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[bioontology-support] help with GAMUTS ontology

Filice, Ross W Ross.W.Filice at
Tue Mar 6 10:07:41 PST 2018

Thanks John. Is there any way to add to these mappings? For example, while LOOM picked up some of the ORDO mappings we also explicitly included these as “sameAs” mappings. They show up as expected when browsing a class (for example but do not show up under the “Mappings” tab. Is there some other way we should be flagging these?

Also, I might humbly suggest you use case-sensitive string matching with LOOM at least with some ontologies. This appears mostly to be a problem (for us at least) with the Ontology of Genes and Genomes where we get “mappings” like:
coma (like I’m unconscious) -> COMA (some gene)
air (like the stuff we breathe) -> AIR (some gene)
cyst (pocket of fluid) -> cysT (some gene)

thanks much,

From: John Graybeal [mailto:jgraybeal at]
Sent: Monday, March 05, 2018 9:21 PM
To: Filice, Ross W
Cc: support at; Kahn, Charles E
Subject: Re: [bioontology-support] help with GAMUTS ontology

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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