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[bioontology-support] [BioPortal] Feedback from Emma Vos

John Graybeal jgraybeal at stanford.edu
Wed Aug 12 16:25:01 PDT 2020


This seems possible. I believe BioPortal *can* display part-of hierarchies, if the ontology is configured to do so. But it is a "choose one" situation, so BioPortal can't support both views.

john

On Aug 12, 2020, at 4:17 PM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

With regard to the display of class hierarchies, there’s a distinct difference between an “asserted" hierarchy and an “inferred" hierarchy. BioPortal is displaying the asserted class hierarchy. If you open the uberon.owl file that OLS serves in the Protege ontology editor, you can see that the “venous blood” class is also show as a leaf term, i.e., in the position that it was manually defined in the asserted hierarchy (screen shot below). You can also see in the same screen shot that the “venous blood” class has a subClassOf axiom:

'part of' some 'hematopoietic system’

This means that "venous blood" will be shown as a subclass of "hematopoietic system” in any instance where an *inferred* hierarchy is displayed. In order to display an inferred hierarchy, you need to perform reasoning on an ontology. I don’t know the internal of the OLS software - however, I’m guessing that somewhere in their pipeline they perform a reasoning task that allows them to display terms in the context of an inferred hierarchy.

The hierarchy that BioPortal displays isn’t incomplete and/or incorrect. The differences you see between the two pieces of software have to do with asserted vs. inferred hierarchies.


Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child.

<PastedGraphic-1.png>


With best regards,
Samson

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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