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[bioontology-support] Annotator returns no hits for sequence ontology terms - can you help?

Trish Whetzel whetzel at stanford.edu
Wed Jun 9 09:46:10 PDT 2010


Hi Helen,

BioPortal previously contained two representations of the sequence  
ontology named the Sequence Ontology and Sequence types and features.  
Per request of the ontology developer, the Sequence Ontology was  
removed from BioPortal and the corresponding update is needed for the  
Annotator in order to remove the Sequence Ontology from the list of  
ontologies for use with the Annotator.

Using the terms allele and diplotype do result in hits from the  
Annotator using the ontology Sequence types and features. However, I  
did notice that this ontology contains many term names that include an  
underscore, e.g. PCR_product (SO:0000006) and therefore to get hits  
for these terms the input would also need to contain underscores.

Trish


On Jun 9, 2010, at 9:03 AM, Helen Johnson wrote:

> Clement, Trish:
>
> Were you able to check the backend of the Annotator
> to see if the Sequence Ontology is in there,
> and further track down why the Annotator does not return hits to  
> this ontology?
>
> -helen
>
> --
> Helen L. Johnson
> Sr. Professional Research Assistant
> Center for Computational Pharmacology,
> University of Colorado Denver, Health Sciences Center
> email:   helen.linguist at gmail.com
>
>
> On Fri, May 28, 2010 at 1:27 PM, Clement Marie Jonquet <jonquet at stanford.edu 
> > wrote:
> Dear Helen,
> I have been looking into your issue.
>
> > In both these attempts the Annotator returned no hits.
>
> Your queries seems ok. I have replicated them and I obtain no  
> annotation
> also.
> I think there is something wrong with this ontology (i.e., Sequence
> ontology), because it is present in the Annotator back end but it's  
> not in
> BP anymore:
> http://bioportal.bioontology.org/virtual/1045
> Trish do you know about this?
>
> I have will have to check the backend DB of the Annotator and tell you
> more.
>
> >> not relevant to my current issues, but what's the difference  
> between
> >> the two websites?
>
> The 2 sites are both client of the web service.
> http://rest.bioontology.org/test_oba.html is a basic HTML client.
> http://bioportal.bioontology.org/annotator is a fancy UI client  
> embedded
> in BioPortal.
> Both POST a message goes to the same web service endpoint at:
> http://rest.bioontology.org/obs/annotator
>
> Hope it helps .
> Clement
>
>
> -----Original Message-----
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Thursday, May 27, 2010 7:55 PM
> To: Nigam Shah; Helen Johnson
> Cc: Cesar Mejia-Munoz; Clement Jonquet; support
> Subject: Re: Annotator returns no hits for sequence ontology terms -  
> can
> you help?
>
> Hi Helen,
>
> I'll be talking with Clement a bit later today and will discuss this
> issue.
>
> Trish
>
>
> On May 27, 2010, at 10:19 AM, Nigam Shah wrote:
>
> > Hi Helen
> >
> > I am traveling on the interview trail and can't troubleshoot right
> > now. I am ccing Clement and Trish who might be able to help. I can
> > look into this next week.
> >
> > Nigam.
> >
> > On May 27, 2010, at 9:27 AM, Helen Johnson
> > <helen.linguist at gmail.com> wrote:
> >
> >> Hi Nigam,
> >>
> >> I am trying to use the NCBO Annotator to recognize
> >> Sequence Ontology (localOntologyID=36782, virtualOntologyID=1045)
> >> terms in text.
> >>
> >> When i ran my experiment on a full text document in our local
> >> application, i found that the Annotator had returned no results.
> >>
> >> I next tried using the web interface
> >> (there are now two urls to the Annotator? i tried both:
> >> http://rest.bioontology.org/test_oba.html
> >> http://bioportal.bioontology.org/annotator#
> >> ), inputting a simple sentence with the terms "allele" (SO:
> >> SO:0001023) and "diplotype" (SO:0001028).
> >> Params: all default, except in "ontologiesToKeepInResults" i input
> >> 36782, and chose "false" for isVirtualOntologyID.
> >> i also tried
> >> Params, all default, except in "ontologiesToKeepInResults" i input
> >> 1045, and chose "true" for isVirtualOntologyID.
> >>
> >> In both these attempts the Annotator returned no hits.
> >>
> >> However, doing an online test with a sentence that contains the
> >> word "cell",
> >> using 42165 for the ontologiesToKeepInResults in one run, and using
> >> the virtualOntologyID 1006 in another run,
> >> both runs return hits to Cell Type Ontology terms.
> >> (both websites were successful, too).
> >>
> >> Do you know:
> >> am i doing something wrong?
> >> or is there something that needs be fixed on the Annotator end?
> >>
> >> not relevant to my current issues, but what's the difference  
> between
> >> the two websites?
> >>
> >> Thanks for helping me out with this.
> >> -helen
> >>
> >>
> >> --
> >> Helen L. Johnson
> >> Sr. Professional Research Assistant
> >> Center for Computational Pharmacology,
> >> University of Colorado Denver, Health Sciences Center
> >> email:   helen.linguist at gmail.com
>
>

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