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

Helen Johnson helen.linguist at gmail.com
Thu Jun 10 14:56:00 PDT 2010


Thank you for your answer.
Let me see if i understand this correctly then:
(by the way - if i should be posting this to the developers list, please let
me know. I've just signed up... i think my memebership approval came
through.)

Instead of using the localOntologyID 36782 that corresponds to the "Sequnce
Ontology" that i was using before,
i need to be using the localOntologyID 42756, which corresponds to the
"Sequence Types and Features" ontology.
The reason for this is that the Sequence Ontology localOntologyID 36782 in
the list of available ontologies to chose from when using the Annotator
was in fact an artifact from when that ontology existed in BioPortal. But it
does not exist there any longer and the ID is invalid. cool.

Question: do you know if the contents of these two ontologies -
the Sequence Ontology localOntologyID 36782 & the Sequence Types and
Features ontology localOntologyID 42516 - cover exactly the same terms?
I tried browsing around at the SO site to find the answer to this, and what
i find there is the use of both titles to describe the resource.
Naively i will at present assume that those resources are in fact covering
the same semantic space until i can figure out otherwise.

Next Question: i tried using both the localOntologyID 42756 and the
virtualOntologyID 1109,
and i am still not getting results for the single world "allele" typed into
the web interface at http://rest.bioontology.org/test_oba.html from the
Sequence types & features ont.
What ontology ID are you using to get results?
What ontology is it matching to?
When i do not restrict the return results to just the Seq types & features,
i get 7 hits back via mgrep, (see attached saved results, html file),
one of which has a very similar LOOKING id (SO:SO_0001023) but which is fact
from a very different ontology named Suggested Ontology for
Pharmacogenomics.

Next, to address the issue of the Sequence Types and Features Ontology
multiword terms containing underscores:
We are currently experimenting with the Annotator to find the Annotator
parameter values that garner the best results on a set of full text
documents.
We are doing this on an ontology-by-ontology basis.
So to be clear, we send one sentence of input at a time to the Annotator,
and we set the Annotator parameter "ontologiesToKeepInResults" to limit the
results to just the ontology we care about - in this case the Sequence types
and features Ontology.

Question: If the ontology's multiword terms are represented with underscores
instead of spaces,
what would we need to do to get a match on a term from our text?
Does the entire sentence need to be sent in with underscores replacing any
whitespace?
By removing white-space word boundaries in this way, would the Annotator be
able to find matches at all?
I assume to find anything, we would have to set the parameter
"wholeWordOnly" to false to get this work,
which would then likely result in a higher false positive hit rate as well?

Next Question:
Assuming this method of sub-ing "_" for " " works to match Seq. terms &
features terms,
what if we are not in experimentation mode anymore and want to use the
Annotator in a real-time situation?
That is, we don't want to limit the return results to just the Sequence
Types and Features,
but rather we want to get matches to any ontologies?
Do we need to send in two queries for each chunk of text we want to search:
one with underscores and one without?
This seems like twice the work it should take and very cumbersome.

Am i missing something here?

Thank you,
-helen johnson






--
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 Wed, Jun 9, 2010 at 10:46 AM, Trish Whetzel <whetzel at stanford.edu> wrote:

> 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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