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[bioontology-support] OBO upload, class browser issue

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Nov 20 11:03:39 PST 2017


Hi Ben,


On Nov 20, 2017, at 7:32 AM, Benjamin Gyori <benjamin_gyori at hms.harvard.edu<mailto:benjamin_gyori at hms.harvard.edu>> wrote:

Dear BioPortal developers,

I am trying to upload an ontology called Bioentities in OBO format. The ontology contains around ~450 terms, with each term having a (1) name (2) list of synonym strings (3) list of mappings to external ontologies (4) list of isa / partof / inverse_isa / has_part relationships to other terms in the same ontology and also external ontologies.

I have uploaded the OBO file, but found that even after it was parsed and indexed, the "Classes" page returned "Problem retrieving classes". Could you help determine how I need to modify the OBO file to work with the class browser? I am attaching a small sample of the overall ontology for reference. The ontology is uploaded at http://bioportal.bioontology.org/ontologies/BE, but is currently set to private - I can share it if it helps find the issue.


There’s no need to change the visibility from private to public. We have admin privileges / full access to your ontology content.

In order to construct / display a term hierarchy, the BioPortal UI first accesses our REST API’s roots endpoint to retrieve the root-level terms. It appears that the roots endpoint for the OBO file you uploaded today is returning an empty set:

http://data.bioontology.org/ontologies/BE/classes/roots

This is the underlying reason the classes page results in a 404 error. I noticed that all of the terms in your ontology have an isa / subclass relationship to "ONT:PROTEIN-FAMILY”. However, ONT:PROTEIN-FAMILY isn’t explicitly defined in the ontology, nor are there any import statements among the document header tags pointing to the external ontology where it’s defined. Probably BioPortal should be able to infer that ONT:PROTEIN-FAMILY is a root term in your ontology, even though ONT:PROTEIN-FAMILY isn't explicitly defined. I will need to enter an issue in our tracker for this and investigate.

In the mean time, if you have an urgent need to view the classes page in BioPortal, I think you would need to submit a version of your ontology to us where that term is either explicitly defined in the ontology source file, or an import statement is added for the external ontology in which the term is defined. If you decide to go that route, feel free to send something to us privately, and we could test it out in our staging environment first.

Kind regards,
Jennifer

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