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[bioontology-support] REST API error

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Mar 24 19:06:38 PDT 2016


Hi Daniela,

Yes, it’s straightforward for us to figure out which ontologies don’t have metrics.  However, thanks for including that attachment - I’ve looked at all of the ontologies that you listed there.

It turns out that you can’t retrieve classes for these ontologies for various reasons, not all of them having to do with metrics.  If it was simply a matter of missing metrics, I regenerated the metrics and verified that the REST call to retrieve classes worked.  For all others, I’ve listed explanations below by category:


Parsing Issues

- AAO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1690).

- BCTTV1: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1700).

- CIINTEADO: : submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1702).

- CU-VO: submitted to BioPortal and passed the parsing process, but our system failed to load the ontology data into the triple store backend.  I’ve entered an issue in our tracker for this (NCBO-1694).

- CISAVIADO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1698).

- IDOBRU:  submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1704).

- IGTO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1696).

- IMMDIS: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1701).

- GTO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1691).

- GTO_TESTING: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1689).

- HAROREADO & HAAURAADO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1695).

- HIV: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1693).

- MOOCCUADO, MOOCCIADO, MOOCULADO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1688).

- NORREG: : submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1703).

- PHFUMIADO & PHMAMMADO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1692).

- PLOSTHES: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1705).

- QIBO: submitted to BioPortal, but failed the parsing process.  I’ve entered an issue in our tracker for this (NCBO-1706).


No Ontology File Submissions

There is metadata for the following ontologies in BioPortal:

- ASLI
- FOD
- INFECTION
- ISO
- JOCHEM
- KARBONAI
- NADAGITAR
- PHARMGKB
- PHENOMEBLAST

… but none of them have submissions of actual ontology source files.  So, there is no class data to retrieve.


Summary-Only Ontologies

These types of ontologies don’t have class data in BioPortal.  You can read more on the wiki: http://www.bioontology.org/wiki/index.php/BioPortal_Help#Browse_Tab.

- CO
- NHSQI2009
- NIC


Spam Ontologies (will be deleted)

- C1902
- CYBERCRIME33
- KASEP
- MOBILE1ST
- RP
- SHAKER
- WANITA

I’m still working on processing metrics for some of the really large ontologies like DRON.  Please follow up with me if there is any one in particular that you’d really like to use and are unable to access.

Jennifer


On Mar 24, 2016, at 11:12 AM, Daniela Oliveira <daniela.oliveira at insight-centre.org<mailto:daniela.oliveira at insight-centre.org>> wrote:

Hi Jennifer,
The FMA ontology works for me too. Sorry, my mistake.  I'm sure you can easily retrieve this information too, but I have a file with all the ontologies in the API which return the same error. I don't know if it's useful, but I'll send it anyway.

Thank you,
Daniela Oliveira

2016-03-24 1:01 GMT+00:00 Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>:
Hi Daniela,

Thanks for the clarification.  The problem is with our REST endpoint, not the Python code.  My colleague Misha explained the problem earlier today in another post:

"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.”

It looks like there are still a few ontologies in BioPortal that don’t have metrics calculated that we missed.  This is the cause of the error you listed below.  We’ll reprocess GO and HP to get metrics calculated for those two, after which the error should be resolved.  You mentioned FMA below, but I can’t reproduce for that ontology.  The REST call of http://data.bioontology.org/ontologies/FMA/classes returns class data for me.

Jennifer


On Mar 23, 2016, at 4:31 PM, Daniela Oliveira <daniela.oliveira at insight-centre.org> wrote:

Sorry, I had tested and forgot to mention that it also doesn't work in the browser, when I go to http://data.bioontology.org/ontologies/GO/classes it says:
{

•
-

"errors"
: [


• "Unable to process due to missing metrics. Contact administrator"

],

• "status"
:

403
}
The

http://data.bioontology.org/ontologies/GO works fine, but the link to the classes gives that error.
In the python code, it's basically just the same command that gives the error. If I run the following, with the get_json script from the python examples:

ontologies = get_json(REST_URL+"/ontologies")
for ontology in ontologies:
    if ontology["acronym"] == "GO":
        get_json(ontology["links"]["classes"])

It returns a HTTPError: HTTP Error 403: Forbidden. This happens to me with several ontologies, but works fine with most of them.

Is there a problem with the way I'm running the script?

Thank you,
Daniela Oliveira

2016-03-23 23:15 GMT+00:00 Jennifer Leigh Vendetti <vendetti at stanford.edu>:
Hi Daniela,

It would be helpful to narrow down if the problem is in the Python code, or if there are particular REST calls that are failing.  Did you try executing the REST calls outside of your program in a browser?  Do they succeed outside of your program?  If they fail outside of your program, please provide an example of the calls that aren’t working for you.

Jennifer


> On Mar 23, 2016, at 8:50 AM, Daniela Oliveira <daniela.oliveira at insight-centre.org> wrote:
>
> Hello,
> I'm using the Bioportal REST API to access classes from several ontologies. Some of the requests work fine, but for some ontologies it is not working. For example, when I try to run get_json(ontology["links"]["classes"]), in Python, it works for ontologies like BFO, DOID and UBERON, but it isn't working for GO, HP and FMA (these were just the one I tested).
>
> Do I need to do something different to handle these ontologies or is there any issue with the server?
>
> Best regards,
> Daniela Oliveira
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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