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[bioontology-support] [BioPortal] Feedback from KRISHNA JULURU

Clement Jonquet jonquet at lirmm.fr
Fri Mar 22 02:43:50 PDT 2019


Hi Krishna, 
CC: the NCIt folks

@Misha, Jennifer: we need to document this on the wiki as the questions comes often. I tried to look up for an already written response in the mailing list archive but with no success. 

Another way to explain is: 
- the filtering by semantic types is a feature that have been developed for terminologies being imported in BioPortal from the UMLS Metathesaurus. Basically because this information is added to concepts by NLM’s experts when a « source » is added to UMLS . 
- thus the Annotator’s filtering by semantic type works ONLY for terminologies in BioPortal extracted from UMLS with the umls2rdf tool (https://github.com/ncbo/umls2rdf) OR for any ontologies that would use the same exact property than the umls2rdf tool generates and that is expected by BioPortal
- thus an ontology (like NCIt) which happened to be included in UMLS (so enriched somehow with semantic types) BUT not leaded in BioPortal from UMLS (in the case directly from an OWL file that NCI generates) will not benefit from the feature. 

One way to fix this would be to : 
- ask the NCIt folks to capture the TUI property the way BioPortal can handle it
- have BioPortal capture semantic type property from multiple possible properties and user will specify at loading time (like for labels or definition)

We have worked on this issue in the SIFR BioPortal to « modify » ourselves the French terminology files loaded in the portal and without proper semantic type declaration. See: https://hal-lirmm.ccsd.cnrs.fr/lirmm-01605517v2 <https://hal-lirmm.ccsd.cnrs.fr/lirmm-01605517v2> 
AFAIK, NCBO never modifies the original files …

Sorry if explanation is a bit quick… I am short on time… 
Could come vback to the discussion next week if needed. 

Best regards
Clement 

-------------------------------------------------------------------------------------------
Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier (LIRMM)
-------------------------------------------------------------------------------------------

> Le 21 mars 2019 à 19:56, Michael Dorf <mdorf at stanford.edu> a écrit :
> 
> Hi Krishna,
> 
> Thank you for contacting us. Our logic for annotating semantic types looks for a property of the class that contains the semantic type code (T191 in this case). Once found, the value is used to set a custom top-level property of the class called “semanticType”. The value of the “semanticType” property is then used when we process classes for the Annotator repository. Looking at the class you provided, there is no property in the class that references the semantic type code. There is one that states the name of the semantic type, “Neoplastic Process”, but that isn’t sufficient for us to classify this as a class belonging to the T191 semantic type:
> 
> http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C9245?display=all&no_links=true&no_context=true <http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C9245?display=all&no_links=true&no_context=true>
> 
> Here is a sample of a different class from SNOMEDCT that does set the semantic type property and thus appears in your annotation query (if you remove the NCIT ontology filter):
> 
> http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F68453008?display=all&no_links=true&no_context=true <http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F68453008?display=all&no_links=true&no_context=true>
> 
> This logic probably could be improved to better recognize the semantic type affiliation, but at this point our small team of two simply doesn’t have the bandwidth to look into this matter more in-depth. I’ve created a bug in our Github issue tracking system that will track this report. Hopefully, we’ll be able to address it in the near future:
> 
> https://github.com/ncbo/ncbo_annotator/issues/5 <https://github.com/ncbo/ncbo_annotator/issues/5>
> 
> Thanks again for your report.
> 
> Michael
> 
> 
> 
>> On Mar 20, 2019, at 7:24 PM, support at bioontology.org <mailto:support at bioontology.org> wrote:
>> 
>> Name: KRISHNA JULURU
>> 
>> Email: juluruk at mskcc.org <mailto:juluruk at mskcc.org>
>> Location: https%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fannotator
>> 
>> 
>> Feedback:
>> 
>> I have been experimenting with the annotator found here: 
>> https://bioportal.bioontology.org/annotator <https://bioportal.bioontology.org/annotator>
>> Settings: 
>> Text entered into annotator: invasive mammary carcinoma 
>> Select ontology: National Cancer Institute Thesaurus (NCIT) 
>> Select UMLS semantic type: neoplastic process
>> 
>> Result: no annotations found
>> 
>> I am not understanding why the result is 'No annotations found'. The term 'invasive mammary carcinoma' does exist in the NCIT, with semantic_type 'Neoplastic process'.
>> 
>> https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C9245 <https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C9245>
>> Can someone please explain what I might be doing wrong?
>> 
>> Thank you.
>> 
>> 
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