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

juluruk at mskcc.org juluruk at mskcc.org
Thu Mar 21 12:09:02 PDT 2019


Hi Michael,

Thanks for the quick reply. Unfortunately, I’m not understanding the explanation (probably because I’m still a novice in this tool).

I have an account on the bioportal site, and I’ve logged in. However, when I follow the links below, I’m getting an error message:

{
·         "status": 401,
·         "error": "You must provide an API Key either using the query-string parameter `apikey` or the `Authorization` header: `Authorization: apikey token=my_apikey`. Your API Key can be obtained by logging in at bioportal.bioontology.org/account"
}

Something I’m doing wrong?

Thanks
Krishna


From: Michael Dorf <mdorf at stanford.edu>
Date: Thursday, March 21, 2019 at 11:56 AM
To: "support at bioontology.org" <support at bioontology.org>
Cc: "Juluru, Krishna/Radiology" <juluruk at mskcc.org>
Subject: [EXTERNAL] Re: [bioontology-support] [BioPortal] Feedback from KRISHNA JULURU

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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