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[bioontology-support] Why is access to some ontologies restricted
Jennifer Leigh Vendetti
vendetti at stanford.edu
Thu Sep 12 15:17:05 PDT 2019
The data.bioontology.org/submissions<http://data.bioontology.org/submissions> endpoint is undocumented in our public facing REST API documentation  because we don’t recommend its usage. BioPortal has over 1,000 ontologies, some of which have large numbers of submission objects, e.g., the GO ontology is up to 1,469 submissions. The endpoint isn’t performant, and is only used for internal debugging purposes.
To access a complete list of the ontologies in BioPortal, please use the ontologies endpoint: http://data.bioontology.org/ontologies. If you want to retrieve all of the submissions for a particular ontology, you would use the pattern /ontologies/:acronym/submissions, e.g.: http://data.bioontology.org/ontologies/BRO/submissions.
There are some ontologies in BioPortal that have licensing restrictions imposed by the authors / maintainers that disallow downloads of the ontology source files. For example, you can access the classes for the SNOMEDCT ontology using the /classes endpoint (http://data.bioontology.org/ontologies/SNOMEDCT/classes), but the /download endpoint (http://data.bioontology.org/ontologies/SNOMEDCT/download) results in a 403 Forbidden error. There are no properties on a submission object that would allow you to check whether or not it’s downloadable - in these cases you would need to handle the 403 error in your code.
On Sep 12, 2019, at 12:29 PM, Sergiu Dumitriu <sergiu at phenotips.org<mailto:sergiu at phenotips.org>> wrote:
Although they are listed in http://data.bioontology.org/ontologies/ and
http://data.bioontology.org/submissions/, some ontologies return a 403
Frobidden status when trying to access them directly, such as FC, SBRO,
VICRA and I'm sure many others.
- Is there a reason for this denial?
- Is there a way to gain access to them?
- Is there a way to identify which ontologies are accessible from other
resources listing them, such as the list of ontologies or the list of
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