Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from kkochut

John Graybeal jgraybeal at stanford.edu
Mon Feb 10 15:40:58 PST 2020


hi Krys,

As we discussed offline, we know we can't upload ontologies above a certain size (not yet quantified, but for sure above 2 GB).

Let's continue to discuss a strategy for troubleshooting this off-line—I think a test with BiblioPortal may be useful.

John

On Feb 7, 2020, at 12:51 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: kkochut

Email: kkochut at uga.edu<mailto:kkochut at uga.edu>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Faccount

Feedback:

Hello,

I created a summary page for a new ontology submission without any problems. It is a Protein Kinase Ontology (PROKINO). However, I am having problems uploading the OWL file. The ontology includes many individuals and the serialized OWL file is quite large (about 2.9 GB).

After failing a couple of times while using the Web browser-based submission form, I tried a command line on a Linux system using the cURL command. It also failed with the following result:

413 Request Entity Too Large

413 Request Entity Too Large

________________________________
nginx/1.16.1


I was executing a POST request (using curl) on the resource /ontologies/PROKINO/submissions, using the -T option and I specified the "chunked" encoding. However, the upload failed after uploading nearly 37% of the file.
Is there an alternative way to upload this ontology?
Thank you.

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200210/a75928ee/attachment.html>


More information about the bioontology-support mailing list