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 Vladimir Mironov

Michael Dorf mdorf at stanford.edu
Mon Nov 23 17:40:01 PST 2015


Another issue worth noting is that we are currently experiencing a disk space issue on one of our REST failover servers. There is a open tracker item (NCBO-1577 - insufficient /tmp space on API servers) on this, and one of our engineers is looking into this issue.  So if timeout isn't the issue here, I would expect this problem to be resolved within the next few days (possible weeks due to the upcoming holidays).

Thank you again, and we'll keep you posted when this tracker items is addressed.

Michael


On Nov 23, 2015, at 17:35, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Vladimir,

As far as I know, there are no hard limit on the ontology upload size. The problem you're most likely running into is that the request times out on the server when you are trying to upload a large file.

Michael

On Nov 22, 2015, at 05:13, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Vladimir Mironov

Email: vladimir.n.mironov at gmail.com<mailto:vladimir.n.mironov at gmail.com>

Location: http://bioportal.bioontology.org/

Feedback:

it is not possible to validate or upload really large OWL ontologies at BioPortal.
I've tested these ones:
-rw-r--r-- 1 mironov metacenter 591M Jan 9 2015 owl/gaz.owl # We're sorry but something has gone wrong. We have been notified of this error.
-rw-r--r-- 1 mironov metacenter 395M Jan 9 2015 owl/chebi.owl # We're sorry but something has gone wrong. We have been notified of this error.
-rw-r--r-- 1 mironov metacenter 213M Sep 30 2014 owl/pr.owl # Errors Problem validating file, please try again
-rw-r--r-- 1 mironov metacenter 147M Jan 9 2015 owl/go.owl # Valid Ontology No errors were found
-rw-r--r-- 1 mironov metacenter 69M May 23 2013 owl/teleost-taxonomy.owl # Valid Ontology No errors were found
-rw-r--r-- 1 mironov metacenter 68M May 29 2013 owl/tto.owl # Valid Ontology No errors were found

The same situation with our own ontologies:
-rw-r--r--. 1 mironov ns9017k 498M Nov 21 15:55 cco.owl # We're sorry but something has gone wrong. We have been notified of this error.
-rw-r--r--. 1 mironov ns9017k 409M Nov 21 17:03 cco-5.owl # We're sorry but something has gone wrong. We have been notified of this error.
-rw-r--r--. 1 mironov ns9017k 347M Nov 21 16:45 cco-4.owl # We're sorry but something has gone wrong. We have been notified of this error.
-rw-r--r--. 1 mironov ns9017k 275M Nov 21 16:35 cco-3.owl # Valid Ontology No errors were found
-rw-r--r--. 1 mironov ns9017k 167M Nov 21 16:28 cco-2.owl # Valid Ontology No errors were found
-rw-r--r--. 1 mironov ns9017k 34M Nov 21 16:21 cco-1.owl # Valid Ontology No errors were found

There seems to be a limit on ontology size around 300M. A couple of years ago we experienced a very similar problem with OBO ontologies. That time the problem was caused by the dearth of RAM available. Couldn't this be the case now?

_______________________________________________
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

_______________________________________________
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20151124/920670ce/attachment-0001.html>


More information about the bioontology-support mailing list