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[bioontology-support] Annotator parameters and documentation

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


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

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] 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

 

Hi,

 

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:

DOID:225       SYNDROME

DOID:0050631           ALLAN-HERNDON-DUDLEY SYNDROME

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
expect. 

http://data.bioontology.org/annotator?
<http://data.bioontology.org/annotator?&ontologies=DOID&stop_words=disease
,syndrome&text=ALLAN-HERNDON-DUDLEY+SYNDROME>
&ontologies=DOID&stop_words=disease,syndrome&text=ALLAN-HERNDON-DUDLEY+SYN
DROME

http://data.bioontology.org/annotator?
<http://data.bioontology.org/annotator?&ontologies=DOID&stop_words=disease
,syndrome&text=ALLAN-HERNDON-DUDLEY+SYNDROME>
&ontologies=DOID&stop_words=syndrome&text=ALLAN-HERNDON-DUDLEY+SYNDROME

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
terms.

 

Could you please help me with this?

 

Many thanks,

Xin

 

On 17 October 2013 07:53, Trish Whetzel <whetzel at ucsd.edu> 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".

 

Trish 



 

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





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.

 

Paul

 

 

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





With the new API release, does the Annotator still use a default list of
stop words? I didn't notice these documented here:
http://data.bioontology.org/documentation#nav_annotator  However, for the
previous API version a default list of stop words could be included and
these were accessed with the call:
http://rest.bioontology.org/obs/stopwords?apikey=
<http://rest.bioontology.org/obs/stopwords?apikey=%3CAPIKey%3E> <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:
http://bioportal.bioontology.org/help?pop=true#Annotator_Tab and links
from here to the "REST API documentation" point to documentation for the
previous API.

 

Thanks for the help, 

Trish 

 

 

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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