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[bioontology-support] Annotator parameters and documentation

Ray Fergerson ray.fergerson at
Fri Nov 1 13:36:19 PDT 2013

This works now (multiple stop words) in yesterday's release.




From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of Xin.H
Sent: Thursday, October 17, 2013 12:35 PM
To: Trish Whetzel
Cc: BioPortal User Support
Subject: Re: [bioontology-support] Annotator parameters and documentation




I got a question about stop_words hope you can help me.


I alway get very short,general terms such as 'SYNDROME' and 'DISEASE' when
doing concept recognizing. For example, 

'ALLAN-HERNDON-DUDLEY SYNDROME' gives me two matches(using Human disease
ontology) but I want to filter out the first one:



Is using stop_words the right way of doing this?


I try to add stop_words to the parameter but, when I use only one stop
word, it work perfectly. When using more than one, it didn't work as

When using only 'disease' as stop word, it filter out the first one, but
when using 'disease,syndrome' as stop_words, it gave me back the two


Could you please help me with this?


Many thanks,



On 17 October 2013 07:53, Trish Whetzel <whetzel at> wrote:

Thanks for the updates. Does the documentation indicate which parameters
are required in the new API? Also, the link for the documentation at the
bottom of the Annotator page links to "stagedata".




On Oct 16, 2013, at 10:29 AM, Paul R Alexander <palexander at>

It does use a default list. We will add these to the documentation.


The Annotator was returning mappings by default due to a bug that has been
fixed. The mappings (when included) come from the entire mapping data set.
In the future there will be options to filter based on source.





On Oct 14, 2013, at 10:53 AM, Trish Whetzel <whetzel at> wrote:

With the new API release, does the Annotator still use a default list of
stop words? I didn't notice these documented here:  However, for the
previous API version a default list of stop words could be included and
these were accessed with the call:
<> <APIKey>


Also, the BioPortal Annotator Web page returns results from term mappings
without selecting a mapping parameter. What is the source of the mappings
the Annotator Web service is using when called from the BioPortal
Annotator Web page? I didn't see information on the mappings here: and links
from here to the "REST API documentation" point to documentation for the
previous API.


Thanks for the help, 




DKnet Project Lead

Ph: (858) 255-0478


University of California, San Diego

9500 Gilman Drive, M/C 0608

La Jolla, CA 92093-0446



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