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[bioontology-support] help with GAMUTS ontology

John Graybeal jgraybeal at
Mon Mar 5 18:21:06 PST 2018

On Mar 5, 2018, at 8:19 AM, Filice, Ross W <Ross.W.Filice at<mailto:Ross.W.Filice at>> wrote:

2) Under “mappings” for GAMUTS it lists three mappings that we did not intend to include – these look like they were auto-populated using case-insensitive string matching. Can we flag something to exclude these mappings? They often are nonsensical.

If you are referring to the syntactic mappings that BioPortal generates (identified as LOOM in the table of mappings for an ontology), they are auto-populated using string matching, and they are often nonsensical (but mostly find useful connections).

This is a well-known result of syntactic mapping services and of BioPortal's automated mapping service, and there is no way (that I know of) for them to be flagged and omitted. Users of BioPortal are cautioned to use those mappings only after taking into account the fundamental limitation of the algorithm.


John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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