Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] preventing wrong mappings

John Graybeal jgraybeal at
Fri Feb 5 19:25:30 PST 2021


That's a great idea!  But no, unfortunately the automated mappings are pretty simple-minded, without any particular augmentation. While we find the mappings are about 85% valid, it is understood by most who use them that they are more in the way of discovery tools, not so much modeling tools. (The mappings created in this way are noted as LOOM mappings in the UI and the API, so they can be identified.)

It is of course still useful information to signal readers and machines that any similarity mappings should be ignored for those relations, and maybe we could pick upon it when we find resources to improve the mappings algorithm. It is not a perfect solution however; there will be cases where two classes should not be mapped as being similar, but in fact their may be some instances that could belong to both classes. Another challenge is that our automated mappings are done across ontologies (not within ontologies, to my knowledge); and you would have to update your disjoint statements regularly to reflect incorrect mappings to newly added ontology terms in BioPortal.


On Feb 5, 2021, at 1:57 AM, Görzig, Heike <heike.goerzig at<mailto:heike.goerzig at>> wrote:

Dear bioontology Team,
we are creating an ontology we are planning to upload to the bioportal.
As the mapping is done automatically on labels and maybe the
description, there might be created some false mappings.
We would like to prevent this. Would owl:disjointWith along a related
ontologie be an option?


Heike Görzig <heike.goerzig at<mailto:heike.goerzig at>>
Helmholtz-Zentrum Berlin für Materialien und Energie (HZB)
Albert-Einstein-Str. 15, 12489 Berlin
Tel.: +49 30 8062 42683
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list