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[bioontology-support] [BioPortal] Feedback from Nedim Durmus

Durmus, Nedim Nedim.Durmus at nyumc.org
Thu Mar 15 11:14:50 PDT 2018


Yes, Jennifer that is the ontology I want. Thank you very much for your valuable information. I will try to convert csv file to that formats. If I can, I will let you know


Best


Nedim


________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Wednesday, March 14, 2018 2:50 PM
To: NCBO User Support
Cc: Durmus, Nedim
Subject: Re: [bioontology-support] [BioPortal] Feedback from Nedim Durmus

Hello Nedim,

Are you referring to this ontology:

http://www.who.int/classifications/icd/adaptations/oncology/en/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.who.int_classifications_icd_adaptations_oncology_en_&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=wXO704yhA1hFGbS2NYYaxvdsCN_fKvBJ0t7ZQCYdkRs&m=ZHiunZlrcAdrzdZXGoBHWRVMwn8lVZt5sPEMKdocDlk&s=mNti3YiSR6foSs4ogL4g7otnkSuDbFYAm_XqV7Orixk&e=>

?

If so, we've had a prior request to upload it to BioPortal. We were unable to do so because it doesn't appear that they publish it in any format that BioPortal handles. BioPortal consumes ontologies in OWL, OBO, or SKOS format. According to the above web page, the only format available is CSV database files. If you're aware of a version of the ontology in a format that BioPortal accepts, we'd be happy to help you try and get it submitted.

Kind regards,
Jennifer



On Mar 9, 2018, at 11:35 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Nedim Durmus

Email: nedim.durmus at nyumc.org<mailto:nedim.durmus at nyumc.org>

Location: http%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=wXO704yhA1hFGbS2NYYaxvdsCN_fKvBJ0t7ZQCYdkRs&m=ZHiunZlrcAdrzdZXGoBHWRVMwn8lVZt5sPEMKdocDlk&s=sQhJaz7B81vgzVvQ3jsqS1H3yjvqotn2N1vsveYf1hY&e=>%2F

Feedback:

Hi,
I am a professional research scientist at New York University. We are now trying to create a database for cancer registry in REDCap. First of all, I want to thank you for this excellent software. It is very useful, wonderful to create databases and also very easy. Thank you very very much for making such a software.

In our database, we want to add a field fro ICD-O-3 codes (International Classification of Diseases for Oncology) which is the third edition of this classification published by World Health Organization. But in your biomedical ontology, this classification does not exist. Can I add this classification to the ontology list or can you add this to the list?

I think it will also be very helpful to the other people because it is mostly used in cancer research. If you want I have the excel list of this ontology. I am attaching the excel file that you can have a look.

Best

Nedim Durmus

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