the results per ontology and show the number of unresolvable targets.
XREFS are supposed to be manually created... thus they are supposed to be good and serve as reference for other (automatic) ontology alignement solutions ;)

I agree with @cmungall point before and included in original post. If we could encourage a bit more the community to adopt standard mapping properties that would be very good.
owl:sameAs, SKOS ones (https://www.w3.org/TR/2009/REC-skos-reference-20090818/#mapping) and finaly, rdfs:seeAlso (that are the weakest indeed).

As a recall the OBO spec provide headers for XREFS:
http://owlcollab.github.io/oboformat/doc/obo-syntax.html (section 4.4.2)
We have found some but not sure how to use them yet.
I will open another tracker to discuss possible equivalence with standard mapping properties.

So how can we do to improve /curate the XREFS?

@cmungall

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commented Jun 29, 2018

@zhengj2007 zhengj2007 changed the title Specify the mapped/equavalent terms Specify the mapped/equivalent terms Dec 3, 2018
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