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

Michael Dorf mdorf at stanford.edu
Thu Mar 21 11:56:31 PDT 2019


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

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

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

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

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

Can someone please explain what I might be doing wrong?

Thank you.

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