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[bioontology-support] OBO upload, class browser issue

John Graybeal jgraybeal at stanford.edu
Wed Nov 22 18:54:11 PST 2017


The AgroPortal group, led by Clement Jonquet, has customized a virtual appliance instance of BioPortal to handle external mappings. Unfortunately, it appears to incur a significant performance hit, that has prevented us from doing the same with BioPortal, at least without a lot of 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.

When you say 'outside ontologies', do you mean outside OBO or outside BioPortal? We should be able to process mappings to other terms in BioPortal (NCIT for example).

With regard to OBO references to terms of ontologies in BioPortal, I am not sure how BioPortal processes the CURIE format for those mappings. (Perhaps a full IRI would be better?)  I'll see if we can dig up any additional answers in that regard. (There might be some information in the OBO support lists also.)

John


On Nov 22, 2017, at 12:52 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Ben,


On Nov 20, 2017, at 8:19 PM, Benjamin Gyori <benjamin_gyori at hms.harvard.edu<mailto:benjamin_gyori at hms.harvard.edu>> wrote:

I modified the root node to be part of the BE ontology, and now the classes are loaded correctly.


OK, good to hear.


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: Could you help figure out what I need to change to make visualization work?


The visualization software you’re referring to is 3rd party, developed by the University of Victoria for BioPortal a few years ago. There’s a known issue that’s cropped up where the software doesn’t work over HTTPS [1]. As of yet, we haven’t been able to secure the resources to take over development and maintenance of their code. There’s a simple workaround in the mean time though. If you modify the URL in the address bar to use HTTP, you’ll be able to see the visualizations:


<Screenshot 2017-11-22 12.42.07.png>




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.

If I understood your question correctly, we don’t offer this kind of functionality. The mappings we generate are between ontology classes from the set of ontologies that exist in BioPortal. I did a quick search and the ontologies you mentioned above don’t appear to have been uploaded into our application, although they could be if they are published in a format we can handle.

I vaguely recall a research group that may have customized a virtual appliance instance of BioPortal to handle external mappings. Let me see if I can track that information down.

Kind regards,
Jennifer

[1] https://github.com/ncbo/biomixer/issues/2


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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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