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[bioontology-support] Ontology Set Up

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Jan 19 11:39:55 PST 2018


Hello Abbie,


On Jan 19, 2018, at 11:23 AM, Ward, Abigail <Abigail_Ward at DFCI.HARVARD.EDU<mailto:Abigail_Ward at DFCI.HARVARD.EDU>> wrote:

Hello!

My name is Abbie Ward and I am one of the research coordinators at Dana-Farber.

For one of our RedCap projects, we would like to utilize the ICD-O ontology set. Our RedCap team advised that I registered for BioPortal, and created an ontology following the instructions. The page for it can be found here:

http://bioportal.bioontology.org/ontologies/ICD-O-3_1

It does not appear that the ontology is ready to be used. What additional steps should I take to ensure that we can use this in our database relatively soon?


I looked at the ontology submission you created in BioPortal. It appears that you specified the ontology should be loaded by our system from the following URL:

http://codes.iarc.fr/codegroup/2

This URL points to an HTML page, rather than an ontology source file. We handle ontologies in OWL, OBO, and SKOS formats. A typical URL for loading an ontology includes the exact path to the ontology source file, including the file name itself, e.g.:

http://www.example.com/my_ontology.owl

It’s unclear to me from looking at their site if they provide their ontology in any of the formats BioPortal is able to load. If you’re able to locate something in one of the above mentioned formats, we could further assist you in trying to get it into BioPortal.


Also, as this is a very well established ontology, is there somewhere else that it is located?


I don’t know of anything offhand, but perhaps other subscribed to this support list know more?

Kind regards,
Jennifer



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