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[bioontology-support] Missing Term in GO?

Erik Fäßler erik.faessler at uni-jena.de
Wed Oct 1 11:15:45 PDT 2014


Hi Manuel,

thanks again for your answer. I  just wanted to mention that those 42 classes weren't missing or not  referenced in the data I had when I reported the initial error. Back then, the reported class was the  only case. Thanks for keeping to look into this!

Best,

Erik



> On 01 Oct 2014, at 18:33, Manuel Salvadores Olaizola <manuelso at stanford.edu> wrote:
> 
> Erik,
> 
> I noticed those 42 missing parents. The error here is slightly different from the one you initially reported because those 42 elements are not in our backend databases. The missing class you initially reported was actually in the database.
> 
> I am looking into this issue and will get back to you with some more clarifications.
> 
> Manuel
> 
> ----- Original Message -----
> From: "Erik Fäßler" <erik.faessler at uni-jena.de>
> To: "Manuel Salvadores Olaizola" <manuelso at stanford.edu>
> Cc: support at bioontology.org
> Sent: Wednesday, October 1, 2014 7:16:18 AM
> Subject: Re: [bioontology-support] Missing Term in GO?
> 
> Hello Manuel,
> 
> thank you so much for looking so deeply into this issue!
> I just re-downloaded all the classes with the exact same script I used before. For the record, these are the parameters I am using:
> 
> "include=prefLabel,synonym,definition,parents,obsolete,notation,semanticType,cui,xref&pagesize=500&no_context=true&no_links=true”
> 
> Now, the original error is gone - however, a whole sequence of new cases has appeared where the parents weren’t present.
> To confirm, I also let your script run. At the end of the mail I paste the output after downloading 833 pages. 42 classes are missing. My own algorithm reports the same classes missing. I again cannot find those classes on the BioPortal webpage. I also noticed the following: When I had the original error, the ontology was reported to have 41839 classes (same number as told by the BioPortal page at the time). Now its only 41601 classes (again same number as told by the BioPortal page, http://bioportal.bioontology.org/ontologies/GO/?p=summary).
> 
> I’d be really grateful if someone could look into this. Thank you!
> 
> Best,
> 
> Erik
> 
> P.S.
> Here the output of your script; I only added my API key and then let it run without further changes.
> 
> Testing  http://purl.obolibrary.org/obo/GO_1903044
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903047
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903146
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903147
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903169
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903289
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903050
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903051
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903052
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903053
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903054
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903055
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903059
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903076
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903077
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903039
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903173
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903095
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903300
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903175
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903174
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903078
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903137
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903293
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903113
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903115
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903114
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903117
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903299
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903209
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903301
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903201
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903060
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903203
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903224
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903205
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903207
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903206
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903061
>    404 Not Found
> Testing  http://www.w3.org/2002/07/owl#Thing
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_1903046
>    404 Not Found
> Testing  http://purl.obolibrary.org/obo/GO_0010191
>    404 Not Found
> 
> 
> 
>> On 01 Oct 2014, at 01:59, Manuel Salvadores Olaizola <manuelso at stanford.edu> wrote:
>> 
>> http://purl.obolibrary.org/obo/GO_0044597
> 
>> On 01 Oct 2014, at 01:59, Manuel Salvadores Olaizola <manuelso at stanford.edu> wrote:
>> 
>> Hi Erik,
>> 
>> I have done some further investigation on this issue. I cannot reproduce your it. The class  http://purl.obolibrary.org/obo/GO_0044597 does come up in when I run my traversal script.
>> 
>> Are you running the classes REST call with some non-default parameters, page size or some other include parameters ?
>> 
>> This is the script that I have created to reproduce your issue.
>> 
>> https://gist.github.com/msalvadores/bc9c874f230ec8100ea6
>> 
>> Is a python script that has two functions:
>> - get_all_classes is a function that dumps all classes in a tsv file. First field is the class id, the rest are the parents.
>> - test_coverage_parents takes the previous file, builds two sets of IDs, one for all class ids and another for all the parent ids.
>> 
>> Please let me know more about how you are using our REST APIs so that I can better reproduce your issue.
>> 
>> Manuel
>> 
>> ----- Original Message -----
>> From: "Manuel Salvadores Olaizola" <manuelso at stanford.edu>
>> To: "Erik Fäßler" <erik.faessler at uni-jena.de>
>> Cc: support at bioontology.org
>> Sent: Friday, September 26, 2014 9:22:24 AM
>> Subject: Re: [bioontology-support] Missing Term in GO?
>> 
>> Hi Erik,
>> 
>> Thanks for reporting this issue. It does look like the REST call is missing that term. Our search index does not have it either and it uses the same capability to traverse all classes from an ontology.
>> 
>> I have created a bug report to address this issue in the next release. We will get back to you with an answer when it is fixed.
>> 
>> Manuel
>> 
>> ----- Original Message -----
>> From: "Erik Fäßler" <erik.faessler at uni-jena.de>
>> To: support at bioontology.org
>> Sent: Friday, September 26, 2014 4:04:43 AM
>> Subject: [bioontology-support] Missing Term in GO?
>> 
>> Dear Bioontology team,
>> 
>> I just downloaded all GO classes via the new REST API. When importing these data into my own database I noticed the class
>> 
>> http://purl.obolibrary.org/obo/GO_0044597
>> 
>> Is referenced as a parent class from the classes
>> 
>> http://purl.obolibrary.org/obo/GO_1901770
>> http://purl.obolibrary.org/obo/GO_1901771
>> 
>> but is not included itself in the REST answer. Also, when I try to find it via the ontology’s page at BioPortal, I am not able to find the class by name, I don’t even get suggestions. However, I get suggestions for its children. When I try to navigate to them by issuing the search, an error occurs.
>> 
>> I think the class should be there, at least I can find it at the original GO homepage.
>> 
>> Best regards,
>> 
>> Erik
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>> 
>> 
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>> 
> 
> 


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