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[bioontology-support] OBO upload, class browser issue

Benjamin Gyori benjamin_gyori at hms.harvard.edu
Mon Nov 20 20:19:55 PST 2017


Hi Jennifer,

Thank you, that's really helpful! I modified the root node to be part of
the BE ontology, and now the classes are loaded correctly. I also really
like the visualization on some of the other ontologies and would like to
make it work for this one. But for some reason I get this blank view when I
click on the Visualization tab:
[image: Inline image 1]
Could you help figure out what I need to change to make visualization work?

Another question I had is about mapping to outside ontologies. In this
ontology xrefs, inverse_is_a and has_part relationships often link to
outside ontologies such as HGNC, UniProt, InterPro, Pfam, Reactome, etc.
What is the preferred way to add links to such outside ontologies in the
OBO file I upload? Currently, I encode them as, for instance "has_part:
HGNC:PRKAA1" and "xref: NCIT:C94701", but it would be nice if these could
be linked out to the given outside resources via the web interface.

Thank you again for your help!

Best,
Ben

On Mon, Nov 20, 2017 at 2:03 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Ben,
>
>
> On Nov 20, 2017, at 7:32 AM, Benjamin Gyori <benjamin_gyori at hms.harvard.ed
> u> 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.bioontolog
> y.org/ontologies/BE
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioportal.bioontology.org_ontologies_BE&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=ix4fLnHrlpV6PLWEgZQBUFTXOiAxDUULFR7mFwfMybU&m=7pTgI3Cg7CSmF0ySLrQpJmaS69W8XcIPkIKthgrcypo&s=XphzNGPyzCDZKwW5OjMqs54jiJh_A-iINam9RwvLK0Y&e=>,
> 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
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_ontologies_BE_classes_roots&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=ix4fLnHrlpV6PLWEgZQBUFTXOiAxDUULFR7mFwfMybU&m=7pTgI3Cg7CSmF0ySLrQpJmaS69W8XcIPkIKthgrcypo&s=6y0988TqAoLirDVYydol3UynCYMYbNVI6z7yYxZcnGc&e=>
>
> 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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