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[bioontology-support] [BioPortal] Feedback from ORDO_Orphanet

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Jul 16 16:09:49 PDT 2018


Hello Marc,


On Jul 16, 2018, at 7:11 AM, Marc Hanauer <marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>> wrote:


Dear John,

Thanks for your reply.

Well the sequence is quiet simple :

Going to bioportal, login/password entered then error message.

I still have access to the account information but can't reach ORDO page (and yes, we would like to edit the ontology information).

I noticed in a screen shot you provided that you’ve configured BioPortal to use a custom ontology set. I tested the steps you provided using a custom ontology set, and I’m now able to reproduce the 500 error.

This issue was reported by another user and recorded in our issue tracker (https://github.com/ncbo/bioportal_web_ui/issues/36). In short, there’s a bug in the BioPortal software that prevents the use of custom ontology sets for ontologies that have views. ORDO has a view attached called "Orphanet Rare Diseases Ontology in OBO”. I will add more information to the issue report, including where exactly the code is failing and associated error messages.

Apologies, but until this issue is fixed and released to our production system, you’ll need to remove your custom ontology set in order to see the ORDO page. You can do that by:

1). Navigating to your account settings page in BioPortal.
2). At the bottom of the account settings page in the “Custom Ontology Set” section, click the “select ontologies” link.
3). Under the “Select Custom Ontologies” text box, click the “clear selection” link.
4). Click the “Save Custom Ontologies” button.

You should then see a message at the top of the page that reads “Custom Ontologies were cleared”. You should also then be able to navigate to the ORDO summary page and make your desired edits.


I've tried with both Firefox and Chrome. At home as well with a different computer and network.

By the way, we've updated our ontology on our own server this friday (as usual, twice a year). The file was correctly processed by EBI OLS tool but not correctly by bioportal: "RDF error”.

I manually reprocessed your ontology in BioPortal. Version 2.6 is now fully parsed and available:

https://bioportal.bioontology.org/ontologies/ORDO?p=summary


[cid:86D2606C-4B3E-4FA7-AD83-AB0FE4624162 at stanford.edu]


I looked at the log files for the initial attempt to process 2.6. It appears that our system was under heavy load and there were issues writing the data to our backend triplestore. Apologies for that inconvenience.


We've already experienced parser issues with bioportal on some previous version. Seems to be a similar situation again.

There was an issue with version 2.4 where the 3rd party library we use for parsing ontologies (OWL API) was generating blank node identifiers with illegal characters. Details were recorded in our GitHub issue tracker:

https://github.com/ncbo/bioportal-project/issues/31

The OWL API developers fixed the issue with blank node identifiers, as detailed in their issue tracker:

https://github.com/owlcs/owlapi/issues/689

I haven’t seen a reoccurrence of this particular issue since those fixes were incorporated into our system.

Kind regards,
Jennifer



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