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[bioontology-support] help with GAMUTS ontology

Filice, Ross W Ross.W.Filice at
Mon Mar 5 08:19:02 PST 2018

Hi - NCBO could you please help? I don't think we received a response (though I may have missed it).
Thanks much,

From: Filice, Ross W
Sent: Thursday, February 22, 2018 2:47 PM
To: support at
Cc: 'Kahn, Charles E'
Subject: help with GAMUTS ontology

Hi - we are having a little trouble with our new, now public, ontology GAMUTS. We've uploaded the ontology in OWL format including mappings to the Orphanet Rare Disease Ontology (ORDO) and it successfully parses, we can annotate text using the web GUI successfully, but we are having several problems:

1) When we try to just browse the ontology, or if we annotate something and try to click through to the matching entity, we get error messages. If we browse other ontologies everything seems to work ok - and I am fairly sure this used to work ok. This error occurs whether I'm logged in as the owner or anonymously. If I use the API I can find all of the annotation data, relationships, ORDO mappings, etc - just seems to be in the web browser version.

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.

3) We also included mappings to ORDO entities using the owl#sameAs property - again, this seems to show up properly when using the API but is not reflected in the Mappings tab. Should we be specifying these mappings in a different way?

Thanks much for your help.

  Ross W. Filice, M.D.
  Associate Professor and Chief, Imaging Informatics
  Department of Radiology, MedStar Georgetown University Hospital
  Chief, Imaging Informatics
  MedStar Medical Group Radiology
  Clinical Informatics Scientist
  National Center for Human Factors in Healthcare, MedStar Institute for Innovation

  3800 Reservoir Road NW, CG 201
  Washington DC, 20007
  202-444-3450<tel:202-444-3450> PHONE
  202-444-4899<tel:202-444-4899> FAX
  ross.w.filice at<mailto:ross.w.filice at>
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