[bioontology-support] [BioPortal] Feedback from kkochut

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[bioontology-support] [BioPortal] Feedback from kkochut

support

Name: kkochut

Email: [hidden email]

Location: https%3A%2F%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.


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Re: [bioontology-support] [BioPortal] Feedback from kkochut

John Graybeal-2
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, [hidden email] wrote:

Name: kkochut

[hidden email]

Location: https%3A%2F%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
[hidden email]
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




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