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[bioontology-support] Related Synonyms

Trish Whetzel plwhetzel at gmail.com
Mon Sep 16 14:05:13 PDT 2013


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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>
>
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