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[bioontology-support] Related Synonyms

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


Yes.

 

Ray

 

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

 

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

Trish 

 

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

Maxwell,

 

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.

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Maxwell Neal
Sent: Wednesday, September 11, 2013 4:22 PM
To: support at bioontology.org
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
(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!

 

M

 

---------------------------------

Maxwell Neal

 

Post-doctoral researcher

Department of Bioengineering

University of Washington

mneal at uw.edu

---------------------------------

 

 

 

 

 

 

 


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