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[bioontology-support] Can't Download NCIT database

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jan 9 14:35:27 PST 2020


Hello Elizabeth,

Gilberto is correct - the issue was on our end. An error occurred in our system on the first attempt to process this latest version of NCIT. I’ve reprocessed the ontology, which is now fully available in BioPortal (including the CSV file).

Apologies for the inconvenience.

Kind regards,
Jennifer

GitHub issue for reference: https://github.com/ncbo/bioportal-project/issues/143


On Jan 9, 2020, at 1:53 PM, Fragoso, Gilberto (NIH/NCI) [E] <fragosog at mail.nih.gov<mailto:fragosog at mail.nih.gov>> wrote:

Hello Elizabeth,

This seems to be an issue at the BioPortal.  I'm cc'ing them as they'll probably need to jump in and examine the ncit.csv.gz file.  I examined the available OWL and RDF/XML files in the BioPortal's NCIT download area and the files look good.  However, although I was able to download the gzipped CSV file, I couldn't extract it from the archive.  The archiver also reports that the decompressed file is 4 GB in size, which seems somewhat high to me.

Depending on what the group at BioPortal finds out we might need to reprocess our file and resubmit it.

For other options in the meantime, and if you don't need the CSV format, you could download the NCIt OWL or RDF/XML files from BioPortal, or the RDF/XML from our FTP site (ftp://ftp1.nci.nih.gov/pub/cacore/EVS/NCI_Thesaurus/), or the OBO edition of the NCIt from http://obofoundry.org/ontology/ncit.html.  We also have a flat file version in our FTP site, but I don't know how it compares to the CSV distribution.

Regards,
Gilberto Fragoso


________________________________
From: Elizabeth Anderson <e13cook at gmail.com<mailto:e13cook at gmail.com>>
Sent: Thursday, January 9, 2020 11:38 AM
To: NCI CBIIT <ncicbiit at mail.nih.gov<mailto:ncicbiit at mail.nih.gov>>
Subject: [bioontology-support] Can't Download NCIT database

To whom it may be concerned,
My name is Elizabeth Anderson and I’m developing a web tool that programmatically accesses information from BioPortal for analyses, and I’ve been using the NCIT database for about nine months (https://bioportal.bioontology.org/ontologies/NCIT). Within the last few days, I’ve been trying to access it and I get a server 500 error that says “Cannot read the latest submission upload file: /srv/ncbo/repository/NCIT/86/NCIT.csv.gz.” I’ve attached an image of the error I receive. It seems like there was an update to the database on December 30 and I was wondering if this might have caused the error.
The NCIT database has been an essential and wonderful asset in the development of my web tool and I am hoping that the error can be fixed so my tool can be used to its full potential. Thank you for all the work you’ve put into it!
Sincerely,
Elizabeth



Elizabeth Cook Anderson
e13cook at gmail.com<mailto:e13cook at gmail.com>



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