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[bioontology-support] Annotator parameters and documentation

Xin.H hxin87 at gmail.com
Thu Oct 17 12:34:30 PDT 2013


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