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[bioontology-support] Annotator issues

Kuttichi Keloth, Vipina vk396 at njit.edu
Mon Nov 11 09:57:29 PST 2019


Hi Michael,

Thank you for the detailed response. I tried to resolve the first issue
that you mentioned - not properly defining the synonyms.
Now for the concept with id 56265001 (Heart disease) we discussed
previously the attached figure shows the modified details.

I have used http://www.w3.org/2004/02/skos/core#altLabel to define synonyms
and below is the term definition now.

 <!-- http://snomed.info/id/56265001 -->

<owl:Class rdf:about="http://snomed.info/id/56265001">
<rdfs:subClassOf rdf:resource="http://snomed.info/id/301095005"/>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Heart
disease</rdfs:label>
<skos:altLabel xml:lang="en">Morbus cordis</skos:altLabel>
<skos:altLabel xml:lang="en">Cardiopathy</skos:altLabel>
<skos:altLabel xml:lang="en">Disorder of heart</skos:altLabel>
<skos:altLabel xml:lang="en">Cardiac disorder</skos:altLabel>
<skos:altLabel xml:lang="en">Heart disease (disorder)</skos:altLabel>
</owl:Class>

Is it not possible to give multiple values to altLabel? I need to have more
than one synonyms. What should I do to achieve this?

In the attached figure Synonyms property shows only Cardiopathy and not the
other values like Morbus Cordis, Disorder of heart, etc. So I guess
Synonyms is taking only the first value of altLabel.

Thank you.
Vipina

On Wed, Oct 23, 2019 at 3:05 PM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Vipina,
>
> There are two issues at play here. The first is that the ontology does not
> properly define synonyms. The second is the earlier mentioned issue that
> prevents regular Annotator refreshes (
> https://github.com/ncbo/ncbo_annotator/issues/8).
>
> The term “Cardiac disorder” contains multiple entries of "
> http://www.w3.org/2000/01/rdf-schema#label”, which does not translate
> into synonyms. By default, BioPortal uses these properties to define its
> own reserved property called “synonym”. A custom synonym property is
> allowed, but the ontology submitter must specify it on the metadata form
> when uploading the ontology.
>
> http://www.w3.org/2004/02/skos/core#altLabel
> http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
> http://purl.obolibrary.org/obo/synonym
> http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
> http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
> http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
>
> The default “prefLabel" property is set using one these properties (unless
> the user specified a custom one):
>
> http://www.w3.org/2004/02/skos/core#prefLabel
> http://www.w3.org/2000/01/rdf-schema#label
> http://data.bioontology.org/metadata/def/prefLabel
>
> As you can see, the "http://www.w3.org/2000/01/rdf-schema#label” property
> is used to determine a prefLabel for the term. When there are multiple
> entries, BioPortal either picks the English one (if multiple languages are
> used), or the very first one as the de-facto prefLabel.
>
> In your older version of the ontology (v6), the term “Cardiac disorder” is
> defined as:
>
>     <!-- http://snomed.info/id/56265001 -->
>
>     <owl:Class rdf:about="http://snomed.info/id/56265001">
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Heart
> disease</rdfs:label>
>     </owl:Class>
>
> In the latest version, the same term is defined as:
>
>     <!-- http://snomed.info/id/56265001 -->
>
>     <owl:Class rdf:about="http://snomed.info/id/56265001">
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cardiac
> disorder</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string
> ">Cardiopathy</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Cardiopathy,
> NOS</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Disorder
> of heart</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Heart
> disease</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Heart
> disease (disorder)</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Heart
> disease, NOS</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Morbus
> cordis</rdfs:label>
>         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Morbus
> cordis, NOS</rdfs:label>
>     </owl:Class>
>
> Because of the Annotator refresh issue, both, the original prefLabel,
> "Heart disease” and the new prefLabel, “Cardiac disorder” are being stored
> in the Annotator, that’s why you're seeing two annotations in your results.
> However, there are NO matches on synonyms, since none are defined. Note the
> result of this API call:
>
>
> http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F56265001?display=all
> <http://data.bioontology.org/ontologies/CC_SNOMED/classes/http://snomed.info/id/56265001?display=all>
>
> As you can see, the “synonym” property contains an empty array.
>
> I am going to try to refresh our Annotator repository in the upcoming
> days, so that at least for the time being it is synchronized with the
> latest version of CC_SNOMED.
>
> Thanks again for your inquiry.
>
> Michael
>
>
> ----------------------------------------------------
> Michael Dorf
> Chief Software Architect
> The National Center for Biomedical Ontology
> Stanford Biomedical Informatics Research
> mdorf at stanford.edu
> O: 650-723-0357
> M: 650-995-4374
> ----------------------------------------------------
>
>
> On Oct 23, 2019, at 9:40 AM, Kuttichikeloth, Vipina <vk396 at njit.edu>
> wrote:
>
> I am sorry about not explaining it properly.
> I am talking about "Cardiac disorder" and sorry that "24 hour ....." was
> highlighted.
> From the synonyms of Cardiac disorder in the attached figure, you can see
> that "Morbus cordis" and "Cardiopathy" and "Heart disease" are synonyms.
> Now when I give the text "*Cardiac disorder, Heart disease, Morbus
> cordis, Cardiopathy*" to the Annotator,  Cardiac disorder and Heart
> disease are annotated to  "Cardiac disorder" (preferred label in this case)
> as you can see in the second screenshot I attached while  "Morbus cordis
> and Cardiopathy" are not annotated.
>
> On Wed, Oct 23, 2019 at 12:28 PM Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Vipina,
>>
>> Thank you for reaching out. I’ve looked at the term you are referring to,
>> but I am seeing a different picture on my end. None of the synonyms from
>> your screenshot are listed under the term “24 hour diastolic blood pressure
>> (observable entity)”:
>>
>> <Screen Shot 2019-10-23 at 9.17.50 AM.png>
>>
>> These synonyms ARE, however, listed under the term “Cardiac disorder”
>> (see below), so your Annotator results appear to be consistent. I’ve
>> flushed our caches, but it hasn’t changed the structure of the “24 hour….”
>> term.
>>
>> <Screen Shot 2019-10-23 at 9.20.10 AM.png>
>>
>>
>> The REST endpoint results are also consistent with my screenshot above:
>>
>>
>> http://data.bioontology.org/ontologies/CC_SNOMED/classes/http%3A%2F%2Fsnomed.info%2Fid%2F314465004?display=all
>> <http://data.bioontology.org/ontologies/CC_SNOMED/classes/http://snomed.info/id/314465004?display=all>
>>
>> Is it possible that that page is somehow browser-cached on your end?
>>
>> Thanks,
>>
>> Michael
>>
>>
>>
>>
>> On Oct 23, 2019, at 8:55 AM, Kuttichikeloth, Vipina <vk396 at njit.edu>
>> wrote:
>>
>> Hi,
>>
>> I am having an issue trying to annotate synonyms. Some synonyms are
>> getting annotated while some others are not.
>> For example, for the concept "Cardiac disorder" the first image attached
>> shows all the alternate labels for the concept in CC_SNOMED.
>> The second image is the result of the Annotator.
>> I read about sort of a similar issue here
>> https://github.com/ncbo/ncbo_annotator/issues/6 and it was mentioned
>> that it has something to do with the way the ontology is designed.
>>
>> Is this also an issue with the design of the ontology? But then why are
>> some synonyms getting annotated.
>>
>> Thank you,
>> Vipina
>>
>> On Thu, Oct 17, 2019 at 5:21 PM Kuttichikeloth, Vipina <vk396 at njit.edu>
>> wrote:
>>
>>> Thank you so much for your help and explanation.
>>>
>>> ~Vipina
>>>
>>>
>>>
>>> On Thu, Oct 17, 2019 at 5:14 PM Michael Dorf <mdorf at stanford.edu> wrote:
>>>
>>>> Hi Vipina,
>>>>
>>>> I was finally able to identify the issue that was causing the behavior
>>>> you reported. The culprit is an earlier version of CC_SNOMED ontology, in
>>>> which the terms in question contained different labels:
>>>>
>>>> Earlier version (cc_v6.owl):
>>>>
>>>>     <!-- http://snomed.info/id/312523009 -->
>>>>
>>>>     <owl:Class rdf:about="http://snomed.info/id/312523009">
>>>>         <rdfs:subClassOf rdf:resource="http://snomed.info/id/279316009
>>>> "/>
>>>>         <rdfs:label rdf:datatype="
>>>> http://www.w3.org/2001/XMLSchema#string">Left</rdfs:label>
>>>>     </owl:Class>
>>>>
>>>> Latest version:
>>>>
>>>>     <!-- http://snomed.info/id/312523009 -->
>>>>
>>>>     <owl:Class rdf:about="http://snomed.info/id/312523009">
>>>>         <rdfs:subClassOf rdf:resource="http://snomed.info/id/279316009
>>>> "/>
>>>>         <rdfs:label rdf:datatype="
>>>> http://www.w3.org/2001/XMLSchema#string">Left (non-mitral)
>>>> atrioventricular valve structure</rdfs:label>
>>>>         <rdfs:label rdf:datatype="
>>>> http://www.w3.org/2001/XMLSchema#string">Left (non-mitral)
>>>> atrioventricular valve structure (body structure)</rdfs:label>
>>>>     </owl:Class>
>>>>
>>>> The same applies to the other false match, the term with the id "
>>>> http://snomed.info/id/312524003”:
>>>>
>>>> Earlier version (cc_v6.owl):
>>>>
>>>>     <!-- http://snomed.info/id/312524003 -->
>>>>
>>>>     <owl:Class rdf:about="http://snomed.info/id/312524003">
>>>>         <rdfs:subClassOf rdf:resource="http://snomed.info/id/279316009
>>>> "/>
>>>>         <rdfs:label rdf:datatype="
>>>> http://www.w3.org/2001/XMLSchema#string">Right</rdfs:label>
>>>>     </owl:Class>
>>>>
>>>> Latest version:
>>>>
>>>>     <!-- http://snomed.info/id/312524003 -->
>>>>
>>>>     <owl:Class rdf:about="http://snomed.info/id/312524003">
>>>>         <rdfs:subClassOf rdf:resource="http://snomed.info/id/279316009
>>>> "/>
>>>>         <rdfs:label rdf:datatype="
>>>> http://www.w3.org/2001/XMLSchema#string">Right (non-tricuspid)
>>>> atrioventricular valve structure</rdfs:label>
>>>>         <rdfs:label rdf:datatype="
>>>> http://www.w3.org/2001/XMLSchema#string">Right (non-tricuspid)
>>>> atrioventricular valve structure (body structure)</rdfs:label>
>>>>     </owl:Class>
>>>>
>>>> We currently have a limitation in the Annotator that prevents us from
>>>> removing older records on ontology re-processing. So when the pref labels
>>>> got changed, both the old and the new values ended up being stored in the
>>>> Annotator. As a workaround for this specific case, I have removed the old
>>>> values from the Annotator datastore. Your text "left right left” no longer
>>>> returns annotations. I’ve logged this issue in our Github repository:
>>>>
>>>> https://github.com/ncbo/ncbo_annotator/issues/8
>>>>
>>>> Thank you again for your patience.
>>>>
>>>> Michael
>>>>
>>>>
>>>> ----------------------------------------------------
>>>> Michael Dorf
>>>> Chief Software Architect
>>>> The National Center for Biomedical Ontology
>>>> Stanford Biomedical Informatics Research
>>>> mdorf at stanford.edu
>>>> O: 650-723-0357
>>>> M: 650-995-4374
>>>> ----------------------------------------------------
>>>>
>>>> On Oct 15, 2019, at 2:01 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>>>>
>>>> Hi Vipina,
>>>>
>>>> Thanks for your report. I need a bit of time to investigate this.
>>>> Indeed, this does not appear to be an expected behavior. I’ll keep you
>>>> posted as soon as I get to the bottom of it.
>>>>
>>>> Thank you for your patience.
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>> ----------------------------------------------------
>>>> Michael Dorf
>>>> Chief Software Architect
>>>> The National Center for Biomedical Ontology
>>>> Stanford Biomedical Informatics Research
>>>> mdorf at stanford.edu
>>>> O: 650-723-0357
>>>> M: 650-995-4374
>>>> ----------------------------------------------------
>>>>
>>>> On Oct 15, 2019, at 9:12 AM, Kuttichikeloth, Vipina <vk396 at njit.edu>
>>>> wrote:
>>>>
>>>> Thank you for the response. I played a little bit more with the
>>>> ontology to add multiple labels to each concept (synonyms) and then
>>>> annotating some text.
>>>> I noticed that every mention of "left" or "right" in the text is
>>>> getting annotated with a concept as shown in the attached image.
>>>> I gave the text to be annotated as "left right left".
>>>> I thought I understood what you said in your response, but in that case
>>>> (and if I understood it correctly), it shouldn't be matching "left" which
>>>> is a part of the entire label
>>>> "Left (non-mitral) atrioventricular valve structure". Am I missing
>>>> something else here?
>>>>
>>>> Thank you.
>>>> Vipina
>>>>
>>>> On Sat, Oct 5, 2019 at 9:37 PM John Graybeal <jgraybeal at stanford.edu>
>>>> wrote:
>>>>
>>>>> Hi Vipina,
>>>>>
>>>>> Our team discussed your experience Friday and I am offering our latest
>>>>> thoughts for the list, and some of my own observations. (I have the
>>>>> specific example you sent Jennifer but have not copied it here.)
>>>>>
>>>>> When I remove '(finding)' from Jennifer's example, I still see an
>>>>> annotation for CC-SNOMED. It does not matter what boxes are or are not
>>>>> checked, this still works.
>>>>>
>>>>> Now, I see that your class (
>>>>> https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http%3A%2F%2Fsnomed.info%2Fid%2F248714006
>>>>> <https://bioportal.bioontology.org/ontologies/CC_SNOMED?p=classes&conceptid=http://snomed.info/id/248714006>) is
>>>>> currently called simply 'abdominal aortic bruit', and so it seems likely
>>>>> that you have removed the parenthetical expressions from your latest
>>>>> submission. Based on some further examples (using 'abdominal' and
>>>>> 'abdominal aortic'), here is the likely explanation.
>>>>>
>>>>> When Annotator is looking for matches, it is only looking for class
>>>>> names that exactly match a string in the source text. (If Annotator matched
>>>>> any class that *contained* a string in your text, there would be an
>>>>> impossibly large number of matches for any significant text, and the vast
>>>>> majority of them would be incorrect.)
>>>>>
>>>>> So for example, Annotator will not match 'abdominal' to the class
>>>>> 'abdominal aortic bruit', because text describing 'abdominal pain' should
>>>>> not result in a match to that detailed class.
>>>>>
>>>>> So if we reconsider your class name that contains '(finding)', if you
>>>>> remove that from the text that you are trying to annotate, the Annotator
>>>>> will no longer consider it a match (because Annotator will not want to
>>>>> assume the more general phrase 'abdominal aortic bruit' matches the more
>>>>> specific phrase 'abdominal aortic bruit (finding)'). This seems
>>>>> appropriately conservative, considering the above example of matching
>>>>> 'abdominal' to the longer phrase.
>>>>>
>>>>> Checking 'Match partial words' does not have any impact on this
>>>>> behavior; it is simply used to enable a short word to match a longer word,
>>>>> for example, to match suffixed words.
>>>>>
>>>>> On another point, if you compare your results with the matches found
>>>>> in SNOMED-CT, there you will find matches to the shorter strings—but only
>>>>> because SNOMED-CT has those exact shorter strings as classes.
>>>>>
>>>>> This matching behavior is different than searching, which will match
>>>>> any appearance of the string in a class name, but will prioritize more
>>>>> complete matches. This is appropriate also, to let people find classes that
>>>>> may have only some of the entered search string.
>>>>>
>>>>> I hope this explains your experience so far. Pleae feel free to follow
>>>>> up with further questions or concerns.
>>>>>
>>>>> John
>>>>>
>>>>>
>>>>> On Wed, Oct 2, 2019 at 2:31 PM Jennifer Leigh Vendetti <
>>>>> vendetti at stanford.edu> wrote:
>>>>>
>>>>>> Hello Vipina,
>>>>>>
>>>>>> Could you give me a specific example of the text you are entering
>>>>>> where you don’t see results that you think should be present? I looked at
>>>>>> your ontology with the Annotator just now. I entered the text of one of
>>>>>> your class names in the Annotator and selected CC_SNOMED under advanced
>>>>>> options. The Annotator returned results as I would have expected:
>>>>>>
>>>>>>
>>>>>> <Screenshot 2019-10-02 11.27.49.png>
>>>>>>
>>>>>> Kind regards,
>>>>>> Jennifer
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina <vk396 at njit.edu>
>>>>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Recently I uploaded an ontology named Cardiology Component of SNOMED
>>>>>> CT (CC_SNOMED). The visibility is set to private. I can see and browse the
>>>>>> classes on BioPortal.
>>>>>>
>>>>>> I want to annotate some medical text using this ontology that I
>>>>>> created. In the advanced options under "select ontologies", I am able to
>>>>>> select CC_SNOMED but when I click "Get annotations" no results appear. I
>>>>>> have tried putting the concepts that exist in CC_SNOMED in the medical text
>>>>>> still no results. Also, if I select SNOMED CT then the text gets annotated
>>>>>> and all these concepts are shown. Is there anything I am missing and please
>>>>>> let me know why this is not working?
>>>>>>
>>>>>> Thank you.
>>>>>> Vipina
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>>
>>>>>>
>>>>> On Oct 2, 2019, at 11:31 AM, Jennifer Leigh Vendetti <
>>>>> vendetti at stanford.edu> wrote:
>>>>>
>>>>> Hello Vipina,
>>>>>
>>>>> Could you give me a specific example of the text you are entering
>>>>> where you don’t see results that you think should be present? I looked at
>>>>> your ontology with the Annotator just now. I entered the text of one of
>>>>> your class names in the Annotator and selected CC_SNOMED under advanced
>>>>> options. The Annotator returned results as I would have expected:
>>>>>
>>>>>
>>>>> <Screenshot 2019-10-02 11.27.49.png>
>>>>>
>>>>> Kind regards,
>>>>> Jennifer
>>>>>
>>>>>
>>>>>
>>>>> On Oct 2, 2019, at 8:57 AM, Kuttichikeloth, Vipina <vk396 at njit.edu>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Recently I uploaded an ontology named Cardiology Component of SNOMED
>>>>> CT (CC_SNOMED). The visibility is set to private. I can see and browse the
>>>>> classes on BioPortal.
>>>>>
>>>>> I want to annotate some medical text using this ontology that I
>>>>> created. In the advanced options under "select ontologies", I am able to
>>>>> select CC_SNOMED but when I click "Get annotations" no results appear. I
>>>>> have tried putting the concepts that exist in CC_SNOMED in the medical text
>>>>> still no results. Also, if I select SNOMED CT then the text gets annotated
>>>>> and all these concepts are shown. Is there anything I am missing and please
>>>>> let me know why this is not working?
>>>>>
>>>>> Thank you.
>>>>> Vipina
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>
>>>>>
>>>>> ========================
>>>>> John Graybeal
>>>>> Technical Program Manager
>>>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>>>>> Stanford Center for Biomedical Informatics Research
>>>>> 650-736-1632
>>>>>
>>>>>
>>>>> <annotator.png>
>>>>
>>>>
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>>
>>>> <cardiac disorder.png><cardiac_annotated.png>
>>
>>
>>
>
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