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[bioontology-support] Missing Term in GO?

Erik Fäßler erik.faessler at uni-jena.de
Wed Oct 1 07:16:18 PDT 2014


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
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

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