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] Related Synonyms

Maxwell Neal mneal at
Wed Sep 11 16:22:04 PDT 2013

Hi all,

I was wondering - is it possible to tweak my NCBO Annotator Java client so that it uses the "RELATED SYNONYM" field in addition to the "Synonyms" field when annotating?

For example, I'd like the service to annotate "Ca2+" with CHEBI:29108 (calcium(2+)). 

"Ca2+" is a RELATED SYNONYM for CHEBI:29108, but its not in the list of plain old Synonyms.

I get no annotations for "Ca2+" with my current client parameter settings:

longestOnly = false
wholeWordOnly = true
filterNumber = false
withDefaultStopWords = false
isStopWordsCaseSensitive = false
minTermSize = 2
scored = true
withSynonyms = true
ontologiesToKeepInResult = 1141, 1053, 1007, 1070, 1009
isVirtualOntologyId = true
levelMax = 0
mappingTypes = null

Many thanks for your help!


Maxwell Neal

Post-doctoral researcher
Department of Bioengineering
University of Washington
mneal at

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

More information about the bioontology-support mailing list