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[bioontology-support] getting information

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Jan 14 09:28:49 PST 2022


Hello Elena,

On Jan 14, 2022, at 2:20 AM, Elena Gelain <elena.gelain at meyer.it<mailto:elena.gelain at meyer.it>> wrote:

Dear all,

this is just an explorative email to ask how the portal works.
If I correctly understand the information (BioPortal help) web page, the browsing of the whole repository is free but the use of the ontologies for the mappings is not permitted for the locked or private repositories, such as SNOMED CT. Hence, to use the terminology I should refer to each Organization.


If an ontology is marked as “private” in BioPortal, the content is only visible to those user accounts that have been granted access to the ontology entry.

There are other ontologies like SNOMEDCT that are marked as “public”, but licensing restrictions prohibit us from providing the ontology source files for download by end users. In other words, there are no “Downloads” columns in the “Submissions” tables on the ontology summary pages.

However, that doesn’t mean that you can’t browse the ontology content for SNOMEDCT in BioPortal. For example, you can see the list of ontologies that have mappings to SNOMEDCT:

https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=mappings

… and, you can see mappings between individual classes, e.g.:

https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F362981000#mappings<https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http://purl.bioontology.org/ontology/SNOMEDCT/362981000#mappings>

The mappings are also available via the BioPortal REST API, e.g.:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F410607006/mappings<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/410607006/mappings>

Kind regards,
Jennifer

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