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[bioontology-support] Related Synonyms

Ray Fergerson ray.fergerson at
Mon Sep 16 15:08:57 PDT 2013





From: Trish Whetzel [mailto:plwhetzel at] 
Sent: Monday, September 16, 2013 2:05 PM
To: Ray Fergerson
Cc: Maxwell Neal; support at
Subject: Re: [bioontology-support] Related Synonyms


Does the NCBO instance of BioPortal still expand part_of relations from
OBO format ontologies?



On Wed, Sep 11, 2013 at 4:57 PM, Ray Fergerson
<ray.fergerson at> wrote:



Sorry but this isn't possible in the production BioPortal. The annotator
specifically uses preferred name and synonyms for annotation. You can
probably hack a VM version on your own hardware to do this. There is a
process that populates the dictionary used for annotation. Currently this
process pulls out only the name and synonyms. You could hack the code to
pull out values from other properties.




From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of
Maxwell Neal
Sent: Wednesday, September 11, 2013 4:22 PM
To: support at
Subject: [bioontology-support] Related Synonyms


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


"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









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