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[bioontology-support] bioportal API issue

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Sep 23 11:24:23 PDT 2016


Hello Steve,

On Sep 23, 2016, at 6:57 AM, Steve Deharo <steve.x.deharo at gsk.com<mailto:steve.x.deharo at gsk.com>> wrote:

Hello,

It appears the following is not currently working:
http://data.bioontology.org/ontologies/HP/classes/ (Internal Server Error)
FYI, this seems to be a re-occurring issue...


The issues you previously reported with MESH and EFO were caused by missing ontology metrics, which are required before users can retrieve classes.

We tracked down the issue you reported today with the HP ontology to an invalid entry in the application’s cache.  We’ve cleared the invalid cache entry and have entered a ticket in our issue tracker to investigate the underlying cause (NCBO-1764).



Could you please let me know once the service is working again?


The classes endpoint for HP is working again.

Regards,
Jennifer




From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 23 March 2016 21:55
To: Steve Deharo
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] bioportal API issue


EXTERNAL

Hi Steve,

Thank you for reporting this issue. One of our recent releases introduced a change that required ontology metrics to be present before the ontology could be considered in a "READY" state. This changes was among the myriad of other changes designed to improve the performance of our REST services (using metrics for class counts avoids making expensive backend calls). Metrics are usually calculated at the ontology processing time, and most ontologies do have them calculated.

Unfortunately (for reasons unknown), this wasn't the case with MESH ontology. I've now corrected it, and the classes endpoint should be operational. I don't expect this issue to reoccur.

http://data.bioontology.org/ontologies/MESH/classes

Thank you again for your patience with this!

Michael


On Mar 23, 2016, at 10:59, Steve Deharo <steve.x.deharo at gsk.com<mailto:steve.x.deharo at gsk.com>> wrote:

Hello,

I have been in touch a few weeks ago about an issue with the API access. Please see the issue in the forwarded email below. The issue was resolved previously but has reoccurred e.g. http://data.bioontology.org/ontologies/MESH/classes has no data, although it can be browsed herehttp://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=root

Would you be able to answer the following questions:
-          Can this be fixed?
-          Is there a long term plan to prevent this issue reoccurring?

Regards,
Steve

From: Steve Deharo
Sent: 25 February 2016 12:03
To: 'support at bioontology.org<mailto:support at bioontology.org>'
Subject: Internal server error

Hello,

I am trying to download the mapping between MeSH and EFO. The following call returns an error:
http://data.bioontology.org/ontologies/EFO/classes/?apikey=<http://data.bioontology.org/ontologies/EFO/classes/?apikey=d072f18c-fcad-418e-8de2-913613bc8d05>[my_key_here]
This worked last month.

The error is “Internal Server Error”.

I have tried the following:
http://data.bioontology.org/ontologies/EFO/notes
http://data.bioontology.org/ontologies/EFO/classes
Both give the same error. However other links from http://data.bioontology.org/ontologies/EFO/ work eg:
http://data.bioontology.org/ontologies/EFO/properties"<http://data.bioontology.org/ontologies/EFO/properties>
http://data.bioontology.org/ontologies/EFO/views

According to http://bioportal.bioontology.org/mappings
2360 MeSH terms are mapped to EFO. The html table is accessible.

Could you please look into this?

Thanks,
Steve


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